[ { "id": "authors:qwsrk-t3828", "collection": "authors", "collection_id": "qwsrk-t3828", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220629-707785000", "type": "article", "title": "Modification of the 4Fe-4S Cluster Charge Transport Pathway Alters RNA Synthesis by Yeast DNA Primase", "author": [ { "family_name": "Salay", "given_name": "Lauren E.", "orcid": "0000-0001-8513-1891", "clpid": "Salay-Lauren-E" }, { "family_name": "Blee", "given_name": "Alexandra M.", "orcid": "0000-0003-4959-5466", "clpid": "Blee-Alexandra-M" }, { "family_name": "Raza", "given_name": "Md Kausar", "orcid": "0000-0002-9175-198X", "clpid": "Raza-Md-Kausar" }, { "family_name": "Gallagher", "given_name": "Kaitlyn S.", "clpid": "Gallagher-Kaitlyn-S" }, { "family_name": "Chen", "given_name": "Huiqing", "clpid": "Chen-Huiqing" }, { "family_name": "Dorfeuille", "given_name": "Andrew J.", "clpid": "Dorfeuille-Andrew-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Chazin", "given_name": "Walter J.", "orcid": "0000-0002-2180-0790", "clpid": "Chazin-Walter-J" } ], "abstract": "DNA synthesis during replication begins with the generation of an \u223c10-nucleotide primer by DNA primase. Primase contains a redox-active 4Fe-4S cluster in the C-terminal domain of the p58 subunit (p58C). The redox state of this 4Fe-4S cluster can be modulated via the transport of charge through the protein and the DNA substrate (redox switching); changes in the redox state of the cluster alter the ability of p58C to associate with its substrate. The efficiency of redox switching in p58C can be altered by mutating tyrosine residues that bridge the 4Fe-4S cluster and the nucleic acid binding site. Here, we report the effects of mutating bridging tyrosines to phenylalanines in yeast p58C. High-resolution crystal structures show that these mutations, even with six tyrosines simultaneously mutated, do not perturb the three-dimensional structure of the protein. In contrast, measurements of the electrochemical properties on DNA-modified electrodes of p58C containing multiple tyrosine to phenylalanine mutations reveal deficiencies in their ability to engage in DNA charge transport. Significantly, this loss of electrochemical activity correlates with decreased primase activity. While single-site mutants showed modest decreases in activity compared to that of the wild-type primase, the protein containing six mutations exhibited a 10-fold or greater decrease. Thus, many possible tyrosine-mediated pathways for charge transport in yeast p58C exist, but inhibiting these pathways together diminishes the ability of yeast primase to generate primers. These results support a model in which redox switching is essential for primase activity.", "doi": "10.1021/acs.biochem.2c00100", "pmcid": "PMC9555021", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "2022-06-07", "series_number": "11", "volume": "61", "issue": "11", "pages": "1113-1123" }, { "id": "authors:4xb7v-75m90", "collection": "authors", "collection_id": "4xb7v-75m90", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211013-163834914", "type": "article", "title": "The [4Fe4S] Cluster of Yeast DNA Polymerase \u03b5 Is Redox Active and Can Undergo DNA-Mediated Signaling", "author": [ { "family_name": "Pinto", "given_name": "Miguel N.", "orcid": "0000-0002-6333-6527", "clpid": "Pinto-Miguel-N" }, { "family_name": "ter Beek", "given_name": "Josy", "orcid": "0000-0003-4165-9277", "clpid": "ter-Beek-Josy" }, { "family_name": "Ekanger", "given_name": "Levi A.", "orcid": "0000-0001-8131-1641", "clpid": "Ekanger-Levi-A" }, { "family_name": "Johansson", "given_name": "Erik", "clpid": "Johansson-Erik-M" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Many DNA replication and DNA repair enzymes have been found to carry [4Fe4S] clusters. The major leading strand polymerase, DNA polymerase \u03b5 (Pol \u03b5) from Saccharomyces cerevisiae, was recently reported to have a [4Fe4S] cluster located within the catalytic domain of the largest subunit, Pol2. Here the redox characteristics of the [4Fe4S] cluster in the context of that domain, Pol2_(CORE), are explored using DNA electrochemistry, and the effects of oxidation and rereduction on polymerase activity are examined. The exonuclease deficient variant D290A/E292A, Pol2_(CORE)exo\u2013, was used to limit DNA degradation. While no redox signal is apparent for Pol2_(CORE)exo\u2013 on DNA-modified electrodes, a large cathodic signal centered at \u2212140 mV vs NHE is observed after bulk oxidation. A double cysteine to serine mutant (C665S/C668S) of Pol2_(CORE)exo\u2013, which lacks the [4Fe4S] cluster, shows no similar redox signal upon oxidation. Significantly, protein oxidation yields a sharp decrease in polymerization, while rereduction restores activity almost to the level of untreated enzyme. Moreover, the addition of reduced EndoIII, a bacterial DNA repair enzyme containing [4Fe4S]\u00b2\u207a, to oxidized Pol2_(CORE)exo\u2013 bound to its DNA substrate also significantly restores polymerase activity. In contrast, parallel experiments with EndoIII^(Y82A), a variant of EndoIII, defective in DNA charge transport (CT), does not show restoration of activity of Pol2_(CORE)exo\u2013. We propose a model in which EndoIII bound to the DNA duplex may shuttle electrons through DNA to the DNA-bound oxidized Pol2_(CORE)exo\u2013 via DNA CT and that this DNA CT signaling offers a means to modulate the redox state and replication by Pol \u03b5.", "doi": "10.1021/jacs.1c07150", "pmcid": "PMC8499023", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2021-10-06", "series_number": "39", "volume": "143", "issue": "39", "pages": "16147-16153" }, { "id": "authors:44nfe-acp33", "collection": "authors", "collection_id": "44nfe-acp33", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210730-174655133", "type": "article", "title": "DNA Electrochemistry: Charge-Transport Pathways through DNA Films on Gold", "author": [ { "family_name": "Nano", "given_name": "Adela", "orcid": "0000-0002-1984-5770", "clpid": "Nano-Adela" }, { "family_name": "Furst", "given_name": "Ariel L.", "orcid": "0000-0001-9583-9703", "clpid": "Furst-Ariel-L" }, { "family_name": "Hill", "given_name": "Michael G.", "clpid": "Hill-Michael-G" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Over the past 25 years, collective evidence has demonstrated that the DNA base-pair stack serves as a medium for charge transport chemistry in solution and on DNA-modified gold surfaces. Since this charge transport depends sensitively upon the integrity of the DNA base pair stack, perturbations in base stacking, as may occur with DNA base mismatches, lesions, and protein binding, interrupt DNA charge transport (DNA CT). This sensitivity has led to the development of powerful DNA electrochemical sensors. Given the utility of DNA electrochemistry for sensing and in response to recent literature, we describe critical protocols and characterizations necessary for performing DNA-mediated electrochemistry. We demonstrate DNA electrochemistry with a fully AT DNA sequence using a thiolated preformed DNA duplex and distinguish this DNA-mediated chemistry from that of electrochemistry of largely single-stranded DNA adsorbed to the surface. We also demonstrate the dependence of DNA CT on a fully stacked duplex. An increase in the percentage of mismatches within the DNA monolayer leads to a linear decrease in current flow for a DNA-bound intercalator, where the reaction is DNA-mediated; in contrast, for ruthenium hexammine, which binds electrostatically to DNA and the redox chemistry is not DNA-mediated, there is no effect on current flow with mismatches. We find that, with DNA as a well hybridized duplex, upon assembly, a DNA-mediated pathway facilitates the electron transfer between a well coupled redox probe and the gold surface. Overall, this report highlights critical points to be emphasized when utilizing DNA electrochemistry and offers explanations and controls for analyzing confounding results.", "doi": "10.1021/jacs.1c04713", "pmcid": "PMC9285625", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2021-08-04", "series_number": "30", "volume": "143", "issue": "30", "pages": "11631-11640" }, { "id": "authors:d5abj-m5a26", "collection": "authors", "collection_id": "d5abj-m5a26", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210609-150237052", "type": "article", "title": "Rhodium Complexes Targeting DNA Mismatches as a Basis for New Therapeutics in Cancers Deficient in Mismatch Repair", "author": [ { "family_name": "Nano", "given_name": "Adela", "orcid": "0000-0002-1984-5770", "clpid": "Nano-Adela" }, { "family_name": "Dai", "given_name": "Joanne", "clpid": "Dai-Joanne" }, { "family_name": "Bailis", "given_name": "Julie M.", "clpid": "Bailis-Julie-M" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Cancers with microsatellite instability (MSI), which include \u226420% of solid tumors, are characterized by resistance to chemotherapy due to deficiency in the DNA mismatch repair (MMR) pathway. Rhodium metalloinsertors make up a class of compounds that bind DNA mismatches with high specificity and show selective cytotoxicity in MSI cancer cells. We determined that rhodium complexes with an N\u2227O coordination showed significantly increased cell potency compared with that of N\u2227N-coordinated compounds, and we identified [Rh(chrysi)(phen)(PPO)]\u00b2\u207a (RhPPO) as the most potent, selective compound in this class. Using matched cell lines that are MMR-deficient (HCT116O) and MMR-proficient (HCT116N), we demonstrated that RhPPO preferentially activates the DNA damage response and inhibits DNA replication and cell proliferation in HCT116O cells, leading to cell death by necrosis. Using a fluorescent conjugate of RhPPO, we established that the metalloinsertor localizes to DNA mismatches in the cell nucleus and causes DNA double-strand breaks at or near the mismatch sites. Evaluation of RhPPO across MMR-deficient and MMR-proficient cell lines confirmed the broad potential for RhPPO to target MSI cancers, with cell potency significantly higher than that of platinum complexes used broadly as chemotherapeutics. Moreover, in a mouse xenograft model of MSI cancer, RhPPO shows promising antitumor activity and increased survival. Thus, our studies indicate that RhPPO is a novel DNA-targeted therapy with improved potency and selectivity over standard-of-care platinum-based chemotherapy and, importantly, that DNA mismatches offer a critical new target in the design of chemotherapeutics for MSI cancers.", "doi": "10.1021/acs.biochem.1c00302", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "2021-07-06", "series_number": "26", "volume": "60", "issue": "26", "pages": "2055-2063" }, { "id": "authors:qtd0v-e8n18", "collection": "authors", "collection_id": "qtd0v-e8n18", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20191213-144717393", "type": "article", "title": "Extracellular DNA Promotes Efficient Extracellular Electron Transfer by Pyocyanin in Pseudomonas aeruginosa Biofilms", "author": [ { "family_name": "Saunders", "given_name": "Scott H.", "orcid": "0000-0003-4224-9106", "clpid": "Saunders-Scott-H" }, { "family_name": "Tse", "given_name": "Edmund C. M.", "orcid": "0000-0002-9313-1290", "clpid": "Tse-Edmund-Chun-Ming" }, { "family_name": "Yates", "given_name": "Matthew D.", "orcid": "0000-0003-4373-3864", "clpid": "Yates-Matthew-D" }, { "family_name": "Jim\u00e9nez Otero", "given_name": "Fernanda", "orcid": "0000-0003-1583-6495", "clpid": "Jim\u00e9nez-Otero-F" }, { "family_name": "Trammell", "given_name": "Scott A.", "orcid": "0000-0002-7996-590X", "clpid": "Trammell-Scott-A" }, { "family_name": "Stemp", "given_name": "Eric D. A.", "orcid": "0000-0003-2098-4214", "clpid": "Stemp-Eric-D-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Tender", "given_name": "Leonard M.", "orcid": "0000-0001-8784-991X", "clpid": "Tender-Leonard-M" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Redox cycling of extracellular electron shuttles can enable the metabolic activity of subpopulations within multicellular bacterial biofilms that lack direct access to electron acceptors or donors. How these shuttles catalyze extracellular electron transfer (EET) within biofilms without being lost to the environment has been a long-standing question. Here, we show that phenazines mediate efficient EET through interactions with extracellular DNA (eDNA) in Pseudomonas aeruginosa biofilms. Retention of pyocyanin (PYO) and phenazine carboxamide in the biofilm matrix is facilitated by eDNA binding. In vitro, different phenazines can exchange electrons in the presence or absence of DNA and can participate directly in redox reactions through DNA. In vivo, biofilm eDNA can also support rapid electron transfer between redox active intercalators. Together, these results establish that PYO:eDNA interactions support an efficient redox cycle with rapid EET that is faster than the rate of PYO loss from the biofilm.", "doi": "10.1016/j.cell.2020.07.006", "pmcid": "PMC7457544", "issn": "0092-8674", "publisher": "Cell Press", "publication": "Cell", "publication_date": "2020-08-20", "series_number": "4", "volume": "182", "issue": "4", "pages": "919-932" }, { "id": "authors:6hx5y-7tz86", "collection": "authors", "collection_id": "6hx5y-7tz86", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200714-092121048", "type": "article", "title": "In vivo anticancer activity of a rhodium metalloinsertor in the HCT116 xenograft tumor model", "author": [ { "family_name": "Threatt", "given_name": "Stephanie D.", "clpid": "Threatt-S-D" }, { "family_name": "Synold", "given_name": "Timothy W.", "clpid": "Synold-T-W" }, { "family_name": "Wu", "given_name": "Jun", "clpid": "Wu-Jun" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Mismatch repair (MMR) deficiencies are a hallmark of various cancers causing accumulation of DNA mutations and mismatches, which often results in chemotherapy resistance. Metalloinsertor complexes, including [Rh(chrysi)(phen)(PPO)]Cl\u2082 (Rh-PPO), specifically target DNA mismatches and selectively induce cytotoxicity within MMR-deficient cells. Here, we present an in vivo analysis of Rh-PPO, our most potent metalloinsertor. Studies with HCT116 xenograft tumors revealed a 25% reduction in tumor volume and 12% increase in survival with metalloinsertor treatment (1 mg/kg; nine intraperitoneal doses over 20 d). When compared to oxaliplatin, Rh-PPO displays ninefold higher potency at tumor sites. Pharmacokinetic studies revealed rapid absorption of Rh-PPO in plasma with notable accumulation in the liver compared to tumors. Additionally, intratumoral metalloinsertor administration resulted in enhanced anticancer effects, pointing to a need for more selective delivery methods. Overall, these data show that Rh-PPO inhibits xenograft tumor growth, supporting the strategy of using Rh-PPO as a chemotherapeutic targeted to MMR-deficient cancers.", "doi": "10.1073/pnas.2006569117", "pmcid": "PMC7395490", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2020-07-28", "series_number": "30", "volume": "117", "issue": "30", "pages": "17535-17542" }, { "id": "authors:shjap-nwd47", "collection": "authors", "collection_id": "shjap-nwd47", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200615-113627458", "type": "article", "title": "UvrC Coordinates an O\u2082-Sensitive [4Fe4S] Cofactor", "author": [ { "family_name": "Silva", "given_name": "Rebekah M. B.", "orcid": "0000-0002-9144-4939", "clpid": "Silva-R-M-B" }, { "family_name": "Grodick", "given_name": "Michael A.", "orcid": "0000-0001-6618-6731", "clpid": "Grodick-M-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Recent advances have led to numerous landmark discoveries of [4Fe4S] clusters coordinated by essential enzymes in repair, replication, and transcription across all domains of life. The cofactor has notably been challenging to observe for many nucleic acid processing enzymes due to several factors, including a weak bioinformatic signature of the coordinating cysteines and lability of the metal cofactor. To overcome these challenges, we have used sequence alignments, an anaerobic purification method, iron quantification, and UV\u2013visible and electron paramagnetic resonance spectroscopies to investigate UvrC, the dual-incision endonuclease in the bacterial nucleotide excision repair (NER) pathway. The characteristics of UvrC are consistent with [4Fe4S] coordination with 60\u201370% cofactor incorporation, and additionally, we show that, bound to UvrC, the [4Fe4S] cofactor is susceptible to oxidative degradation with aggregation of apo species. Importantly, in its holo form with the cofactor bound, UvrC forms high affinity complexes with duplexed DNA substrates; the apparent dissociation constants to well-matched and damaged duplex substrates are 100 \u00b1 20 nM and 80 \u00b1 30 nM, respectively. This high affinity DNA binding contrasts reports made for isolated protein lacking the cofactor. Moreover, using DNA electrochemistry, we find that the cluster coordinated by UvrC is redox-active and participates in DNA-mediated charge transport chemistry with a DNA-bound midpoint potential of 90 mV vs NHE. This work highlights that the [4Fe4S] center is critical to UvrC.", "doi": "10.1021/jacs.0c01671", "pmcid": "PMC7392197", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2020-06-24", "series_number": "25", "volume": "142", "issue": "25", "pages": "10964-10977" }, { "id": "authors:7mh1p-5xd62", "collection": "authors", "collection_id": "7mh1p-5xd62", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200122-124618192", "type": "article", "title": "Cell-Selective Cytotoxicity of a Fluorescent Rhodium Metalloinsertor Conjugate Results from Irreversible DNA Damage at Base Pair Mismatches", "author": [ { "family_name": "Nano", "given_name": "Adela", "orcid": "0000-0002-1984-5770", "clpid": "Nano-Adela" }, { "family_name": "Bailis", "given_name": "Julie M.", "clpid": "Bailis-J-M" }, { "family_name": "Mariano", "given_name": "Natalie F.", "clpid": "Mariano-N-F" }, { "family_name": "Pham", "given_name": "Elizabeth D.", "clpid": "Pham-E-D" }, { "family_name": "Threatt", "given_name": "Stephanie D.", "clpid": "Threatt-S-D" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Up to 20% of solid tumors are characterized by DNA mismatch repair (MMR) deficiency and microsatellite instability that confer resistance to standard of care chemotherapy. MMR-deficient cancers have an increased mutation rate, and DNA mismatches accumulate as part of these cancers. We previously described a class of compounds, rhodium metalloinsertors, that bind DNA mismatches with high specificity and selectivity and have potential as targeted therapy. [Rh(chrysi)(phen)(PPO)]2+ (RhPPO) is the most potent, selective compound in this class and acts by targeting DNA mismatches, resulting in preferential cytotoxicity to MMR-deficient cancers. To explore further the cellular mechanism of action of RhPPO, we conjugated the metal complex to a fluorescent probe, cyanine 3 (Cy3). RhPPO-Cy3 binds DNA mismatches and retains the selectivity and potent cytotoxic activity of RhPPO for MMR-deficient cell lines. RhPPO-Cy3 forms discrete foci in the cell nucleus that overlap with sites of DNA damage, suggesting that the lesions occur at or near DNA mismatch sites. RhPPO-Cy3 foci persist over time, despite initial processing of the lesion and recruitment of repair proteins, consistent with the idea that the complex binding to a mismatch prevents repair. RhPPO-Cy3 binding does not lead to activation of p53 and the apoptotic pathway. Together, these findings support the idea that RhPPO-Cy3 binding leads to irreversible DNA damage at DNA mismatches that enables selective cytotoxicity to MMR-deficient cells.", "doi": "10.1021/acs.biochem.9b01037", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "2020-02-11", "series_number": "5", "volume": "59", "issue": "5", "pages": "717-726" }, { "id": "authors:qz0c8-31p72", "collection": "authors", "collection_id": "qz0c8-31p72", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190624-083057369", "type": "article", "title": "Redox Chemistry in the Genome: Emergence of the [4Fe4S] Cofactor in Repair and Replication", "author": [ { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Silva", "given_name": "Rebekah M. B.", "orcid": "0000-0002-9144-4939", "clpid": "Silva-Rebekah-M-B" }, { "family_name": "O'Brien", "given_name": "Elizabeth", "clpid": "O'Brien-Elizabeth" } ], "abstract": "Many DNA-processing enzymes have been shown to contain a [4Fe4S] cluster, a common redox cofactor in biology. Using DNA electrochemistry, we find that binding of the DNA polyanion promotes a negative shift in [4Fe4S] cluster potential, which corresponds thermodynamically to a \u223c500-fold increase in DNA-binding affinity for the oxidized [4Fe4S]^(3+) cluster versus the reduced [4Fe4S]^(2+) cluster. This redox switch can be activated from a distance using DNA charge transport (DNA CT) chemistry. DNA-processing proteins containing the [4Fe4S] cluster are enumerated, with possible roles for the redox switch highlighted. A model is described where repair proteins may signal one another using DNA-mediated charge transport as a first step in their search for lesions. The redox switch in eukaryotic DNA primases appears to regulate polymerase handoff, and in DNA polymerase \u03b4, the redox switch provides a means to modulate replication in response to oxidative stress. We thus describe redox signaling interactions of DNA-processing [4Fe4S] enzymes, as well as the most interesting potential players to consider in delineating new DNA-mediated redox signaling networks.", "doi": "10.1146/annurev-biochem-013118-110644", "pmcid": "PMC6590699", "issn": "0066-4154", "publisher": "Annual Reviews", "publication": "Annual Review of Biochemistry", "publication_date": "2019-06", "volume": "88", "pages": "163-190" }, { "id": "authors:htqdw-jxk49", "collection": "authors", "collection_id": "htqdw-jxk49", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190809-145602002", "type": "article", "title": "Primer handoff between DNA primase and DNA polymerase \u03b1", "author": [ { "family_name": "Zhong", "given_name": "Aoshu", "clpid": "Zhong-Aoshu" }, { "family_name": "Salay", "given_name": "Lauren E.", "clpid": "Salay-L-E" }, { "family_name": "Chazinb", "given_name": "Walter J.", "clpid": "Chazinb-W-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "DNA replication is a fundamental process. In eukaryotes, the\nfirst step in daughter strand synthesis is the generation of a\nshort (~10 nt) RNA primer by DNA primase, followed by\ntransfer of the primer to DNA polymerase \u03b1 (Pol \u03b1) for extension\nby ~20 nts (O'Brien et al., 2017; Burgers & Kunkel, 2017;\nPellegrini, 2012; O'Brien et al., 2018; O'Brien, Holt, Salay,\nChazin, & Barton, 2018). Although the catalytic activity and\nstructures of primase and Pol a have been extensively\nstudied (Burgers & Kunkel, 2017; Pellegrini, 2012; O'Brien\net al., 2018; O'Brien, Holt, Salay, Chazin, & Barton, 2018), the\nmolecular mechanism of primer handoff between primase\nand Pol \u03b1 remains largely unknown. We have proposed that\nredox switching of the [4Fe4S] cluster in primase is important\nfor primer truncation and handoff to Pol a (O'Brien et al.,\n2017; O'Brien et al., 2018). Eukaryotic Pol \u03b1 is composed of a catalytic subunit (p180) and a regulatory subunit (p68). The p180 subunit contains a [4Fe4S] cluster.", "doi": "10.1080/07391102.2019.1604468", "issn": "0739-1102", "publisher": "Taylor & Francis", "publication": "Journal of Biomolecular Structure and Dynamics", "publication_date": "2019-05-27", "series_number": "S1", "volume": "37", "issue": "S1", "pages": "63-64" }, { "id": "authors:99ryg-92b35", "collection": "authors", "collection_id": "99ryg-92b35", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190809-152328895", "type": "article", "title": "The role of the redox active 4Fe\u20134S cluster of yeast Dna2", "author": [ { "family_name": "Gaustad MacArdle", "given_name": "Siobh\u00e1n", "clpid": "MacArdle-S" }, { "family_name": "Barton", "given_name": "Jacqueline", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Dna2 is an essential nuclease-helicase conserved throughout eukaryotic organisms with an impressive repertoire of DNA maintenance activity (Budd & Campbell, 1995). Due to its major roles in Okazaki fragment processing during DNA replication, double strand break repair, telomere maintenance and mitochondrial DNA maintenance, it is not surprising that both Dna2 upregulation and mutation have been observed in various types of cancer (Lee, Kim, Yoo, & Lee, 2010; Strauss, 2014).", "doi": "10.1080/07391102.2019.1604468", "issn": "0739-1102", "publisher": "Taylor & Francis", "publication": "Journal of Biomolecular Structure and Dynamics", "publication_date": "2019-05-27", "series_number": "S1", "volume": "37", "issue": "S1", "pages": "63" }, { "id": "authors:mss9k-agb85", "collection": "authors", "collection_id": "mss9k-agb85", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190114-083314706", "type": "article", "title": "Cellular Target of a Rhodium Metalloinsertor is the DNA Base Pair Mismatch", "author": [ { "family_name": "Boyle", "given_name": "Kelsey M.", "orcid": "0000-0002-6728-8403", "clpid": "Boyle-Kelsey-M" }, { "family_name": "Nano", "given_name": "Adela", "orcid": "0000-0002-1984-5770", "clpid": "Nano-Adela" }, { "family_name": "Day", "given_name": "Catherine", "clpid": "Day-Catherine" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Defects in DNA mismatch repair (MMR) are commonly found in various cancers, especially in colorectal cancers. Despite the high prevalence of MMR\u2010deficient cancers, mismatch\u2010targeted therapeutics are limited and diagnostic tools are indirect. Here, we examine the cytotoxic properties of a rhodium metalloinsertor, [Rh(phen)(chrysi)(PPO)]^(2+)(RhPPO) in 27 diverse colorectal cancer cell lines. Despite the low frequency of genomic mismatches and the non\u2010covalent nature of the RhPPO\u2010DNA lesion, RhPPO is on average five times more potent than cisplatin. Importantly, the biological target and profile for RhPPO differs from that of cisplatin. A fluorescent metalloinsertor, RhCy3, was used to demonstrate that the cellular target of RhPPO is the DNA mismatch. RhCy3 represents a direct probe for MMR\u2010deficiency and correlates directly with the cytotoxicity of RhPPOacross different cell lines. Overall, our studies clearly indicate that RhPPO and RhCy3 are promising anticancer and diagnostic probes for MMR\u2010deficient cancers, respectively.", "doi": "10.1002/chem.201900042", "issn": "0947-6539", "publisher": "John Wiley & Sons", "publication": "Chemistry: a European Journal", "publication_date": "2019-02-26", "series_number": "12", "volume": "25", "issue": "12", "pages": "3014-3019" }, { "id": "authors:et6gb-8cj94", "collection": "authors", "collection_id": "et6gb-8cj94", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190111-103734017", "type": "article", "title": "Effective Distance for DNA-Mediated Charge Transport between Repair Proteins", "author": [ { "family_name": "Tse", "given_name": "Edmund C. M.", "orcid": "0000-0002-9313-1290", "clpid": "Tse-Edmund-C-M" }, { "family_name": "Zwang", "given_name": "Theodore J.", "clpid": "Zwang-Theodore-J" }, { "family_name": "Bedoya", "given_name": "Sebastian", "clpid": "Bedoya-Sebastian" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The stacked aromatic base pairs within the DNA double helix facilitate charge transport down its length in the absence of lesions, mismatches, and other stacking perturbations. DNA repair proteins containing [4Fe4S] clusters can take advantage of DNA charge transport (CT) chemistry to scan the genome for mistakes more efficiently. Here we examine the effective length over which charge can be transported along DNA between these repair proteins. We define the effective CT distance as the length of DNA within which two proteins are able to influence their ensemble affinity to the DNA duplex via CT. Endonuclease III, a DNA repair glycosylase containing a [4Fe4S] cluster, was incubated with DNA duplexes of different lengths (1.5\u20139 kb), and atomic force microscopy was used to quantify the binding of proteins to these duplexes to determine how the relative protein affinity changes with increasing DNA length. A sharp change in binding slope is observed at 3509 base pairs, or about 1.2 \u03bcm, that supports the existence of two regimes for protein binding, one within the range for DNA CT, one outside of the range for CT; DNA CT between the redox proteins bound to DNA effectively decreases the ensemble binding affinity of oxidized and reduced proteins to DNA. Utilizing an Endonuclease III mutant Y82A, which is defective in carrying out DNA CT, shows only one regime for protein binding. Decreasing the temperature to 4 \u00b0C or including metallointercalators on the duplex, both of which should enhance base stacking and decrease DNA floppiness, leads to extending the effective length for DNA charge transport to \u223c5300 bp or 1.8 \u03bcm. These results thus support DNA charge transport between repair proteins over kilobase distances. The results furthermore highlight the ability of DNA repair proteins to search the genome quickly and efficiently using DNA charge transport chemistry.", "doi": "10.1021/acscentsci.8b00566", "pmcid": "PMC6346725", "issn": "2374-7943", "publisher": "American Chemical Society", "publication": "ACS Central Science", "publication_date": "2019-01-23", "series_number": "1", "volume": "5", "issue": "1", "pages": "65-72" }, { "id": "authors:b5wsp-px732", "collection": "authors", "collection_id": "b5wsp-px732", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181213-083058525", "type": "article", "title": "Yeast require redox switching in DNA primase", "author": [ { "family_name": "O'Brien", "given_name": "Elizabeth", "clpid": "O'Brien-Elizabeth" }, { "family_name": "Salay", "given_name": "Lauren E.", "clpid": "Salay-Lauren-E" }, { "family_name": "Epum", "given_name": "Esther A.", "clpid": "Epum-Esther-A" }, { "family_name": "Friedman", "given_name": "Katherine L.", "clpid": "Friedman-Katherine-L" }, { "family_name": "Chazin", "given_name": "Walter J.", "orcid": "0000-0002-2180-0790", "clpid": "Chazin-Walter-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Eukaryotic DNA primases contain a [4Fe4S] cluster in the C-terminal domain of the p58 subunit (p58C) that affects substrate affinity but is not required for catalysis. We show that, in yeast primase, the cluster serves as a DNA-mediated redox switch governing DNA binding, just as in human primase. Despite a different structural arrangement of tyrosines to facilitate electron transfer between the DNA substrate and [4Fe4S] cluster, in yeast, mutation of tyrosines Y395 and Y397 alters the same electron transfer chemistry and redox switch. Mutation of conserved tyrosine 395 diminishes the extent of p58C participation in normal redox-switching reactions, whereas mutation of conserved tyrosine 397 causes oxidative cluster degradation to the [3Fe4S]^+ species during p58C redox signaling. Switching between oxidized and reduced states in the presence of the Y397 mutations thus puts primase [4Fe4S] cluster integrity and function at risk. Consistent with these observations, we find that yeast tolerate mutations to Y395 in p58C, but the single-residue mutation Y397L in p58C is lethal. Our data thus show that a constellation of tyrosines for protein-DNA electron transfer mediates the redox switch in eukaryotic primases and is required for primase function in vivo.", "doi": "10.1073/pnas.1810715115", "pmcid": "PMC6310810", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2018-12-26", "series_number": "52", "volume": "115", "issue": "52", "pages": "13186-13191" }, { "id": "authors:ph56x-jj932", "collection": "authors", "collection_id": "ph56x-jj932", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181115-142248448", "type": "article", "title": "Substrate Binding Regulates Redox Signaling in Human DNA Primase", "author": [ { "family_name": "O'Brien", "given_name": "Elizabeth", "clpid": "O'Brien-Elizabeth" }, { "family_name": "Holt", "given_name": "Marilyn E.", "orcid": "0000-0002-3164-869X", "clpid": "Holt-Marilyn-E" }, { "family_name": "Salay", "given_name": "Lauren E.", "clpid": "Salay-Lauren-E" }, { "family_name": "Chazin", "given_name": "Walter J.", "orcid": "0000-0002-2180-0790", "clpid": "Chazin-Walter-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Generation of daughter strands during DNA replication requires the action of DNA primase to synthesize an initial short RNA primer on the single-stranded DNA template. Primase is a heterodimeric enzyme containing two domains whose activity must be coordinated during primer synthesis: an RNA polymerase domain in the small subunit (p48) and a [4Fe4S] cluster-containing C-terminal domain of the large subunit (p58C). Here we examine the redox switching properties of the [4Fe4S] cluster in the full p48/p58 heterodimer using DNA electrochemistry. Unlike with isolated p58C, robust redox signaling in the primase heterodimer requires binding of both DNA and NTPs; NTP binding shifts the p48/p58 cluster redox potential into the physiological range, generating a signal near 160 mV vs NHE. Preloading of primase with NTPs enhances catalytic activity on primed DNA, suggesting that primase configurations promoting activity are more highly populated in the NTP-bound protein. We propose that p48/p58 binding of anionic DNA and NTPs affects the redox properties of the [4Fe4S] cluster; this electrostatic change is likely influenced by the alignment of primase subunits during activity because the configuration affects the [4Fe4S] cluster environment and coupling to DNA bases for redox signaling. Thus, both binding of polyanionic substrates and configurational dynamics appear to influence [4Fe4S] redox signaling properties. These results suggest that these factors should be considered generally in characterizing signaling networks of large, multisubunit DNA-processing [4Fe4S] enzymes.", "doi": "10.1021/jacs.8b09914", "pmcid": "PMC6470046", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2018-12-12", "series_number": "49", "volume": "140", "issue": "49", "pages": "17153-17162" }, { "id": "authors:951bb-z6136", "collection": "authors", "collection_id": "951bb-z6136", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190102-135257451", "type": "article", "title": "Functional and structural similarity of human DNA primase [4Fe4S] cluster domain constructs", "author": [ { "family_name": "Holt", "given_name": "Marilyn E.", "orcid": "0000-0002-3164-869X", "clpid": "Holt-M-E" }, { "family_name": "Salay", "given_name": "Lauren E.", "clpid": "Salay-L-E" }, { "family_name": "O'Brien", "given_name": "Elizabeth", "clpid": "O'Brien-E" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Chazin", "given_name": "Walter J.", "orcid": "0000-0002-2180-0790", "clpid": "Chazin-W-J" } ], "abstract": "The regulatory subunit of human DNA primase has a C-terminal domain (p58C) that contains a [4Fe4S] cluster and binds DNA. Previous electrochemical analysis of a p58C construct revealed that its affinity for DNA is sensitive to the redox state of the [4Fe4S] cluster. Concerns about the validity of this conclusion have been raised, based in part on differences in X-ray crystal structures of the p58C_(272-464) construct used for that study and that of a N-terminally shifted p58C_(266-456) construct and consequently, an assumption that p58C_(272-464) has abnormal physical and functional properties. To address this controversy, a new p58C_(266-464) construct containing all residues was crystallized under the conditions previously used for crystallizing p58C_(272-464), and the solution structures of both constructs were assessed using circular dichroism and NMR spectroscopy. In the new crystal structure, p58C_(266-464) exhibits the same elements of secondary structure near the DNA binding site as observed in the crystal structure of p58C_(272-464). Moreover, in solution, circular dichroism and ^(15)N,^1H-heteronuclear single quantum coherence (HSQC) NMR spectra show there are no significant differences in the distribution of secondary structures or in the tertiary structure or the two constructs. To validate that the two constructs have the same functional properties, binding of a primed DNA template was measured using a fluorescence-based DNA binding assay, and the affinities for this substrate were the same (3.4 \u00b1 0.5 \u03bcM and 2.7 \u00b1 0.3 \u03bcM, respectively). The electrochemical properties of p58C_(266-464) were also measured and this p58C construct was able to engage in redox switching on DNA with the same efficiency as p58C_(272-464). Together, these results show that although p58C can be stabilized in different conformations in the crystalline state, in solution there is effectively no difference in the structure and functional properties of p58C constructs of different lengths.", "doi": "10.1371/journal.pone.0209345", "pmcid": "PMC6298731", "issn": "1932-6203", "publisher": "Public Library of Science", "publication": "PLoS ONE", "publication_date": "2018-12", "series_number": "12", "volume": "13", "issue": "12", "pages": "Art. No. e0209345" }, { "id": "authors:k4n2j-kcv87", "collection": "authors", "collection_id": "k4n2j-kcv87", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180827-094622072", "type": "article", "title": "Nitric Oxide Modulates Endonuclease III Redox Activity by a 800 mV Negative Shift upon [Fe\u2084S\u2084] Cluster Nitrosylation", "author": [ { "family_name": "Ekanger", "given_name": "Levi A.", "orcid": "0000-0001-8131-1641", "clpid": "Ekanger-Levi-A" }, { "family_name": "Oyala", "given_name": "Paul H.", "orcid": "0000-0002-8761-4667", "clpid": "Oyala-Paul-H" }, { "family_name": "Moradian", "given_name": "Annie", "orcid": "0000-0002-0407-2031", "clpid": "Moradian-Annie" }, { "family_name": "Sweredoski", "given_name": "Michael J.", "orcid": "0000-0003-0878-3831", "clpid": "Sweredoski-Michael-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Here we characterize the [Fe\u2084S\u2084] cluster nitrosylation of a DNA repair enzyme, endonuclease III (EndoIII), using DNA-modified gold electrochemistry and protein film voltammetry, electrophoretic mobility shift assays, mass spectrometry of whole and trypsin-digested protein, and a variety of spectroscopies. Exposure of EndoIII to nitric oxide under anaerobic conditions transforms the [Fe\u2084S\u2084] cluster into a dinitrosyl iron complex, [(Cys)_2Fe(NO)_2]\u2212, and Roussin's red ester, [(\u03bc-Cys)_2Fe_2(NO)\u2084], in a 1:1 ratio with an average retention of 3.05 \u00b1 0.01 Fe per nitrosylated cluster. The formation of the dinitrosyl iron complex is consistent with previous reports, but the Roussin's red ester is an unreported product of EndoIII nitrosylation. Hyperfine sublevel correlation (HYSCORE) pulse EPR spectroscopy detects two distinct classes of NO with ^(14)N hyperfine couplings consistent with the dinitrosyl iron complex and reduced Roussin's red ester. Whole-protein mass spectrometry of EndoIII nitrosylated with ^(14)NO and ^(15)NO support the assignment of a protein-bound [(\u03bc-Cys)_2Fe_2(NO))_4] Roussin's red ester. The [Fe\u2084S\u2084]^(2+/3+) redox couple of DNA-bound EndoIII is observable using DNA-modified gold electrochemistry, but nitrosylated EndoIII does not display observable redox activity using DNA electrochemistry on gold despite having a similar DNA-binding affinity as the native protein. However, direct electrochemistry of protein films on graphite reveals the reduction potential of native and nitrosylated EndoIII to be 127 \u00b1 6 and \u2212674 \u00b1 8 mV vs NHE, respectively, corresponding to a shift of approximately \u2212800 mV with cluster nitrosylation. Collectively, these data demonstrate that DNA-bound redox activity, and by extension DNA-mediated charge transport, is modulated by [Fe\u2084S\u2084] cluster nitrosylation.", "doi": "10.1021/jacs.8b07362", "pmcid": "PMC6186442", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2018-09-19", "series_number": "37", "volume": "140", "issue": "37", "pages": "11800-11810" }, { "id": "authors:4h21e-z5y10", "collection": "authors", "collection_id": "4h21e-z5y10", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180222-102406884", "type": "article", "title": "A human MUTYH variant linking colonic polyposis to redox degradation of the [4Fe4S]\u00b2\u207a cluster", "author": [ { "family_name": "McDonnell", "given_name": "Kevin J.", "orcid": "0000-0002-4942-8943", "clpid": "McDonnell-K-J" }, { "family_name": "Chemler", "given_name": "Joseph A.", "clpid": "Chemler-J-A" }, { "family_name": "Bartels", "given_name": "Phillip L.", "clpid": "Bartels-P-L" }, { "family_name": "O'Brien", "given_name": "Elizabeth", "clpid": "O'Brien-Elizabeth" }, { "family_name": "Marvin", "given_name": "Monica L.", "clpid": "Marvin-M-L" }, { "family_name": "Ortega", "given_name": "Janice", "clpid": "Ortega-Janice" }, { "family_name": "Stern", "given_name": "Ralph H.", "clpid": "Stern-R-H" }, { "family_name": "Raskin", "given_name": "Leon", "clpid": "Raskin-L" }, { "family_name": "Li", "given_name": "Guo-Min", "orcid": "0000-0002-9842-4578", "clpid": "Li-Guo-Min" }, { "family_name": "Sherman", "given_name": "David H.", "orcid": "0000-0001-8334-3647", "clpid": "Sherman-D-H" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Gruber", "given_name": "Stephen B.", "clpid": "Gruber-S-B" } ], "abstract": "The human DNA repair enzyme MUTYH excises mispaired adenine residues in oxidized DNA. Homozygous MUTYH mutations underlie the autosomal, recessive cancer syndrome MUTYH-associated polyposis. We report a MUTYH variant, p.C306W (c.918C>G), with a tryptophan residue in place of native cysteine, that ligates the [4Fe4S] cluster in a patient with colonic polyposis and family history of early age colon cancer. In bacterial MutY, the [4Fe4S] cluster is redox active, allowing rapid localization to target lesions by long-range, DNA-mediated signalling. In the current study, using DNA electrochemistry, we determine that wild-type MUTYH is similarly redox-active, but MUTYH C306W undergoes rapid oxidative degradation of its cluster to [3Fe4S]^+, with loss of redox signalling. In MUTYH C306W, oxidative cluster degradation leads to decreased DNA binding and enzyme function. This study confirms redox activity in eukaryotic DNA repair proteins and establishes MUTYH C306W as a pathogenic variant, highlighting the essential role of redox signalling by the [4Fe4S] cluster.", "doi": "10.1038/s41557-018-0068-x", "pmcid": "PMC6060025", "issn": "1755-4330", "publisher": "Nature Publishing Group", "publication": "Nature Chemistry", "publication_date": "2018-08", "series_number": "8", "volume": "10", "issue": "8", "pages": "873-880" }, { "id": "authors:71wcn-2eb03", "collection": "authors", "collection_id": "71wcn-2eb03", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180524-092613150", "type": "article", "title": "Sensing DNA through DNA Charge Transport", "author": [ { "family_name": "Zwang", "given_name": "Theodore J.", "orcid": "0000-0002-6815-4482", "clpid": "Zwang-Theodore-J" }, { "family_name": "Tse", "given_name": "Edmund C. M.", "orcid": "0000-0002-9313-1290", "clpid": "Tse-Edmund-C-M" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "DNA charge transport chemistry involves the migration of charge over long molecular distances through the aromatic base pair stack within the DNA helix. This migration depends upon the intimate coupling of bases stacked one with another, and hence any perturbation in that stacking, through base modifications or protein binding, can be sensed electrically. In this review, we describe the many ways DNA charge transport chemistry has been utilized to sense changes in DNA, including the presence of lesions, mismatches, DNA-binding proteins, protein activity, and even reactions under weak magnetic fields. Charge transport chemistry is remarkable in its ability to sense the integrity of DNA.", "doi": "10.1021/acschembio.8b00347", "pmcid": "PMC6080280", "issn": "1554-8929", "publisher": "American Chemical Society", "publication": "ACS Chemical Biology", "publication_date": "2018-07-20", "series_number": "7", "volume": "13", "issue": "7", "pages": "1799-1809" }, { "id": "authors:hfgvq-7x764", "collection": "authors", "collection_id": "hfgvq-7x764", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180405-142009074", "type": "article", "title": "A Family of Rhodium Complexes with Selective Toxicity towards Mismatch Repair-Deficient Cancers", "author": [ { "family_name": "Boyle", "given_name": "Kelsey M.", "orcid": "0000-0002-6728-8403", "clpid": "Boyle-Kelsey-M" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Rhodium metalloinsertors are a unique set of metal complexes that bind specifically to DNA base pair mismatches in vitro and kill mismatch repair (MMR)-deficient cells at lower concentrations than their MMR-proficient counterparts. A family of metalloinsertors containing rhodium\u2013oxygen ligand coordination, termed \"Rh\u2013O\" metalloinsertors, has been prepared and shown to have a significant increase in both overall potency and selectivity toward MMR-deficient cells regardless of structural changes in the ancillary ligands. Here we describe DNA-binding and cellular studies with the second generation of Rh\u2013O metalloinsertors in which an ancillary ligand is varied in both steric bulk and lipophilicity. These complexes, of the form [Rh(L)(chrysi)(PPO)]^(2+), all include the O-containing PPO ligand (PPO = 2-(pyridine-2-yl)propan-2-ol) and the aromatic inserting ligand chrysi (5,6-chrysene quinone diimine) but differ in the identity of their ancillary ligand L, where L is a phenanthroline or bipyridyl derivative. The Rh\u2013O metalloinsertors in this family all show micromolar binding affinities for a 29-mer DNA hairpin containing a single CC mismatch. The complexes display comparable lipophilic tendencies and pK_a values of 8.1\u20139.1 for dissociation of an imine proton on the chrysi ligand. In cellular proliferation and cytotoxicity assays with MMR-deficient cells (HCT116O) and MMR-proficient cells (HCT116N), the complexes containing the phenanthroline-derived ligands show highly selective cytotoxic preference for the MMR-deficient cells at nanomolar concentrations. Using mass spectral analyses, it is shown that the complexes are taken into cells through a passive mechanism and exhibit low accumulation in mitochondria, an off-target organelle that, when targeted by parent metalloinsertors, can lead to nonselective cytotoxicity. Overall, these Rh\u2013O metalloinsertors have distinct and improved behavior compared to previous generations of parent metalloinsertors, making them ideal candidates for further therapeutic assessment.", "doi": "10.1021/jacs.8b02271", "pmcid": "PMC5965675", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2018-04-25", "series_number": "16", "volume": "140", "issue": "16", "pages": "5612-5624" }, { "id": "authors:e0y7y-4ta30", "collection": "authors", "collection_id": "e0y7y-4ta30", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180312-100907248", "type": "article", "title": "A Compass at Weak Magnetic Fields Using Thymine Dimer Repair", "author": [ { "family_name": "Zwang", "given_name": "Theodore J.", "orcid": "0000-0002-6815-4482", "clpid": "Zwang-Theodore-J" }, { "family_name": "Tse", "given_name": "Edmund C. M.", "orcid": "0000-0002-9313-1290", "clpid": "Tse-Edmund-Chun-Ming" }, { "family_name": "Zhong", "given_name": "Dongping", "clpid": "Zhong-Dongping" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "How birds sense the variations in Earth's magnetic field for navigation is poorly understood, although cryptochromes, proteins homologous to photolyases, have been proposed to participate in this magnetic sensing. Here, in electrochemical studies with an applied magnetic field, we monitor the repair of cyclobutane pyrimidine dimer lesions in duplex DNA by photolyase, mutants of photolyase, and a modified cryptochrome. We find that the yield of dimer repair is dependent on the strength and angle of the applied magnetic field even when using magnetic fields weaker than 1 gauss. This high sensitivity to weak magnetic fields depends upon a fast radical pair reaction on the thymines leading to repair. These data illustrate chemically how cyclobutane pyrimidine dimer repair may be used in a biological compass informed by variations in Earth's magnetic field.", "doi": "10.1021/acscentsci.8b00008", "pmcid": "PMC5879481", "issn": "2374-7943", "publisher": "American Chemical Society", "publication": "ACS Central Science", "publication_date": "2018-03-28", "series_number": "3", "volume": "4", "issue": "3", "pages": "405-412" }, { "id": "authors:jga11-5d250", "collection": "authors", "collection_id": "jga11-5d250", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180510-091834521", "type": "article", "title": "Probing Phenazine Electron Transfer and Retention in Pseudomonas Aeruginosa Biofilms", "author": [ { "family_name": "Saunders", "given_name": "Scott H.", "orcid": "0000-0003-4224-9106", "clpid": "Saunders-Scott-H" }, { "family_name": "Yates", "given_name": "Matthew D.", "orcid": "0000-0003-4373-3864", "clpid": "Yates-Matthew-D" }, { "family_name": "Tse", "given_name": "Edmund C. M.", "clpid": "Tse-Edmund-C-M" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Tender", "given_name": "Leonard M.", "orcid": "0000-0001-8784-991X", "clpid": "Tender-Leonard-M" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "The opportunistic pathogen Pseudomonas aeruginosa forms metabolically stratified biofilms. Redox-active phenazine metabolites shuttle metabolic electrons from the oxygen depleted biofilm interior to the oxygen saturated exterior, facilitating anoxic survival. We are testing the hypothesis that phenazine retention and/or charge transfer through the biofilm matrix are mediated by extracellular DNA (eDNA), which is the most abundant polymer in the P. aeruginosa matrix and is known to provide structural integrity to the biofilm. Specifically, we are growing biofilms on electrode arrays and performing in vitro studies of phenazine interactions with DNA. Biofilm experiments show that conductivity through the matrix is mediated by sequential electron transfer between phenazine molecules. Transferring electrode grown biofilms to fresh liquid medium demonstrates that some phenazines are retained tightly in the biofilm matrix, while others rapidly diffuse away. The retention of different phenazines corresponds to their affinity for DNA in vitro, consistent with the idea that some phenazines might bind the eDNA in the biofilm. We are testing whether phenazines bound to DNA can also mediate charge transfer. Collectively, these experiments are helping us better understand how P. aeruginosa utilizes its self-produced extracellular electron shuttles to survive biofilm oxidant limitation, and are opening up new perspectives on the role(s) that eDNA may play in the biofilm matrix.", "doi": "10.1016/j.bpj.2017.11.198", "issn": "0006-3495", "publisher": "Biophysical Society", "publication": "Biophysical Journal", "publication_date": "2018-02-02", "series_number": "3", "volume": "114", "issue": "3", "pages": "28a" }, { "id": "authors:d2s3h-bhg15", "collection": "authors", "collection_id": "d2s3h-bhg15", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171211-090046935", "type": "article", "title": "A Redox Role for the [4Fe4S] Cluster of Yeast DNA Polymerase \u03b4", "author": [ { "family_name": "Bartels", "given_name": "Phillip L.", "clpid": "Bartels-P-L" }, { "family_name": "Stodola", "given_name": "Joseph L.", "clpid": "Stodola-J-L" }, { "family_name": "Burgers", "given_name": "Peter M. J.", "clpid": "Burgers-P-M-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "A [4Fe4S]^(2+) cluster in the C-terminal domain of the catalytic subunit of the eukaryotic B-family DNA polymerases is essential for the formation of active multi-subunit complexes. Here we use a combination of electrochemical and biochemical methods to assess the redox activity of the [4Fe4S]^(2+) cluster in Saccharomyces cerevisiae polymerase (Pol) \u03b4, the lagging strand DNA polymerase. We find that Pol \u03b4 bound to DNA is indeed redox-active at physiological potentials, generating a DNA-mediated signal electrochemically with a midpoint potential of 113 \u00b1 5 mV versus NHE. Moreover, biochemical assays following electrochemical oxidation of Pol \u03b4 reveal a significant slowing of DNA synthesis that can be fully reversed by reduction of the oxidized form. A similar result is apparent with photooxidation using a DNA-tethered anthraquinone. These results demonstrate that the [4Fe4S] cluster in Pol \u03b4 can act as a redox switch for activity, and we propose that this switch can provide a rapid and reversible way to respond to replication stress.", "doi": "10.1021/jacs.7b10284", "pmcid": "PMC5881389", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2017-12-20", "series_number": "50", "volume": "139", "issue": "50", "pages": "18339-18348" }, { "id": "authors:k9jwd-r1m73", "collection": "authors", "collection_id": "k9jwd-r1m73", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171115-104208193", "type": "article", "title": "A rhodium-cyanine fluorescent probe: detection and signaling of mismatches in DNA", "author": [ { "family_name": "Nano", "given_name": "Adela", "orcid": "0000-0002-1984-5770", "clpid": "Nano-Adela" }, { "family_name": "Boynton", "given_name": "Adam N.", "orcid": "0000-0003-4427-513X", "clpid": "Boynton-Adam-Nathaniel" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "We report a bifunctional fluorescent probe that combines a rhodium metalloinsertor with a cyanine dye as the fluorescent reporter. The conjugate shows weak luminescence when free in solution or with well matched DNA but exhibits a significant luminescence increase in the presence of a 27-mer DNA duplex containing a central CC mismatch. DNA photocleavage experiments demonstrate that, upon photoactivation, the conjugate cleaves the DNA backbone specifically near the mismatch site on a 27-mer fragment, consistent with mismatch targeting. Fluorescence titrations with the 27-mer duplex containing the CC mismatch reveal a DNA binding affinity of 3.1 \u00d7 10^6 M^(\u20131), similar to that of other rhodium metalloinsertors. Fluorescence titrations using genomic DNA extracted from various cell lines demonstrate a clear discrimination in fluorescence between those cell lines that are proficient or deficient in mismatch repair. This differential luminescence reflects the sensitive detection of the mismatchrepair-deficient phenotype.", "doi": "10.1021/jacs.7b10639", "pmcid": "PMC5892186", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2017-12-06", "series_number": "48", "volume": "139", "issue": "48", "pages": "17301-17304" }, { "id": "authors:z1fec-24d82", "collection": "authors", "collection_id": "z1fec-24d82", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180112-074331185", "type": "article", "title": "The Mechanisms for counting and handoff by human DNA primase: a role for the 4Fe-4S cluster?", "author": [ { "family_name": "Chazin", "given_name": "Walter", "orcid": "0000-0002-2180-0790", "clpid": "Chazin-W-J" }, { "family_name": "Barton", "given_name": "Jacqueline", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Thompson", "given_name": "Matthew", "clpid": "Thompson-M-K" }, { "family_name": "O'Brien", "given_name": "Elizabeth", "clpid": "O'Brien-Elizabeth" }, { "family_name": "Holt", "given_name": "Marilyn", "orcid": "0000-0002-3164-869X", "clpid": "Holt-M-E" }, { "family_name": "Salay", "given_name": "Lauren", "clpid": "Salay-L-E" }, { "family_name": "Ehlinger", "given_name": "Aaron", "clpid": "Ehlinger-A-C" } ], "abstract": "[No abstract]", "doi": "10.1002/pro.3349", "issn": "0961-8368", "publisher": "Wiley", "publication": "Protein Science", "publication_date": "2017-12", "series_number": "S1", "volume": "26", "issue": "S1", "pages": "147-148" }, { "id": "authors:km6j9-02594", "collection": "authors", "collection_id": "km6j9-02594", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170818-103108794", "type": "article", "title": "The Oxidation State of [4Fe4S] Clusters Modulates the DNA-Binding Affinity of DNA Repair Proteins", "author": [ { "family_name": "Tse", "given_name": "Edmund C. M.", "orcid": "0000-0002-9313-1290", "clpid": "Tse-Edmund-C-M" }, { "family_name": "Zwang", "given_name": "Theodore J.", "orcid": "0000-0002-6815-4482", "clpid": "Zwang-Theodore-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "A central question important to understanding DNA repair is how certain proteins are able to search for, detect, and fix DNA damage on a biologically relevant time scale. A feature of many base excision repair proteins is that they contain [4Fe4S] clusters that may aid their search for lesions. In this paper, we establish the importance of the oxidation state of the redox-active [4Fe4S] cluster in the DNA damage detection process. We utilize DNA-modified electrodes to generate repair proteins with [4Fe4S] clusters in the 2+ and 3+ states by bulk electrolysis under an O_2-free atmosphere. Anaerobic microscale thermophoresis results indicate that proteins carrying [4Fe4S]^(3+) clusters bind to DNA 550 times more tightly than those with [4Fe4S]^(2+) clusters. The measured increase in DNA-binding affinity matches the calculated affinity change associated with the redox potential shift observed for [4Fe4S] cluster proteins upon binding to DNA. We further devise an electrostatic model that shows this change in DNA-binding affinity of these proteins can be fully explained by the differences in electrostatic interactions between DNA and the [4Fe4S] cluster in the reduced versus oxidized state. We then utilize atomic force microscopy (AFM) to demonstrate that the redox state of the [4Fe4S] clusters regulates the ability of two DNA repair proteins, Endonuclease III and DinG, to bind preferentially to DNA duplexes containing a single site of DNA damage (here a base mismatch) which inhibits DNA charge transport. Together, these results show that the reduction and oxidation of [4Fe4S] clusters through DNA-mediated charge transport facilitates long-range signaling between [4Fe4S] repair proteins. The redox-modulated change in DNA-binding affinity regulates the ability of [4Fe4S] repair proteins to collaborate in the lesion detection process.", "doi": "10.1021/jacs.7b07230", "pmcid": "PMC5929122", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2017-09-13", "series_number": "36", "volume": "139", "issue": "36", "pages": "12784-12792" }, { "id": "authors:z7hxn-92t93", "collection": "authors", "collection_id": "z7hxn-92t93", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170719-101916396", "type": "article", "title": "Sulfur K-Edge XAS Studies of the Effect of DNA Binding on the [Fe_4S_4] Site in EndoIII and MutY", "author": [ { "family_name": "Ha", "given_name": "Yang", "clpid": "Ha-Yang" }, { "family_name": "Arnold", "given_name": "Anna R.", "clpid": "Arnold-Anna-R" }, { "family_name": "Nu\u00f1ez", "given_name": "Nicole N.", "clpid": "Nu\u00f1ez-Nicole-N" }, { "family_name": "Bartels", "given_name": "Phillip L.", "clpid": "Bartels-Phillip-L" }, { "family_name": "Zhou", "given_name": "Andy", "clpid": "Zhou-Andy" }, { "family_name": "David", "given_name": "Sheila S.", "orcid": "0000-0001-5873-7935", "clpid": "David-Sheila-S" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Hedman", "given_name": "Britt", "clpid": "Hedman-Britt" }, { "family_name": "Hodgson", "given_name": "Keith O.", "clpid": "Hodgson-Keith-O" }, { "family_name": "Solomon", "given_name": "Edward I.", "orcid": "0000-0003-0291-3199", "clpid": "Solomon-Edward-I" } ], "abstract": "S K-edge X-ray absorption spectroscopy (XAS) was used to study the [Fe_4S_4] clusters in the DNA repair glycosylases EndoIII and MutY to evaluate the effects of DNA binding and solvation on Fe\u2013S bond covalencies (i.e., the amount of S 3p character mixed into the Fe 3d valence orbitals). Increased covalencies in both iron\u2013thiolate and iron\u2013sulfide bonds would stabilize the oxidized state of the [Fe_4S_4] clusters. The results are compared to those on previously studied [Fe_4S_4] model complexes, ferredoxin (Fd), and to new data on high-potential iron\u2013sulfur protein (HiPIP). A limited decrease in covalency is observed upon removal of solvent water from EndoIII and MutY, opposite to the significant increase observed for Fd, where the [Fe_4S_4] cluster is solvent exposed. Importantly, in EndoIII and MutY, a large increase in covalency is observed upon DNA binding, which is due to the effect of its negative charge on the iron\u2013sulfur bonds. In EndoIII, this change in covalency can be quantified and makes a significant contribution to the observed decrease in reduction potential found experimentally in DNA repair proteins, enabling their HiPIP-like redox behavior.", "doi": "10.1021/jacs.7b03966", "pmcid": "PMC5568943", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2017-08-23", "series_number": "33", "volume": "139", "issue": "33", "pages": "11434-11442" }, { "id": "authors:ahngd-2am75", "collection": "authors", "collection_id": "ahngd-2am75", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170720-130038340", "type": "article", "title": "Response to Comments on \"The [4Fe4S] cluster of human DNA primase functions as a redox switch using DNA charge transport\"", "author": [ { "family_name": "O'Brien", "given_name": "Elizabeth", "clpid": "O'Brien-Elizabeth" }, { "family_name": "Holt", "given_name": "Marilyn E.", "orcid": "0000-0002-3164-869X", "clpid": "Holt-Marilyn-E" }, { "family_name": "Thompson", "given_name": "Matthew K.", "clpid": "Thompson-Matthew-K" }, { "family_name": "Salay", "given_name": "Lauren E.", "clpid": "Salay-Lauren-E" }, { "family_name": "Ehlinger", "given_name": "Aaron C.", "clpid": "Ehlinger-Aaaron-C" }, { "family_name": "Chazin", "given_name": "Walter J.", "orcid": "0000-0002-2180-0790", "clpid": "Chazin-Walter-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Baranovskiy et al. and Pellegrini argue that, based on structural data, the path for charge transfer through the [4Fe4S] domain of primase is not feasible. Our manuscript presents electrochemical data directly showing charge transport through DNA to the [4Fe4S] cluster of a primase p58C construct and a reversible switch in the DNA-bound signal with oxidation/reduction, which is inhibited by mutation of three tyrosine residues. Although the dispositions of tyrosines differ in different constructs, all are within range for microsecond electron transfer.", "doi": "10.1126/science.aan2762", "pmcid": "PMC5935490", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2017-07-20", "series_number": "6348", "volume": "357", "issue": "6348", "pages": "Art. No. 2762" }, { "id": "authors:khd4k-zta92", "collection": "authors", "collection_id": "khd4k-zta92", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170705-085833705", "type": "article", "title": "A Ruthenium(II) Complex as a Luminescent Probe for DNA Mismatches and Abasic Sites", "author": [ { "family_name": "Boynton", "given_name": "Adam N.", "orcid": "0000-0003-4427-513X", "clpid": "Boynton-Adam-Nathaniel" }, { "family_name": "Marc\u00e9lis", "given_name": "Lionel", "orcid": "0000-0002-6324-477X", "clpid": "Marc\u00e9lis-Lionel" }, { "family_name": "McConnell", "given_name": "Anna J.", "orcid": "0000-0001-7329-4319", "clpid": "McConnell-Anna-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "[Ru(bpy)_2(BNIQ)]^(2+) (BNIQ = Benzo[c][1,7]naphthyridine-1-isoquinoline), which incorporates the sterically expansive BNIQ ligand, is a highly selective luminescent probe for DNA mismatches and abasic sites, possessing a 500-fold higher binding affinity toward these destabilized regions relative to well-matched base pairs. As a result of this higher binding affinity, the complex exhibits an enhanced steady-state emission in the presence of DNA duplexes containing a single base mismatch or abasic site compared to fully well-matched DNA. Luminescence quenching experiments with Cu(phen)_2^(2+) and [Fe(CN)_6]^(3\u2013) implicate binding of the complex to a mismatch from the minor groove via metalloinsertion. The emission response of the complex to different single base mismatches, binding preferentially to the more destabilized mismatches, is also consistent with binding by metalloinsertion. This work shows that high selectivity toward destabilized regions in duplex DNA can be achieved through the rational design of a complex with a sterically expansive aromatic ligand.", "doi": "10.1021/acs.inorgchem.7b01037", "pmcid": "PMC5516787", "issn": "0020-1669", "publisher": "American Chemical Society", "publication": "Inorganic Chemistry", "publication_date": "2017-07-17", "series_number": "14", "volume": "56", "issue": "14", "pages": "8381-8389" }, { "id": "authors:920hn-jde20", "collection": "authors", "collection_id": "920hn-jde20", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170622-100942401", "type": "article", "title": "Rhodium metalloinsertor binding generates a lesion with selective cytotoxicity for mismatch repair-deficient cells", "author": [ { "family_name": "Bailis", "given_name": "Julie M.", "clpid": "Bailis-Julie-M" }, { "family_name": "Weidmann", "given_name": "Alyson G.", "clpid": "Weidmann-Alyson-G" }, { "family_name": "Mariano", "given_name": "Natalie F.", "clpid": "Mariano-Natalie-F" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The DNA mismatch repair (MMR) pathway recognizes and repairs errors in base pairing and acts to maintain genome stability. Cancers that have lost MMR function are common and comprise an important clinical subtype that is resistant to many standard of care chemotherapeutics such as cisplatin. We have identified a family of rhodium metalloinsertors that bind DNA mismatches with high specificity and are preferentially cytotoxic to MMR-deficient cells. Here, we characterize the cellular mechanism of action of the most potent and selective complex in this family, [Rh(chrysi)(phen)(PPO)]^(2+) (Rh-PPO). We find that Rh-PPO binding induces a lesion that triggers the DNA damage response (DDR). DDR activation results in cell-cycle blockade and inhibition of DNA replication and transcription. Significantly, the lesion induced by Rh-PPO is not repaired in MMR-deficient cells, resulting in selective cytotoxicity. The Rh-PPO mechanism is reminiscent of DNA repair enzymes that displace mismatched bases, and is differentiated from other DNA-targeted chemotherapeutics such as cisplatin by its potency, cellular mechanism, and selectivity for MMR-deficient cells.", "doi": "10.1073/pnas.1706665114", "pmcid": "PMC5502648", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2017-07-03", "series_number": "27", "volume": "114", "issue": "27", "pages": "6948-6953" }, { "id": "authors:en86e-jb249", "collection": "authors", "collection_id": "en86e-jb249", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170306-132005349", "type": "article", "title": "Electrochemistry of the [4Fe4S] Cluster in Base Excision Repair Proteins: Tuning the Redox Potential with DNA", "author": [ { "family_name": "Bartels", "given_name": "Phillip L.", "clpid": "Bartels-Phillip-L" }, { "family_name": "Zhou", "given_name": "Andy", "clpid": "Zhou-Andy" }, { "family_name": "Arnold", "given_name": "Anna R.", "clpid": "Arnold-Anna-R" }, { "family_name": "Nu\u00f1ez", "given_name": "Nicole N.", "clpid": "Nu\u00f1ez-Nicole-N" }, { "family_name": "Crespilho", "given_name": "Frank N.", "clpid": "Crespilho-Frank-N" }, { "family_name": "David", "given_name": "Sheila S.", "orcid": "0000-0001-5873-7935", "clpid": "David-Sheila-S" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Escherichia coli endonuclease III (EndoIII) and MutY are DNA glycosylases that contain [4Fe4S] clusters and that serve to maintain the integrity of the genome after oxidative stress. Electrochemical studies on highly oriented pyrolytic graphite (HOPG) revealed that DNA binding by EndoIII leads to a large negative shift in the midpoint potential of the cluster, consistent with stabilization of the oxidized [4Fe4S]^(3+) form. However, the smooth, hydrophobic HOPG surface is nonideal for working with proteins in the absence of DNA. In this work, we use thin film voltammetry on a pyrolytic graphite edge electrode to overcome these limitations. Improved adsorption leads to substantial signals for both EndoIII and MutY in the absence of DNA, and a large negative potential shift is retained with DNA present. In contrast, the EndoIII mutants E200K, Y205H, and K208E, which provide electrostatic perturbations in the vicinity of the cluster, all show DNA-free potentials within error of wild type; similarly, the presence of negatively charged poly-L-glutamate does not lead to a significant potential shift. Overall, binding to the DNA polyanion is the dominant effect in tuning the redox potential of the [4Fe4S] cluster, helping to explain why all DNA-binding proteins with [4Fe4S] clusters studied to date have similar DNA-bound potentials.", "doi": "10.1021/acs.langmuir.6b04581", "pmcid": "PMC5423460", "issn": "0743-7463", "publisher": "American Chemical Society", "publication": "Langmuir", "publication_date": "2017-03-14", "series_number": "10", "volume": "33", "issue": "10", "pages": "2523-2530" }, { "id": "authors:263g7-pcc67", "collection": "authors", "collection_id": "263g7-pcc67", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170223-150518455", "type": "article", "title": "The [4Fe4S] cluster of human DNA primase functions as a redox switch using DNA charge transport", "author": [ { "family_name": "O'Brien", "given_name": "Elizabeth", "clpid": "O'Brien-Elizabeth" }, { "family_name": "Holt", "given_name": "Marilyn E.", "orcid": "0000-0002-3164-869X", "clpid": "Holt-Marilyn-E" }, { "family_name": "Thompson", "given_name": "Matthew K.", "clpid": "Thompson-Matthew-K" }, { "family_name": "Salay", "given_name": "Lauren E.", "clpid": "Salay-Lauren-E" }, { "family_name": "Ehlinger", "given_name": "Aaron C.", "clpid": "Ehlinger-Aaron-C" }, { "family_name": "Chazin", "given_name": "Walter J.", "orcid": "0000-0002-2180-0790", "clpid": "Chazin-Walter-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "DNA charge transport chemistry offers a means of long-range, rapid redox signaling. We demonstrate that the [4Fe4S] cluster in human DNA primase can make use of this chemistry to coordinate the first steps of DNA synthesis. Using DNA electrochemistry, we found that a change in oxidation state of the [4Fe4S] cluster acts as a switch for DNA binding. Single-atom mutations that inhibit this charge transfer hinder primase initiation without affecting primase structure or polymerization. Generating a single base mismatch in the growing primer duplex, which attenuates DNA charge transport, inhibits primer truncation. Thus, redox signaling by [4Fe4S] clusters using DNA charge transport regulates primase binding to DNA and illustrates chemistry that may efficiently drive substrate handoff between polymerases during DNA replication.", "doi": "10.1126/science.aag1789", "pmcid": "PMC5338353", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2017-02-24", "series_number": "6327", "volume": "355", "issue": "6327", "pages": "Art. No. eaag1789" }, { "id": "authors:g3f47-e8502", "collection": "authors", "collection_id": "g3f47-e8502", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170112-075221809", "type": "article", "title": "Ahmed H. Zewail", "author": [ { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "[no abstract]", "issn": "0009-2347", "publisher": "American Chemical Society", "publication": "Chemical & Engineering News", "publication_date": "2016-12-19", "series_number": "49", "volume": "94", "issue": "49", "pages": "43" }, { "id": "authors:2z7m4-vxh66", "collection": "authors", "collection_id": "2z7m4-vxh66", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161117-080611089", "type": "article", "title": "Helix-dependent Spin Filtering through the DNA Duplex", "author": [ { "family_name": "Zwang", "given_name": "Theodore J.", "orcid": "0000-0002-6815-4482", "clpid": "Zwang-Theodore-J" }, { "family_name": "H\u00fcrlimann", "given_name": "Sylvia", "clpid": "H\u00fcrlimann-Sylvia" }, { "family_name": "Hill", "given_name": "Michael G.", "clpid": "Hill-Michael-G" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Recent work suggests that electrons can travel through DNA and other chiral molecules in a spin-selective manner, but little is known about the origin of this spin selectivity. Here we describe experiments on magnetized DNA-modified electrodes to explore spin-selective electron transport through hydrated duplex DNA. Our results show that the two spins migrate through duplex DNA with different yield, and that spin selectivity requires charge transport through the DNA duplex. Significantly, shifting the same duplex DNA between right-handed B- and left-handed Z-forms leads to a diode-like switch in spin-selectivity; which spin moves more efficiently through the duplex depends upon the DNA helicity. With DNA, the supramolecular organization of chiral moieties, rather than the chirality of the individual monomers, determines the selectivity in spin, and thus a conformational change can switch the spin selectivity.", "doi": "10.1021/jacs.6b10538", "pmcid": "PMC5175457", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2016-12-07", "series_number": "48", "volume": "138", "issue": "48", "pages": "15551-15554" }, { "id": "authors:k5qze-qke18", "collection": "authors", "collection_id": "k5qze-qke18", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160125-103800513", "type": "article", "title": "Targeting DNA mismatches with rhodium metalloinsertors", "author": [ { "family_name": "Boyle", "given_name": "Kelsey M.", "orcid": "0000-0002-6728-8403", "clpid": "Boyle-Kelsey-M" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "DNA has been exploited as a biological target of chemotherapeutics since the 1940s. Traditional chemotherapeutics, such as cisplatin and DNA-alkylating agents, rely primarily on increased uptake by rapidly proliferating cancer cells for therapeutic effects, but this strategy can result in off-target toxicity in healthy tissue. Recently, research interests have shifted towards targeted chemotherapeutics, in which a drug targets a specific biological signature of cancer, resulting in selective toxicity towards cancerous cells. Here, we review a family of complexes, termed rhodium metalloinsertors, that selectively target DNA base pair mismatches, a hallmark of mismatch repair (MMR)-deficient cancers. These rhodium metalloinsertors bind DNA mismatches with high specificity and display high selectively in killing MMR-deficient versus MMR-proficient cells. This cell selectivity is unique among small molecules that bind DNA. Current generations of rhodium metalloinsertors have shown nanomolar potency along with high selectivity towards MMR-deficient cells, and show promise as a foundation for a new family of chemotherapeutics for MMR-deficient cancers.", "doi": "10.1016/j.ica.2016.01.021", "pmcid": "PMC5061454", "issn": "0020-1693", "publisher": "Elsevier", "publication": "Inorganica Chimica Acta", "publication_date": "2016-10-01", "volume": "452", "pages": "3-11" }, { "id": "authors:2djz8-d4540", "collection": "authors", "collection_id": "2djz8-d4540", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161128-100708366", "type": "article", "title": "Redox Signaling through DNA", "author": [ { "family_name": "O'Brien", "given_name": "Elizabeth", "clpid": "O'Brien-Elizabeth" }, { "family_name": "Silva", "given_name": "Rebekah M. B.", "orcid": "0000-0002-9144-4939", "clpid": "Silva-Rebekah-M-B" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Biological electron transfer reactions between metal cofactors are critical to many essential processes within the cell. Duplex DNA is, moreover, capable of mediating the transport of charge through its \u03c0-stacked nitrogenous bases. Increasingly, [4Fe4S] clusters, generally redox-active cofactors, have been found to be associated with enzymes involved in DNA processing. DNA-binding enzymes containing [4Fe4S] clusters can thus utilize DNA charge transport (DNA CT) for redox signaling to coordinate reactions over long molecular distances. In particular, DNA CT signaling may represent the first step in the search for DNA lesions by proteins containing [4Fe4S] clusters that are involved in DNA repair. Here we describe research carried out to examine the chemical characteristics and biological consequences of DNA CT. We are finding that DNA CT among metalloproteins represents powerful chemistry for redox signaling at long range within the cell.", "doi": "10.1002/ijch.201600022", "pmcid": "PMC5225960", "issn": "0021-2148", "publisher": "Laser Pages Publishing Ltd", "publication": "Israel Journal of Chemistry", "publication_date": "2016-10", "series_number": "9-10", "volume": "56", "issue": "9-10", "pages": "705-723" }, { "id": "authors:fyhhf-cr965", "collection": "authors", "collection_id": "fyhhf-cr965", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160907-083741647", "type": "article", "title": "Characterization of the DNA-Mediated Oxidation of Dps, A Bacterial Ferritin", "author": [ { "family_name": "Arnold", "given_name": "Anna R.", "clpid": "Arnold-Anna-R" }, { "family_name": "Zhou", "given_name": "Andy", "clpid": "Zhou-Andy" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Dps proteins are bacterial ferritins that protect DNA from oxidative stress and have been implicated in bacterial survival and virulence. In addition to direct oxidation of the Dps iron sites by diffusing oxidants, oxidation from a distance via DNA charge transport (CT), where electrons and electron holes are rapidly transported through the base-pair \u03c0-stack, could represent an efficient DNA protection mechanism utilized by Dps. Here, we spectroscopically characterize the DNA-mediated oxidation of ferrous iron-loaded Dps. X-band EPR was used to monitor the oxidation of DNA-bound Dps after DNA photooxidation using an intercalating ruthenium photooxidant and the flash-quench technique. Upon irradiation with poly(dGdC)_2, a signal arises with g = 4.3, consistent with the formation of mononuclear high-spin Fe(III) sites of low symmetry, the expected oxidation product of Dps with one iron bound at each ferroxidase site. When poly(dGdC)_2 is substituted with poly(dAdT)_2, the yield of Dps oxidation is decreased significantly, consistent with guanine radical intermediates facilitating Dps oxidation. We have also explored possible protein electron transfer (ET) intermediates in the DNA-mediated oxidation of ferrous iron-loaded Dps. Dps proteins contain a conserved tryptophan residue in close proximity to the iron-binding ferroxidase site (W52 in E. coli Dps). In EPR studies of the oxidation of ferrous iron-loaded Dps following DNA photooxidation, a W52A Dps mutant was significantly deficient compared to WT Dps in forming the characteristic EPR signal at g = 4.3, consistent with W52 acting as an ET hopping intermediate. This effect is mirrored in vivo in E. coli survival in response to hydrogen peroxide, where mutation of W52 leads to decreased survival under oxidative stress.", "doi": "10.1021/jacs.6b06507", "pmcid": "PMC5014645", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2016-09-07", "series_number": "35", "volume": "138", "issue": "35", "pages": "11290-11298" }, { "id": "authors:x827g-d0b38", "collection": "authors", "collection_id": "x827g-d0b38", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160418-100658436", "type": "article", "title": "[Ru(Me\u2084phen)\u2082dppz]\u00b2\u207a, a Light Switch for DNA Mismatches", "author": [ { "family_name": "Boynton", "given_name": "Adam N.", "orcid": "0000-0003-4427-513X", "clpid": "Boynton-Adam-Nathaniel" }, { "family_name": "Marc\u00e9lis", "given_name": "Lionel", "orcid": "0000-0002-6324-477X", "clpid": "Marc\u00e9lis-Lionel" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "[Ru(Me\u2084phen)\u2082dppz]\u00b2\u207a serves as a luminescent \"light switch\" for single base mismatches in DNA. The preferential luminescence enhancement observed with mismatches results from two factors: (i) the complex possesses a 26-fold higher binding affinity toward the mismatch compared to well-matched base pairs, and (ii) the excited state emission lifetime of the ruthenium bound to the DNA mismatch is 160 ns versus 35 ns when bound to a matched site. Results indicate that the complex binds to the mismatch through a metalloinsertion binding mode. Cu(phen)\u2082\u00b2\u207a quenching experiments show that the complex binds to the mismatch from the minor groove, characteristic of metalloinsertion. Additionally, the luminescence intensity of the complex with DNA containing single base mismatches correlates with the thermodynamic destabilization of the mismatch, also consistent with binding through metalloinsertion. This complex represents a potentially new early cancer diagnostic for detecting deficiencies in mismatch repair.", "doi": "10.1021/jacs.6b02022", "pmcid": "PMC4989906", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2016-04-20", "series_number": "15", "volume": "138", "issue": "15", "pages": "5020-5023" }, { "id": "authors:ht1e9-vp666", "collection": "authors", "collection_id": "ht1e9-vp666", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160606-074814901", "type": "article", "title": "DNA-Mediated Redox Signaling in Bacterial Nucleotide Excision Repair by UvrC", "author": [ { "family_name": "Silva", "given_name": "Rebekah M. B.", "clpid": "Silva-R-M-B" }, { "family_name": "Zhou", "given_name": "Andy", "clpid": "Zhou-Andy" }, { "family_name": "Grodick", "given_name": "Michael A.", "clpid": "Grodick-M-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Our laboratory has proposed redox signaling among DNA repair proteins containing 4Fe-4S clusters through DNA charge transport (DNA CT) as a first step in lesion detection. Recently, we have explored whether UvrC, the endonuclease in Nucleotide Excision Repair (NER), may also contain a 4Fe-4S cluster. A new purification route was developed to express an MBP-UvrC fusion protein, and evidence of a 4Fe-4S cluster was seen by UV-Visible (UV-Vis) and Electron Paramagnetic Resonance (EPR) spectroscopy. Like other 4Fe-4S repair proteins studied in our lab, MBP-UvrC can participate in DNA CT chemistry, as evidenced by its electrochemical activity on DNA-modified gold electrodes. Complementing in vivo genetic assays have been developed and indicate that DNA-mediated signaling between UvrC and other DNA-processing enzymes containing 4Fe-4S clusters is occurring. Taken together, these results have suggested that UvrC is part of a network of 4Fe-4S proteins that communicate using DNA CT to find lesions and maintain genomic integrity. Additional in vitro and in vivo characterization is underway to understand further the biological implications of the newly-discovered, DNA-mediated redox chemistry of UvrC.", "doi": "10.1016/j.bpj.2015.11.403", "issn": "0006-3495", "publisher": "Biophysical Society", "publication": "Biophysical Journal", "publication_date": "2016-02-16", "series_number": "3", "volume": "110", "issue": "3", "pages": "62A-63A" }, { "id": "authors:34sfb-tqw76", "collection": "authors", "collection_id": "34sfb-tqw76", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160603-153447332", "type": "article", "title": "Cracking Open a Molecular Calculator: DNA Charge Transport and Primase", "author": [ { "family_name": "Holt", "given_name": "Marilyn E.", "orcid": "0000-0002-3164-869X", "clpid": "Holt-M-E" }, { "family_name": "O'Brien", "given_name": "Elizabeth", "clpid": "O'Brien-Elizabeth" }, { "family_name": "Salay", "given_name": "Lauren", "clpid": "Salay-L" }, { "family_name": "Thompson", "given_name": "Matthew", "clpid": "Thompson-M" }, { "family_name": "Ehlinger", "given_name": "Aaron", "clpid": "Ehlinger-A-C" }, { "family_name": "Barton", "given_name": "Jacqueline", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Chazin", "given_name": "Walter", "orcid": "0000-0002-2180-0790", "clpid": "Chazin-W-J" } ], "abstract": "De novo initiation of DNA synthesis by DNA polymerases requires formation of an initial \"primer\" on the template. In eukaryotes, this function is provided by a distinct DNA primase. Primase, a DNA-dependent RNA polymerase, generates short (8-12 nt) RNA primers on ssDNA templates. These initial RNA primers are handed off to DNA polymerase \u03b1 (pol \u03b1), which extends the primer by \u223c20 nts. This primed RNA/DNA substrate is then handed off to processive polymerases \u03b5 or \u03b4, which synthesize the vast majority of new DNA on the leading and lagging strands. X-ray crystal structures of human primase have been used to propose models for the catalytic mechanism. However, the molecular basis for primer counting and handoff remains unclear. Primase contains a 4Fe-4S cluster in the p58C domain critical to pol-prim loading and activity, but its specific function is not known. We are investigating the hypothesis that the function of the cluster is to drive primer length counting. Well-stacked duplex DNA has been shown capable of transporting charge over long distances, and it has been proposed this phenomenon enables communication between Fe-S cluster-containing proteins. In this study, we show the 4Fe-4S cluster in wild-type p58C is capable of mediating charge transport (CT) with DNA. DNA-modified electrodes were used to characterize the electrochemistry of p58C. Based on previously determined WT structures, we identified a possible pathway from the cluster to the DNA binding site in p58C and designed mutants of key residues in this pathway. Mutation of Tyr345 to Phe greatly diminishes DNA CT. Primase activity assays with WT and mutant proteins revealed substantial differences in product length distribution. These data suggest charge transport is involved in primer length counting and may signal for primer template handoff to pol \u03b1.", "doi": "10.1016/j.bpj.2015.11.172", "issn": "0006-3495", "publisher": "Biophysical Society", "publication": "Biophysical Journal", "publication_date": "2016-02-16", "series_number": "3", "volume": "110", "issue": "3", "pages": "21A" }, { "id": "authors:7hy11-gjf26", "collection": "authors", "collection_id": "7hy11-gjf26", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160307-094405041", "type": "article", "title": "DNA Charge Transport: from Chemical Principles to the Cell", "author": [ { "family_name": "Arnold", "given_name": "Anna R.", "clpid": "Arnold-Anna-R" }, { "family_name": "Grodick", "given_name": "Michael A.", "orcid": "0000-0001-6618-6731", "clpid": "Grodick-Michael-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The DNA double helix has captured the imagination of many, bringing it to the forefront of biological research. DNA has unique features that extend our interest into areas of chemistry, physics, material science, and engineering. Our laboratory has focused on studies of DNA charge transport (CT), wherein charges can efficiently travel long molecular distances through the DNA helix while maintaining an exquisite sensitivity to base pair \u03c0-stacking. Because DNA CT chemistry reports on the integrity of the DNA duplex, this property may be exploited to develop electrochemical devices to detect DNA lesions and DNA-binding proteins. Furthermore, studies now indicate that DNA CT may also be used in the cell by, for example, DNA repair proteins, as a cellular diagnostic, in order to scan the genome to localize efficiently to damage sites. In this review, we describe this evolution of DNA CT chemistry from the discovery of fundamental chemical principles to applications in diagnostic strategies and possible roles in biology.", "doi": "10.1016/j.chembiol.2015.11.010", "pmcid": "PMC4803044", "issn": "2451-9456", "publisher": "Cell Press", "publication": "Cell Chemical Biology", "publication_date": "2016-01-21", "series_number": "1", "volume": "23", "issue": "1", "pages": "183-197" }, { "id": "authors:4pgdb-hmh88", "collection": "authors", "collection_id": "4pgdb-hmh88", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150928-090441652", "type": "article", "title": "A Monofunctional Platinum Complex Coordinated to a Rhodium Metalloinsertor Selectively Binds Mismatched DNA in the Minor Groove", "author": [ { "family_name": "Weidmann", "given_name": "Alyson G.", "orcid": "0000-0003-3876-2847", "clpid": "Weidmann-Alyson-G" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "We report the synthesis and characterization of a bimetallic complex derived from a new family of potent and selective metalloinsertors containing an unusual Rh\u2013O axial coordination. This complex incorporates a monofunctional platinum center containing only one labile site for coordination to DNA, rather than two, and coordinates DNA nonclassically through adduct formation in the minor groove. This conjugate displays bifunctional, interdependent binding of mismatched DNA via metalloinsertion at a mismatch as well as covalent platinum binding. DNA sequencing experiments revealed that the preferred site of platinum coordination is not the traditional N7-guanine site in the major groove, but rather N3-adenine in the minor groove. The complex also displays enhanced cytotoxicity in mismatch repair-deficient and mismatch repair-proficient human colorectal carcinoma cell lines compared to the chemotherapeutic cisplatin, and it triggers cell death via an apoptotic pathway, rather than the necrotic pathway induced by rhodium metalloinsertors.", "doi": "10.1021/acs.inorgchem.5b01722", "pmcid": "PMC4618505", "issn": "0020-1669", "publisher": "American Chemical Society", "publication": "Inorganic Chemistry", "publication_date": "2015-10-05", "series_number": "19", "volume": "54", "issue": "19", "pages": "9626-9636" }, { "id": "authors:05tka-d5p21", "collection": "authors", "collection_id": "05tka-d5p21", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150625-120207586", "type": "article", "title": "DNA Electrochemistry Shows DNMT1 Methyltransferase Hyperactivity in Colorectal Tumors", "author": [ { "family_name": "Furst", "given_name": "Ariel L.", "orcid": "0000-0001-9583-9703", "clpid": "Furst-Ariel-L" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "DNMT1, the most abundant human methyltransferase, is responsible for translating the correct methylation pattern during DNA replication, and aberrant methylation by DNMT1 has been linked to tumorigenesis. We have developed a sensitive signal-on electrochemical assay for the measurement of DNMT1 activity in crude tissue lysates. We have further analyzed ten tumor sets and have found a direct correlation between DNMT1 hyperactivity and tumorous tissue. In the majority of samples analyzed, the tumorous tissue has significantly higher DNMT1 activity than the healthy adjacent tissue. No such correlation is observed in measurements of DNMT1 expression by qPCR, DNMT1 protein abundance by western blotting, or DNMT1 activity using a radiometric DNA labeling assay. DNMT1 hyperactivity can result from both protein overexpression and enzyme hyperactivity. DNMT1 activity measured electrochemically provides a direct measure of activity in cell lysates and, as a result, provides a sensitive and early indication of cancerous transformation.", "doi": "10.1016/j.chembiol.2015.05.019", "pmcid": "PMC4518711", "issn": "1074-5521", "publisher": "Cell Press", "publication": "Chemistry and Biology", "publication_date": "2015-07-23", "series_number": "7", "volume": "22", "issue": "7", "pages": "938-945" }, { "id": "authors:j73wd-g9a27", "collection": "authors", "collection_id": "j73wd-g9a27", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150615-083148726", "type": "article", "title": "A Multiplexed, Two-Electrode Platform for Biosensing Based on DNA-Mediated Charge Transport", "author": [ { "family_name": "Furst", "given_name": "Ariel L.", "orcid": "0000-0001-9583-9703", "clpid": "Furst-Ariel-L" }, { "family_name": "Hill", "given_name": "Michael G.", "clpid": "Hill-Michael-G" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "We have developed a thin layer, multiplexed biosensing platform that features two working-electrode arrays for detecting small molecules, nucleic acid sequences, and DNA-binding proteins. DNA duplexes are patterned onto the primary electrode array, while a secondary electrode array is used both to initiate DNA monolayer formation and for electrochemical readout via DNA-mediated charge transport (DNA CT) chemistry. Electrochemical reduction of Cu(phendione)_2^(2+) (phendione is 1,10-phenanthroline-5,6-dione) at the secondary electrodes induces covalent attachment via click chemistry of ethynyl-labeled DNA probe duplexes onto the primary electrodes that have been treated with azide-terminated alkylthiols. Electrochemical impedance spectroscopy and cyclic voltammetry confirm that catalyst activation at the secondary electrode is essential to maintain the integrity of the DNA monolayer. Electrochemical readout of DNA CT processes that occur at the primary electrode is accomplished also at the secondary electrode. The two-electrode system enables the platform to function as a collector\u2013generator using either ferrocyanide or ferricyanide as mediators with methylene blue and DNA charge transport. Electrochemical measurements at the secondary electrode eliminate the need for large background corrections. The resulting sensitivity of this platform enables the reliable and simultaneous detection of femtomoles of the transcription factors TATA-binding protein and CopG on a single multiplexed device.", "doi": "10.1021/acs.langmuir.5b00829", "pmcid": "PMC4587567", "issn": "0743-7463", "publisher": "American Chemical Society", "publication": "Langmuir", "publication_date": "2015-06-16", "series_number": "23", "volume": "31", "issue": "23", "pages": "6554-6562" }, { "id": "authors:7ahw2-t8661", "collection": "authors", "collection_id": "7ahw2-t8661", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150414-131730851", "type": "article", "title": "Luminescent ruthenium probe for DNA mismatches", "author": [ { "family_name": "Boynton", "given_name": "Adam N.", "orcid": "0000-0003-4427-513X", "clpid": "Boynton-Adam-Nathaniel" }, { "family_name": "McConnell", "given_name": "Anna J.", "orcid": "0000-0001-7329-4319", "clpid": "McConnell-Anna-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Our lab. has focused on the design of metalloinsertors in an effort to prep. new chemotherapeutic agents targeted towards\nmismatch repair (MMR) - deficient cells. Metalloinsertors bind selectively to DNA mismatches and show preferential selectivity\nin MMR- deficient cells. We have also been interested in designing luminescent ruthenium complexes that could function as\ndiagnostic probes for DNA mismatches. It is known that the complex [Ru(bpy)_2(dppz)]^(2+) while non- emissive in aq. soln.,\nexhibits a restored luminescence upon binding to duplex DNA. In this work, a new sterically expansive ligand (BNIQ) was\nsynthesized and coordinated to ruthenium to create a new luminescent complex [Ru(bpy)_2(BNIQ)]^(2+). The luminescent\nproperties of this complex in the presence of well- matched and mismatched DNA duplexes were examd. using steady state and\nemission lifetime measurements. The complex exhibits an enhanced luminescence in the presence of mismatched DNA relative\nto well- matched DNA, suggesting that this complex may be utilized as a novel probe for DNA mismatches.", "issn": "0065-7727", "publisher": "American Chemical Society", "publication": "Abstracts of Papers of the American Chemical Society", "publication_date": "2015-03", "volume": "249", "pages": "INOR-584" }, { "id": "authors:f2wb0-9pq24", "collection": "authors", "collection_id": "f2wb0-9pq24", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150422-094854656", "type": "article", "title": "New family of rhodium metalloinsertors with improved selectivity and potency against DNA mismatch repair deficient cell lines", "author": [ { "family_name": "Boyle", "given_name": "Kelsey M.", "orcid": "0000-0002-6728-8403", "clpid": "Boyle-Kelsey-M" }, { "family_name": "Komor", "given_name": "Alexis", "clpid": "Komor-A-C" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Rhodium metalloinsertors are a unique family of complexes that selectively bind DNA base pair mismatches. We have\nseen crystallog. that insertion of the sterically expansive chrysi (5, 6- chrysenequinone diimine) ligand into DNA at a\nmismatched site leads to the ejection of the mismatched bases. This unique lesion may serve as the biol. target within the cell.\nPreviously, it has been shown that rhodium metalloinsertors preferentially increase cell death and inhibit proliferation of\nmismatch repair (MMR) - deficient colorectal cancer cell lines over their MMR- proficient counterparts. Recently, a new\nfamily of rhodium metalloinsertors contg. a rhodium- oxygen bond has been shown to have improved potency in the\nnanomolar range as well as increased cytotoxic selectivity toward MMR- deficient cells. This family appears distinct from\nprevious metalloinsertors in that both the \u0394- and %\u03bb- isomers of these complexes bind mismatched DNA with similar\naffinities. Current research is focused on extending the family to include new complexes that will allow us to explain in detail\nthe basis for the high cell selectivity and potency of this new family.", "issn": "0065-7727", "publisher": "American Chemical Society", "publication": "Abstracts of Papers of the American Chemical Society", "publication_date": "2015-03", "volume": "249", "pages": "INOR-169" }, { "id": "authors:42czn-8gb46", "collection": "authors", "collection_id": "42czn-8gb46", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150424-080918487", "type": "article", "title": "DNA-mediated redox signaling by UvrC", "author": [ { "family_name": "Grodick", "given_name": "Michael A.", "clpid": "Grodick-M-A" }, { "family_name": "Silva", "given_name": "Rebekah M.", "clpid": "Silva-R-M" }, { "family_name": "Zhou", "given_name": "Andy", "clpid": "Zhou-Andy" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The E. coli UvrC protein is an integral part of the DNA nucleotide excision repair pathway. Our lab. has focused on studies of\nredox DNA signaling among DNA repair proteins contg. 4Fe- 4S clusters. We have now explored whether UvrC may also\ncontain a 4Fe- 4S cluster. A new purifn. route was developed to express an MBP- UvrC fusion. The purified protein shows a UVvisible\nabsorbance spectrum consistent with that of a 4Fe- 4S cluster. ESR expts. of reduced UvrC give rise to a signal\nindicative of a 4Fe- 4S cluster. Electrochem. expts. indicate that the protein is electrochem. active on DNA- modified gold\nelectrodes. Finally, genetic methods to study possible DNA- mediated signaling between UvrC and other DNA- processing\nenzymes contg. 4Fe- 4S clusters are being examd.", "issn": "0065-7727", "publisher": "American Chemical Society", "publication": "Abstracts of Papers of the American Chemical Society", "publication_date": "2015-03", "volume": "249", "pages": "BIOL-113" }, { "id": "authors:4ct37-5v194", "collection": "authors", "collection_id": "4ct37-5v194", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150423-132051717", "type": "article", "title": "Electron transfer and DNA replication: Assessing the functional role of the yeast DNA polymerase \u03b4 [4Fe- 4S] 2+ cluster", "author": [ { "family_name": "Bartels", "given_name": "Phillip L.", "clpid": "Bartels-P-L" }, { "family_name": "Stodola", "given_name": "Joseph L.", "clpid": "Stodola-J-L" }, { "family_name": "Burgers", "given_name": "Peter M. J.", "clpid": "Burgers-P-M-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Eukaryotic B- family DNA polymerases have recently been shown to contain a conserved [4Fe- 4S]2+ cluster in the C- terminus\nof the catalytic subunit. This cofactor has been most completely characterized in yeast DNA polymerase \u03b4 (Pol \u03b4) , the\nenzyme responsible for lagging strand DNA synthesis. Multiple lines of evidence point to a role for the cluster beyond\nstructural integrity, but the nature of this function is not obvious. Clues to what this function might be come from previous\nwork in the Barton lab, which showed that [4Fe- 4S]2+ clusters in bacterial base excision repair enzymes undergo a shift in\npotential favoring oxidn. upon binding to DNA, allowing them to utilize DNA- mediated redox signaling to coordinate their\nactivities and find their targets. Building on this earlier work, we have investigated the capability of the Pol \u03b4 [4Fe- 4S]2+\ncluster to undergo reversible electron transfer using DNA- modified electrodes, and have designed assays to test the effect\nof redox state on enzymic activity.", "issn": "0065-7727", "publisher": "American Chemical Society", "publication": "Abstracts of Papers of the American Chemical Society", "publication_date": "2015-03", "volume": "249", "pages": "BIOL-129" }, { "id": "authors:ch3jx-s1h45", "collection": "authors", "collection_id": "ch3jx-s1h45", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150414-131045800", "type": "article", "title": "Development of rhodium metalloinsertors as chemotherapeutic agents", "author": [ { "family_name": "Komor", "given_name": "Alexis", "clpid": "Komor-A-C" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Deficiencies in the mismatch repair (MMR) pathway have been assocd. with various cancers, and many commonly used\nchemotherapeutics have decreased effectiveness against MMR- deficient cancers. Rhodium metalloinsertors are octahedral\ncomplexes that bind DNA mismatches with high affinity and specificity through metalloinsertion, a binding mode through which\nthe compds. insert into the DNA duplex from the minor groove and eject the mismatched bases. These compds. also exhibit\nunique cell- selective cytotoxicity, preferentially inducing necrosis in mismatch repair (MMR) - deficient cells over MMR- proficient\ncells. This chemotherapeutic activity, which has been confirmed across multiple assays and in different systems for\ncomparing MMR deficiency to proficiency, has been found to be the result of specific targeting of the metalloinsertors to\nnuclear DNA mismatches. Most recently, a new generation of metalloinsertors with enhanced potency and selectivity has\nbeen discovered which display Rh- O coordination and a possible different binding disposition in the mismatch site as compared\nto earlier generation metalloinsertors.", "issn": "0065-7727", "publisher": "American Chemical Society", "publication": "Abstracts of Papers of the American Chemical Society", "publication_date": "2015-03", "volume": "249", "pages": "INOR-793" }, { "id": "authors:tza0z-z3131", "collection": "authors", "collection_id": "tza0z-z3131", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150408-100209650", "type": "article", "title": "DNA-mediated signaling by the E. coli helicase, DinG", "author": [ { "family_name": "Grodick", "given_name": "Michael A.", "clpid": "Grodick-M-A" }, { "family_name": "Zwang", "given_name": "Theodore J.", "clpid": "Zwang-Theodore-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The protein DinG is an ATP-dependent helicase from E. coli that contains a 4Fe-4S cluster. DNA-modified\ngold electrodes were used to measure the midpoint redox potential of the DNA-bound protein, which was found\nto be \u223c80 mV vs. Using a 20-mer with a 15-mer single-stranded overhang as a helicase substrate on the\nDNA-modified electrodes, it was shown that enzymic activity via the hydrolysis of ATP increased the intensity of\nthe electrochem. signal intensity. Whether DinG and EndoIII, a base excision repair enzyme also contg. a 4Fe-\n4S cluster, use DNA-mediated charge transport (CT) chem. for inter-protein signaling was tested using\nseveral techniques. Using a single mol. at. force microscopy assay, it was shown that DinG and EndoIII\npreferentially redistribute to strands of DNA that contain DNA damage via long-range DNA-mediated CT. To\ntest this signaling within cells, genetics expts. were used that strongly suggest that DinG and EndoIII utilize\nDNA-mediated signaling to cooperate in redistributing DinG to its target lesion.", "issn": "0065-7727", "publisher": "American Chemical Society", "publication": "Abstracts of Papers of the American Chemical Society", "publication_date": "2015-03", "volume": "249", "pages": "INOR-926" }, { "id": "authors:9z0v3-nzn67", "collection": "authors", "collection_id": "9z0v3-nzn67", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150424-080637938", "type": "article", "title": "Investigating the redox properties of human DNA primase", "author": [ { "family_name": "O'Brien", "given_name": "Elizabeth", "clpid": "O'Brien-Elizabeth" }, { "family_name": "Holt", "given_name": "Marilyn", "clpid": "Holt-M" }, { "family_name": "Ehlinger", "given_name": "Aaron", "clpid": "Ehlinger-A-C" }, { "family_name": "Chazin", "given_name": "Walter J.", "orcid": "0000-0002-2180-0790", "clpid": "Chazin-W-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Human DNA primase is a heterodimeric, DNA- dependent RNA polymerase that initiates replication on single- stranded DNA.\nPrimase has been shown previously to contain a [4Fe4S] cluster cofactor in the C terminal domain of its large subunit (p58C) .\nHere we measure the redox activity of the [4Fe4S] domain of primase (p58C) using electrochem. on a DNA- modified gold\nelectrode. P58C is found to be electrochem. active on duplex DNA substrates with a single- stranded DNA overhang. Binding\nof p58C to the DNA substrate, moreover, is found to be dependent both on oxidn. state of the [4Fe4S] cluster and on the\npresence of nucleotide triphosphates (NTPs) . Through these studies, we are exploring how DNA charge transport may be\nexploited by DNA primase in order to execute the multistep, coordinated process of replication initiation.", "issn": "0065-7727", "publisher": "American Chemical Society", "publication": "Abstracts of Papers of the American Chemical Society", "publication_date": "2015-03", "volume": "249", "pages": "BIOL-126" }, { "id": "authors:6pj83-bak04", "collection": "authors", "collection_id": "6pj83-bak04", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150424-081137913", "type": "article", "title": "Magnetic field effects on charge transport through DNA", "author": [ { "family_name": "Zwang", "given_name": "Theodore J.", "clpid": "Zwang-Theodore-J" }, { "family_name": "Hurlimann", "given_name": "Sylvia", "clpid": "Hurlimann-S" }, { "family_name": "Hill", "given_name": "Michael G.", "clpid": "Hill-M-G" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Our lab has performed electrochem. studies of ground state charge transport through DNA, and now we have begun to examine the effects of magnetic fields on this charge transport process. DNA films were attached to nickel surfaces and\nimmersed in buffer. A p.d. was applied that induced charge to move through the DNA, between the nickel surface and a\nredox reporter. We have found that an external magnetic field has a significant effect on charge transport within this\nsystem. This information has significant implications for magnetic field effects in biol. systems.", "issn": "0065-7727", "publisher": "American Chemical Society", "publication": "Abstracts of Papers of the American Chemical Society", "publication_date": "2015-03", "volume": "249", "pages": "BIOL-70" }, { "id": "authors:868p4-cc905", "collection": "authors", "collection_id": "868p4-cc905", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150408-082055756", "type": "article", "title": "Construction and application of a Rh-Pt DNA metalloinsertor conjugate", "author": [ { "family_name": "Weidmann", "given_name": "Alyson G.", "clpid": "Weidmann-A-G" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The success of cisplatin as an anticancer agent has led to the development of a multitude of inorg. complexes for chemotherapy.\nIn particular, rhodium metalloinsertor complexes, which selectively target base pair mismatches in DNA, have been shown to\nexhibit exceptional and selective cytotoxic activity in cancer cells that are deficient in mismatch repair (MMR). Here, we have\nsynthesized and characterized a bifunctional metalloinsertor conjugate (RhPt), consisting of a rhodium mismatch recognition\ncomponent tethered to a deriv. of the chemotherapeutic oxaliplatin. The RhPt complex exhibits dual binding to a DNA duplex\ncontg. a mismatch, first through metalloinsertion at the mismatched site followed by the formation of covalent Pt-DNA adducts.\nIt was found that RhPt displays enhanced cytotoxicity in MMR-deficient HCT116O cells compared to cisplatin and oxaliplatin as\nwell as relative to the individual subunits. Cytotoxicity assays with caspase and poly-ADP ribose polymerase inhibitors revealed\nthat RhPt induces apoptotic cell death, rather than the necrotic pathway triggered by metalloinsertors. Cellular uptake was\nprobed using inductively coupled plasma mass spectrometry, and it was found that RhPt exhibits increased cellular uptake\ncompared to control complexes, likely contributing to its enhanced activity. This and other Rh-Pt complexes will be discussed in\nthe application of bifunctional complexes as chemotherapeutic agents.", "issn": "0065-7727", "publisher": "American Chemical Society", "publication": "Abstracts of Papers of the American Chemical Society", "publication_date": "2015-03", "volume": "249", "pages": "INOR-935" }, { "id": "authors:6zc60-fe983", "collection": "authors", "collection_id": "6zc60-fe983", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150423-131845489", "type": "article", "title": "Oxidation of p53 via DNA-mediated charge transport", "author": [ { "family_name": "Schaefer", "given_name": "Kathryn N.", "clpid": "Schaefer-K-N" }, { "family_name": "Geil", "given_name": "Wendy M.", "clpid": "Geil-W-M" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Transcription factor p53 plays a crit. role in the cellular response to stress stimuli. Previous studies have shown that p53\ndissocs. from its response element upon oxidative DNA- mediated charge transport (CT) . This oxidative dissocn. of p53 via\nDNA CT depends on the integrity of the \u03c0- stacked DNA bases and guanine locations within the response element. Greater\np53 dissocn. is obsd. from sequences contg. low redox potential purine regions, particularly guanine doublets and triplets.\nOxidative DNA damage is inhibited in the presence of p53, but only at sites in direct contact with p53. To det. residues\nwithin p53 that enable oxidative dissocn. by DNA CT, select p53 mutations were explored. Electrophoretic mobility shift\nassays using oligonucleotides contg. tethered anthraquinone for long- range photooxidn. were used to det. the influence of each\nmutation on oxidative dissocn. Differential thiol labeling and multiple reaction monitoring mass spectrometry were used to\ninvestigate cysteine oxidn. within p53 from a distance via DNA CT. It is proposed that disulfide formation involving C275 is\ncrit. for inducing oxidative dissocn. of p53 from DNA.", "issn": "0065-7727", "publisher": "American Chemical Society", "publication": "Abstracts of Papers of the American Chemical Society", "publication_date": "2015-03", "volume": "249", "pages": "BIOL-170" }, { "id": "authors:xsebc-1bp61", "collection": "authors", "collection_id": "xsebc-1bp61", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150408-095933576", "type": "article", "title": "Label-free electrochemical detection of human methyltransferase from tumors", "author": [ { "family_name": "Furst", "given_name": "Ariel L.", "clpid": "Furst-A-L" }, { "family_name": "Muren", "given_name": "Natalie", "clpid": "Muren-N-B" }, { "family_name": "Hill", "given_name": "Michael G.", "clpid": "Hill-M-G" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Abnormal DNA methyltransferase activity has been implicated in cancerous transformations and tumorigenesis; efficient\ndetection of methyltransferase activity could provide an early cancer diagnostic. Currently, most detection platforms\ninvolve fluorescence or radioactivity, making them cumbersome. Electrochem. platforms, in contrast, offer high portability,\nsensitivity, and ease of use. We have developed an electrochem. DNA array platform that is formed and addressed using a\nsecondary electrode, allowing for both formation of dil. DNA monolayers and optimized detection through DNA-mediated\ncharge transport with electrocatalysis. This label-free electrochem. platform has been used to successfully detect the activity\nof the most abundant human methyltransferase, DNMT1, in crude lysates from both cultured human colorectal cancer cells\n(HCT116) and colorectal tissue samples. We addnl. distinguish colorectal carcinoma tissue from healthy adjacent tissue through\ndifferences in DNMT1 activity, demonstrating the utility of this two-electrode platform for clin. applications.", "issn": "0065-7727", "publisher": "American Chemical Society", "publication": "Abstracts of Papers of the American Chemical Society", "publication_date": "2015-03", "volume": "249", "pages": "INOR-929" }, { "id": "authors:byqc1-zmg80", "collection": "authors", "collection_id": "byqc1-zmg80", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150202-150621170", "type": "article", "title": "DNA Charge Transport within the Cell", "author": [ { "family_name": "Grodick", "given_name": "Michael A.", "clpid": "Grodick-M-A" }, { "family_name": "Muren", "given_name": "Natalie B.", "clpid": "Muren-N-B" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The unique characteristics of DNA charge transport (CT) have prompted an examination of roles for this chemistry within a biological context. Not only can DNA CT facilitate long-range oxidative damage of DNA, but redox-active proteins can couple to the DNA base stack and participate in long-range redox reactions using DNA CT. DNA transcription factors with redox-active moieties such as SoxR and p53 can use DNA CT as a form of redox sensing. DNA CT chemistry also provides a means to monitor the integrity of the DNA, given the sensitivity of DNA CT to perturbations in base stacking as arise with mismatches and lesions. Enzymes that utilize this chemistry include an interesting and ever-growing class of DNA-processing enzymes involved in DNA repair, replication, and transcription that have been found to contain 4Fe-4S clusters. DNA repair enzymes containing 4Fe-4S clusters, that include endonuclease III (EndoIII), MutY, and DinG from bacteria, as well as XPD from archaea, have been shown to be redox-active when bound to DNA, share a DNA-bound redox potential, and can be reduced and oxidized at long-range via DNA CT. Interactions between DNA and these proteins in solution, in addition to genetics experiments within Escherichia coli, suggest that DNA-mediated CT can be used as a means of cooperative signaling among DNA repair proteins that contain 4Fe-4S clusters as a first step in finding DNA damage, even within cells. On the basis of these data, we can consider also how DNA-mediated CT may be used as a means of signaling to coordinate DNA processing across the genome.", "doi": "10.1021/bi501520w", "pmcid": "PMC4587570", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "2015-02-03", "series_number": "4", "volume": "54", "issue": "4", "pages": "962-973" }, { "id": "authors:g0n2w-ayc20", "collection": "authors", "collection_id": "g0n2w-ayc20", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150120-083007297", "type": "article", "title": "Oxidation of p53 through DNA Charge Transport Involves a Network of Disulfides within the DNA-Binding Domain", "author": [ { "family_name": "Schaefer", "given_name": "Kathryn N.", "clpid": "Schaefer-K-N" }, { "family_name": "Geil", "given_name": "Wendy M.", "clpid": "Geil-W-M" }, { "family_name": "Sweredoski", "given_name": "Michael J.", "orcid": "0000-0003-0878-3831", "clpid": "Sweredoski-M-J" }, { "family_name": "Moradian", "given_name": "Annie", "orcid": "0000-0002-0407-2031", "clpid": "Moradian-A" }, { "family_name": "Hess", "given_name": "Sonja", "orcid": "0000-0002-5904-9816", "clpid": "Hess-S" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Transcription factor p53 plays a critical role in the cellular response to stress stimuli. We have seen that p53 dissociates selectively from various promoter sites as a result of oxidation at long-range through DNA-mediated charge transport (CT). Here, we examine this chemical oxidation and determine the residues in p53 that are essential for oxidative dissociation, focusing on the network of cysteine residues adjacent to the DNA-binding site. Of the eight mutants studied, only the C275S mutation shows decreased affinity for the Gadd45 promoter site. However, both mutations C275S and C277S result in substantial attenuation of oxidative dissociation, with C275S causing the most severe attenuation. Differential thiol labeling was used to determine the oxidation states of cysteine residues within p53 after DNA-mediated oxidation. Reduced cysteines were iodoacetamide-labeled, whereas oxidized cysteines participating in disulfide bonds were ^(13)C_2D_2-iodoacetamide-labeled. Intensities of respective iodoacetamide-modified peptide fragments were analyzed by mass spectrometry. A distinct shift in peptide labeling toward ^(13)C_2D_2-iodoacetamide-labeled cysteines is observed in oxidized samples, confirming that chemical oxidation of p53 occurs at long range. All observable cysteine residues trend toward the heavy label under conditions of DNA CT, indicating the formation of multiple disulfide bonds among the cysteine network. On the basis of these data, it is proposed that disulfide formation involving C275 is critical for inducing oxidative dissociation of p53 from DNA.", "doi": "10.1021/bi501424v", "pmcid": "PMC4310631", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "2015-01-27", "series_number": "3", "volume": "54", "issue": "3", "pages": "932-941" }, { "id": "authors:r0k0e-42241", "collection": "authors", "collection_id": "r0k0e-42241", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140811-081446490", "type": "article", "title": "Electrocatalysis in DNA sensors", "author": [ { "family_name": "Furst", "given_name": "Ariel L.", "clpid": "Furst-A-L" }, { "family_name": "Hill", "given_name": "Michael G.", "clpid": "Hill-M-G" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Electrocatalysis is often thought of solely in the inorganic realm, most often applied to energy conversion in fuel cells. However, the ever-growing field of bioelectrocatalysis has made great strides in advancing technology for both biofuel cells as well as biological detection platforms. Within the context of bioelectrocatalytic detection systems, DNA-based platforms are especially prevalent. One subset of these platforms, the one we have developed, takes advantage of the inherent charge transport properties of DNA. Electrocatalysis coupled with DNA-mediated charge transport has enabled specific and sensitive detection of lesions, mismatches and DNA-binding proteins. Even greater signal amplification from these platforms is now being achieved through the incorporation of a secondary electrode to the platform both for patterning DNA arrays and for detection. Here, we describe the evolution of this new DNA sensor technology.", "doi": "10.1016/j.poly.2014.07.005", "pmcid": "PMC4243183", "issn": "0277-5387", "publisher": "Elsevier", "publication": "Polyhedron", "publication_date": "2014-12-14", "volume": "84", "pages": "150-159" }, { "id": "authors:qvmeg-xc632", "collection": "authors", "collection_id": "qvmeg-xc632", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141009-075720084", "type": "article", "title": "Label-free electrochemical detection of human methyltransferase from tumors", "author": [ { "family_name": "Furst", "given_name": "Ariel L.", "clpid": "Furst-A-L" }, { "family_name": "Muren", "given_name": "Natalie B.", "clpid": "Muren-N-B" }, { "family_name": "Hill", "given_name": "Michael G.", "clpid": "Hill-M-G" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The role of abnormal DNA methyltransferase activity in the development and progression of cancer is an essential and rapidly growing area of research, both for improved diagnosis and treatment. However, current technologies for the assessment of methyltransferase activity, particularly from crude tumor samples, limit this work because they rely on radioactivity or fluorescence and require bulky instrumentation. Here, we report an electrochemical platform that overcomes these limitations for the label-free detection of human DNA(cytosine-5)-methyltransferase1 (DNMT1) methyltransferase activity, enabling measurements from crude cultured colorectal cancer cell lysates (HCT116) and biopsied tumor tissues. Our multiplexed detection system involving patterning and detection from a secondary electrode array combines low-density DNA monolayer patterning and electrocatalytically amplified DNA charge transport chemistry to measure selectively and sensitively DNMT1 activity within these complex and congested cellular samples. Based on differences in DNMT1 activity measured with this assay, we distinguish colorectal tumor tissue from healthy adjacent tissue, illustrating the effectiveness of this two-electrode platform for clinical applications.", "doi": "10.1073/pnas.1417351111", "pmcid": "PMC4210341", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2014-10-21", "series_number": "42", "volume": "111", "issue": "42", "pages": "14985-14989" }, { "id": "authors:kfkv8-ext87", "collection": "authors", "collection_id": "kfkv8-ext87", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140929-091130056", "type": "article", "title": "An Unusual Ligand Coordination Gives Rise to a New Family of Rhodium Metalloinsertors with Improved Selectivity and Potency", "author": [ { "family_name": "Komor", "given_name": "Alexis C.", "clpid": "Komor-A-C" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Rhodium metalloinsertors are octahedral complexes that bind DNA mismatches with high affinity and specificity and exhibit unique cell-selective cytotoxicity, targeting mismatch repair (MMR)-deficient cells over MMR-proficient cells. Here we describe a new generation of metalloinsertors with enhanced biological potency and selectivity, in which the complexes show Rh\u2013O coordination. In particular, it has been found that both \u0394- and \u039b-[Rh(chrysi)(phen)(DPE)]2+ (where chrysi =5,6 chrysenequinone diimmine, phen =1,10-phenanthroline, and DPE = 1,1-di(pyridine-2-yl)ethan-1-ol) bind to DNA containing a single CC mismatch with similar affinities and without racemization. This is in direct contrast with previous metalloinsertors and suggests a possible different binding disposition for these complexes in the mismatch site. We ascribe this difference to the higher pK_a of the coordinated immine of the chrysi ligand in these complexes, so that the complexes must insert into the DNA helix with the inserting ligand in a buckled orientation; spectroscopic studies in the presence and absence of DNA along with the crystal structure of the complex without DNA support this assignment. Remarkably, all members of this new family of compounds have significantly increased potency in a range of cellular assays; indeed, all are more potent than cisplatin and N-methyl-N\u2032-nitro-nitrosoguanidine (MNNG, a common DNA-alkylating chemotherapeutic agent). Moreover, the activities of the new metalloinsertors are coupled with high levels of selective cytotoxicity for MMR-deficient versus proficient colorectal cancer cells.", "doi": "10.1021/ja5072064", "pmcid": "PMC4195389", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2014-10-08", "series_number": "40", "volume": "136", "issue": "40", "pages": "14160-14172" }, { "id": "authors:w6t2y-e0s19", "collection": "authors", "collection_id": "w6t2y-e0s19", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140721-085331031", "type": "article", "title": "Construction and Application of a Rh\u2013Pt DNA Metalloinsertor Conjugate", "author": [ { "family_name": "Weidmann", "given_name": "Alyson G.", "clpid": "Weidmann-A-G" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "We report the synthesis and characterization of a bimetallic conjugate (RhPt) in which an oxaliplatin derivative is tethered to a rhodium metalloinsertor through an aminomalonate leaving group ligand. The complex interacts with DNA through metalloinsertion at a base pair mismatch followed by formation of a covalent Pt\u2013DNA adduct. Characterization of RhPt in mismatch repair-deficient HCT116O cells reveals increased cytotoxicity compared to cisplatin and oxaliplatin as well as relative to the unconjugated rhodium and platinum counterparts. Caspase and poly-ADP ribose polymerase inhibition assays indicate that RhPt induces apoptotic cell death. Inductively coupled plasma mass spectrometry (ICP-MS) experiments reveal that RhPt exhibits enhanced cellular uptake properties that contribute to its increased efficacy.", "doi": "10.1021/ic501509x", "pmcid": "PMC4123934", "issn": "0020-1669", "publisher": "American Chemical Society", "publication": "Inorganic Chemistry", "publication_date": "2014-08-04", "series_number": "15", "volume": "53", "issue": "15", "pages": "7812-7814" }, { "id": "authors:h4f8p-5cy24", "collection": "authors", "collection_id": "h4f8p-5cy24", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140528-093946157", "type": "article", "title": "DNA-Mediated Oxidation of p53", "author": [ { "family_name": "Schaefer", "given_name": "Kathryn N.", "clpid": "Schaefer-K-N" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Transcription factor p53 is the most commonly altered gene in human cancer. As a redox-active protein in direct contact with DNA, p53 can directly sense oxidative stress through DNA-mediated charge transport. Electron hole transport occurs over long distances through the \u03c0-stacked bases and leads to the oxidative dissociation of p53. The extent of protein dissociation depends upon the redox potential of the DNA in direct contact with each p53 monomer. The DNA sequence dependence of p53 oxidative dissociation was examined by electrophoretic mobility shift assays using oligonucleotides containing both synthetic and human p53 consensus sequences with an appended photooxidant, anthraquinone. Greater p53 dissociation is observed from sequences containing low-redox potential purine regions, particularly guanine triplets. Using denaturing polyacrylamide gel electrophoresis of irradiated anthraquinone-modified DNA, the DNA damage sites corresponding to sites of preferred electron hole localization were determined. The resulting DNA damage preferentially localizes to guanine doublets and triplets. Oxidative DNA damage is inhibited in the presence of p53, but only at sites in direct contact with p53. From these data, predictions about the sensitivity of human p53-binding sites to oxidative stress as well as possible biological implications have been made. On the basis of our data, the guanine pattern within the purine region of each p53-binding site determines the response of p53 to DNA oxidation, yielding for some sequences the oxidative dissociation of p53 from a distance and thereby providing another potential role for DNA charge transport chemistry within the cell.", "doi": "10.1021/bi5003184", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "2014-06-03", "series_number": "21", "volume": "53", "issue": "21", "pages": "3467-3475" }, { "id": "authors:21stj-t6y12", "collection": "authors", "collection_id": "21stj-t6y12", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141024-100939620", "type": "article", "title": "Targeted Chemotherapy with Metal Complexes", "author": [ { "family_name": "Weidmann", "given_name": "Alyson G.", "clpid": "Weidmann-A-G" }, { "family_name": "Komor", "given_name": "Alexis C.", "clpid": "Komor-A-C" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Classical chemotherapeutics, such as cisplatin and its analogues, have been highly successful in the clinic, yet improvements can certainly be made, given the significant side effects associated with the killing of healthy cells. Recent advances in the field of chemotherapy include the development of targeted anticancer agents, compounds that are directed towards a specific biomarker of cancer, with the hopes that such targeted therapies might have reduced side effects given their greater selectivity. Here we discuss several transition metal complexes that are tailored towards various biomolecules associated with cancer. Most notably, the success of rhodium metalloinsertors, which specifically bind to nucleic acid base mismatches in DNA, highlight the enormous potential of this exciting new strategy.", "doi": "10.1080/02603594.2014.890099", "pmcid": "PMC4309285", "issn": "0260-3594", "publisher": "Taylor & Francis", "publication": "Comments on Inorganic Chemistry", "publication_date": "2014-05-01", "series_number": "3-4", "volume": "34", "issue": "3-4", "pages": "114-123" }, { "id": "authors:zzfz5-d1211", "collection": "authors", "collection_id": "zzfz5-d1211", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140422-093606577", "type": "article", "title": "DNA-Mediated Signaling by Proteins with 4Fe\u22124S Clusters Is Necessary for Genomic Integrity", "author": [ { "family_name": "Grodick", "given_name": "Michael A.", "clpid": "Grodick-M-A" }, { "family_name": "Segal", "given_name": "Helen M.", "clpid": "Segal-H-M" }, { "family_name": "Zwang", "given_name": "Theodore J.", "clpid": "Zwang-Theodore-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Iron\u2013sulfur clusters have increasingly been found to be associated with enzymes involved in DNA processing. Here we describe a role for these redox clusters in DNA-mediated charge-transport signaling in E. coli between DNA repair proteins from distinct pathways. DNA-modified electrochemistry shows that the 4Fe\u20134S cluster of DNA-bound DinG, an ATP-dependent helicase that repairs R-loops, is redox-active at cellular potentials and ATP hydrolysis increases DNA-mediated redox signaling. Atomic force microscopy experiments demonstrate that DinG and Endonuclease III (EndoIII), a base excision repair enzyme, cooperate at long-range using DNA charge transport to redistribute to regions of DNA damage. Genetics experiments, moreover, reveal that this DNA-mediated signaling among proteins also occurs within the cell and, remarkably, is required for cellular viability under conditions of stress. Silencing the gene encoding EndoIII in a strain of E. coli where repair by DinG is essential results in a significant growth defect that is rescued by complementation with EndoIII but not with an EndoIII mutant that is enzymatically active but unable to carry out DNA charge transport. This work thus elucidates a fundamental mechanism to coordinate the activities of DNA repair enzymes across the genome.", "doi": "10.1021/ja501973c", "pmcid": "PMC4017601", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2014-04-30", "series_number": "17", "volume": "136", "issue": "17", "pages": "6470-6478" }, { "id": "authors:c53v8-ehj83", "collection": "authors", "collection_id": "c53v8-ehj83", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150316-095808555", "type": "article", "title": "DNA signaling among proteins with iron-sulfur clusters", "author": [ { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "DNA-mediated charge transport can yield redox chem. over long mol. distances in a reaction that reports on the integrity of the\nintervening base stack. Moreover, increasingly, proteins involved in DNA replication and repair have been found to contain\n4Fe-4S clusters, common redox cofactors in biol. DNA- modified electrodes have been utilized to det. redox potentials for\nthese metalloproteins bound to DNA; this electrochem. establishes the ability of the metalloproteins to carry out redox chem. at\nphysiol. potentials in the DNA- bound form. Studies are also described to characterize how these DNA-binding proteins contg.\n4Fe-4S clusters may utilize DNA charge transport chem. for long range redox signaling.", "issn": "0065-7727", "publisher": "American Chemical Society", "publication": "Abstracts of Papers of the American Chemical Society", "publication_date": "2014-03-16", "volume": "247", "pages": "440-INOR" }, { "id": "authors:2pj20-9sq48", "collection": "authors", "collection_id": "2pj20-9sq48", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20131224-071741505", "type": "article", "title": "DNA-Modified Electrodes Fabricated Using Copper-Free Click Chemistry for Enhanced Protein Detection", "author": [ { "family_name": "Furst", "given_name": "Ariel L.", "clpid": "Furst-A-L" }, { "family_name": "Hill", "given_name": "Michael G.", "clpid": "Hill-M-G" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "A method of DNA monolayer formation has been developed using copper-free click chemistry that yields enhanced surface homogeneity and enables variation in the amount of DNA assembled; extremely low-density DNA monolayers, with as little as 5% of the monolayer being DNA, have been formed. These DNA-modified electrodes (DMEs) were characterized visually, with AFM, and electrochemically, and were found to facilitate DNA-mediated reduction of a distally bound redox probe. These low-density monolayers were found to be more homogeneous than traditional thiol-modified DNA monolayers, with greater helix accessibility through an increased surface area-to-volume ratio. Protein binding efficiency of the transcriptional activator TATA-binding protein (TBP) was also investigated on these surfaces and compared to that on DNA monolayers formed with standard thiol-modified DNA. Our low-density monolayers were found to be extremely sensitive to TBP binding, with a signal decrease in excess of 75% for 150 nM protein. This protein was detectable at 4 nM, on the order of its dissociation constant, with our low-density monolayers. The improved DNA helix accessibility and sensitivity of our low-density DNA monolayers to TBP binding reflects the general utility of this method of DNA monolayer formation for DNA-based electrochemical sensor development.", "doi": "10.1021/la403262v", "pmcid": "PMC3947573", "issn": "0743-7463", "publisher": "American Chemical Society", "publication": "Langmuir", "publication_date": "2013-12-31", "series_number": "52", "volume": "29", "issue": "52", "pages": "16141-16149" }, { "id": "authors:zgj86-d3729", "collection": "authors", "collection_id": "zgj86-d3729", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20131223-100408108", "type": "article", "title": "Electrochemical Patterning and Detection of DNA Arrays on a Two-Electrode Platform", "author": [ { "family_name": "Furst", "given_name": "Ariel", "clpid": "Furst-A" }, { "family_name": "Landefeld", "given_name": "Sally", "clpid": "Landefeld-S" }, { "family_name": "Hill", "given_name": "Michael G.", "clpid": "Hill-M-G" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "We report a novel method of DNA array formation that is electrochemically formed and addressed with a two-electrode platform. Electrochemical activation of a copper catalyst, patterned with one electrode, enables precise placement of multiple sequences of DNA onto a second electrode surface. The two-electrode patterning and detection platform allows for both spatial resolution of the patterned DNA array and optimization of detection through DNA-mediated charge transport with electrocatalysis. This two-electrode platform has been used to form arrays that enable differentiation between well-matched and mismatched sequences, the detection of TATA-binding protein, and sequence-selective DNA hybridization.", "doi": "10.1021/ja410902j", "pmcid": "PMC4026266", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2013-12-12", "series_number": "51", "volume": "135", "issue": "51", "pages": "19099-19102" }, { "id": "authors:4528g-xng10", "collection": "authors", "collection_id": "4528g-xng10", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20131205-093720227", "type": "article", "title": "Electrochemical Assay for the Signal-On Detection of Human DNA Methyltransferase Activity", "author": [ { "family_name": "Muren", "given_name": "Natalie B.", "clpid": "Muren-N-B" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Strategies to detect human DNA methyltransferases are needed, given that aberrant methylation by these enzymes is associated with cancer initiation and progression. Here we describe a nonradioactive, antibody-free, electrochemical assay in which methyltransferase activity on DNA-modified electrodes confers protection from restriction for signal-on detection. We implement this assay with a multiplexed chip platform and show robust detection of both bacterial (SssI) and human (Dnmt1) methyltransferase activity. Essential to work with human methyltransferases, our unique assay design allows activity measurements on both unmethylated and hemimethylated DNA substrates. We validate this assay by comparison with a conventional radioactive method. The advantages of electrochemistry over radioactivity and fluorescence make this assay an accessible and promising new approach for the sensitive, label-free detection of human methyltransferase activity.", "doi": "10.1021/ja4085918", "pmcid": "PMC3899840", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2013-11-06", "series_number": "44", "volume": "135", "issue": "44", "pages": "16632-16640" }, { "id": "authors:3vfp1-t5243", "collection": "authors", "collection_id": "3vfp1-t5243", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20131205-114027493", "type": "article", "title": "An Inducible, Isogenic Cancer Cell Line System for Targeting the State of Mismatch Repair Deficiency", "author": [ { "family_name": "Bailis", "given_name": "Julie M.", "clpid": "Bailis-J-M" }, { "family_name": "Gordon", "given_name": "Marcia L.", "clpid": "Gordon-M-L" }, { "family_name": "Gurgel", "given_name": "Jesse L.", "clpid": "Gurgel-J-L" }, { "family_name": "Komor", "given_name": "Alexis C.", "clpid": "Komor-A-C" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Kirsch", "given_name": "Ilan R.", "clpid": "Kirsch-I-R" } ], "abstract": "The DNA mismatch repair system (MMR) maintains genome stability through recognition and repair of single-base mismatches and small insertion-deletion loops. Inactivation of the MMR pathway causes microsatellite instability and the accumulation of genomic mutations that can cause or contribute to cancer. In fact, 10-20% of certain solid and hematologic cancers are MMR-deficient. MMR-deficient cancers do not respond to some standard of care chemotherapeutics because of presumed increased tolerance of DNA damage, highlighting the need for novel therapeutic drugs. Toward this goal, we generated isogenic cancer cell lines for direct comparison of MMR-proficient and MMR-deficient cells. We engineered NCI-H23 lung adenocarcinoma cells to contain a doxycycline-inducible shRNA designed to suppress the expression of the mismatch repair gene MLH1, and compared single cell subclones that were uninduced (MLH1-proficient) versus induced for the MLH1 shRNA (MLH1-deficient). Here we present the characterization of these MMR-inducible cell lines and validate a novel class of rhodium metalloinsertor compounds that differentially inhibit the proliferation of MMR-deficient cancer cells.", "doi": "10.1371/journal.pone.0078726", "pmcid": "PMC3812133", "issn": "1932-6203", "publisher": "Public Library of Science", "publication": "PLoS ONE", "publication_date": "2013-10-29", "series_number": "10", "volume": "8", "issue": "10", "pages": "Art. No. e78726" }, { "id": "authors:yqazn-8e590", "collection": "authors", "collection_id": "yqazn-8e590", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20131206-091447174", "type": "article", "title": "DNA Protection by the Bacterial Ferritin Dps via DNA Charge\n Transport", "author": [ { "family_name": "Arnold", "given_name": "Anna R.", "clpid": "Arnold-A-R" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Dps proteins, bacterial mini-ferritins that protect DNA from oxidative stress, are implicated in the survival and virulence of pathogenic bacteria. Here we examine the mechanism of E. coli Dps protection of DNA, specifically whether this DNA-binding protein can utilize DNA charge transport through the base pair \u03c0-stack to protect the genome from a distance. An intercalating ruthenium photooxidant was employed to generate DNA damage localized to guanine repeats, the sites of lowest potential in DNA. We find that Dps loaded with ferrous iron, in contrast to Apo-Dps and ferric iron-loaded Dps, significantly attenuates the yield of oxidative DNA damage. These data demonstrate that ferrous iron-loaded Dps is selectively oxidized to fill guanine radical holes, thereby restoring the integrity of the DNA. Luminescence studies indicate no direct interaction between the ruthenium photooxidant and Dps, supporting the DNA-mediated oxidation of ferrous iron-loaded Dps. Thus DNA charge transport may be a mechanism by which Dps efficiently protects the genome of pathogenic bacteria from a distance.", "doi": "10.1021/ja408760w", "pmcid": "PMC3899832", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2013-10-23", "series_number": "42", "volume": "135", "issue": "42", "pages": "15726-15729" }, { "id": "authors:n7hqa-k6d28", "collection": "authors", "collection_id": "n7hqa-k6d28", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20131105-140620927", "type": "article", "title": "Intraduplex DNA-Mediated Electrochemistry of Covalently Tethered Redox-Active Reporters", "author": [ { "family_name": "Pheeney", "given_name": "Catrina G.", "clpid": "Pheeney-C-G" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Intraduplex DNA-mediated reduction is established as a general mechanism for the reduction of distally bound stacked redox-active species covalently tethered to DNA through flexible alkane linkages. Methylene Blue (MB), Nile Blue (NB), and Anthraquinone (AQ) were covalently tethered to DNA with three different covalent linkages. Using these reporters DNA electrochemistry was shown to be both DNA-mediated and intra-, rather than inter-, duplex. Significantly, the charge transport pathway occurring through the DNA \u03c0-stack is established by using an intervening AC mismatch to break this path. The fact that the DNA-mediated reduction of MB occurs primarily via intraduplex intercalation is established through varying the proximity and integrity of the neighboring duplex DNA.", "doi": "10.1021/ja408135g", "pmcid": "PMC3899830", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2013-09-30", "series_number": "40", "volume": "135", "issue": "40", "pages": "14944-14947" }, { "id": "authors:va0a5-cf585", "collection": "authors", "collection_id": "va0a5-cf585", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20131204-111813799", "type": "article", "title": "Luminescence of [Ru(bpy)_2(dppz)]^(2+) Bound to RNA Mismatches", "author": [ { "family_name": "McConnell", "given_name": "Anna J.", "orcid": "0000-0001-7329-4319", "clpid": "McConnell-Anna-J" }, { "family_name": "Song", "given_name": "Hang", "clpid": "Song-Hang" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The luminescence of rac-[Ru(bpy)_2(dppz)]^(2+) (bpy = 2,2\u2032-bipyridine and dppz = dipyrido[3,2-a:2\u2032,3\u2032-c]phenazine) was explored in the presence of RNA oligonucleotides containing a single RNA mismatch (CA and GG) in order to develop a probe for RNA mismatches. While there is minimal luminescence of [Ru(bpy)_2(dppz)]^(2+) in the presence of matched RNA due to weak binding, the luminescence is significantly enhanced in the presence of a single CA mismatch. The luminescence differential between CA mismatched and matched RNA is substantially higher compared to the DNA analogue, and therefore, [Ru(bpy)_2(dppz)]^(2+) appears to be also a sensitive light switch probe for a CA mismatch in duplex RNA. Although the luminescence intensity is lower in the presence of RNA than DNA, F\u00f6rster resonance energy transfer (FRET) between the donor ruthenium complex and FRET acceptor SYTO 61 is successfully exploited to amplify the luminescence in the presence of the mismatch. Luminescence and quenching studies with sodium iodide suggest that [Ru(bpy)_2(dppz)]^(2+) binds to these mismatches via metalloinsertion from the minor groove. This work provides further evidence that metalloinsertion is a general binding mode of octahedral metal complexes to thermodynamically destabilized mismatches not only in DNA but also in RNA.", "doi": "10.1021/ic401531r", "pmcid": "PMC3823503", "issn": "0020-1669", "publisher": "American Chemical Society", "publication": "Inorganic Chemistry", "publication_date": "2013-09-02", "series_number": "17", "volume": "52", "issue": "17", "pages": "10131-10136" }, { "id": "authors:vh0kw-0ck43", "collection": "authors", "collection_id": "vh0kw-0ck43", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130913-110347612", "type": "article", "title": "Multiplexed Electrochemistry of DNA-Bound Metalloproteins", "author": [ { "family_name": "Pheeney", "given_name": "Catrina G.", "clpid": "Pheeney-C-G" }, { "family_name": "Arnold", "given_name": "Anna R.", "clpid": "Arnold-A-R" }, { "family_name": "Grodick", "given_name": "Michael A.", "clpid": "Grodick-M-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Here we describe a multiplexed electrochemical characterization of DNA-bound proteins containing [4Fe-4S] clusters. DNA-modified electrodes have become an essential tool for the characterization of the redox chemistry of DNA repair proteins containing redox cofactors, and multiplexing offers a means to probe different complex samples and substrates in parallel to elucidate this chemistry. Multiplexed analysis of endonuclease III (EndoIII), a DNA repair protein containing a [4Fe-4S] cluster known to be accessible via DNA-mediated charge transport, shows subtle differences in the electrochemical behavior as a function of DNA morphology. The peak splitting, signal broadness, sensitivity to \u03c0-stack perturbations, and kinetics were all characterized for the DNA-bound reduction of EndoIII on both closely and loosely packed DNA films. DNA-bound EndoIII is seen to have two different electron transfer pathways for reduction, either through the DNA base stack or through direct surface reduction; closely packed DNA films, where the protein has limited surface accessibility, produce electrochemical signals reflecting electron transfer that is DNA-mediated. Multiplexing furthermore permits the comparison of the electrochemistry of EndoIII mutants, including a new family of mutations altering the electrostatics surrounding the [4Fe-4S] cluster. While little change in the midpoint potential was found for this family of mutants, significant variations in the efficiency of DNA-mediated electron transfer were apparent. On the basis of the stability of these proteins, examined by circular dichroism, we propose that the electron transfer pathway can be perturbed not only by the removal of aromatic residues but also through changes in solvation near the cluster.", "doi": "10.1021/ja4041779", "pmcid": "PMC3899834", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2013-08-14", "series_number": "32", "volume": "135", "issue": "32", "pages": "11869-11878" }, { "id": "authors:7vkm8-c2z75", "collection": "authors", "collection_id": "7vkm8-c2z75", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130718-095506376", "type": "article", "title": "Biological effects of simple changes in functionality on rhodium metalloinsertors", "author": [ { "family_name": "Weidmann", "given_name": "Alyson G.", "clpid": "Weidmann-A-G" }, { "family_name": "Komor", "given_name": "Alexis C.", "clpid": "Komor-A-C" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "DNA mismatch repair (MMR) is crucial to ensuring the fidelity of the genome. The inability to correct single base mismatches leads to elevated mutation rates and carcinogenesis. Using metalloinsertors\u2013bulky metal complexes that bind with high specificity to mismatched sites in the DNA duplex\u2013our laboratory has adopted a new chemotherapeutic strategy through the selective targeting of MMR-deficient cells, that is, those that have a propensity for cancerous transformation. Rhodium metalloinsertors display inhibitory effects selectively in cells that are deficient in the MMR machinery, consistent with this strategy. However, a highly sensitive structure\u2013function relationship is emerging with the development of new complexes that highlights the importance of subcellular localization. We have found that small structural modifications, for example a hydroxyl versus a methyl functional group, can yield profound differences in biological function. Despite similar binding affinities and selectivities for DNA mismatches, only one metalloinsertor shows selective inhibition of cellular proliferation in MMR-deficient versus -proficient cells. Studies of whole-cell, nuclear and mitochondrial uptake reveal that this selectivity depends upon targeting DNA mismatches in the cell nucleus.", "doi": "10.1098/rsta.2012.0117", "pmcid": "PMC3685451", "issn": "1364-503X", "publisher": "Royal Society of London", "publication": "Philosophical Transactions A: Mathematical, Physical and Engineering Sciences", "publication_date": "2013-07-28", "series_number": "1995", "volume": "371", "issue": "1995", "pages": "Art. No. 20120117" }, { "id": "authors:qyp3v-t1v78", "collection": "authors", "collection_id": "qyp3v-t1v78", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130503-130417175", "type": "article", "title": "The path for metal complexes to a DNA target", "author": [ { "family_name": "Komor", "given_name": "Alexis C.", "clpid": "Komor-A-C" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The discovery of cisplatin as a therapeutic agent stimulated a new era in the application of transition\nmetal complexes for therapeutic design. Here we describe recent results on a variety of transition metal\ncomplexes targeted to DNA to illustrate many of the issues involved in new therapeutic design. We\ndescribe first structural studies of complexes bound covalently and non-covalently to DNA to identify\npotential lesions within the cell. We then review the biological fates of these complexes, illustrating the\nkey elements in obtaining potent activity, the importance of uptake and subcellular localization of the\ncomplexes, as well as the techniques used to delineate these characteristics. Genomic DNA provides a\nchallenging but valuable target for new transition metal-based therapeutics.", "doi": "10.1039/c3cc00177f", "pmcid": "PMC3660861", "issn": "1359-7345", "publisher": "Royal Society of Chemistry", "publication": "Chemical Communications", "publication_date": "2013-02-20", "series_number": "35", "volume": "49", "issue": "35", "pages": "3617-3630" }, { "id": "authors:wz0e4-frp04", "collection": "authors", "collection_id": "wz0e4-frp04", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130425-131548699", "type": "article", "title": "DNA-Mediated Signaling", "author": [ { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Many experiments have now shown that double helical DNA can serve as a conduit for efficient charge transport over long distances. We have seen, for example, that oxidative damage to DNA can be promoted from a distance as a DNA-mediated redox process. Photophysical, electrochemical and biochemical experiments have been conducted to characterize this chemistry. Uniquely, this chemistry is exquisitely sensitive to perturbations in the DNA base stack, such as arise with base mismatches, lesions, and protein binding. We have explored how this chemistry may be used within the cell for long range signaling. Studies are described where DNA charge transport is utilized in signaling DNA-bound proteins, both to regulate transcription and to activate repair of base lesions under conditions of oxidative stress. DNA charge transport chemistry provides an opportunity to carry out redox chemistry at a distance.", "doi": "10.1016/j.bpj.2012.11.031", "issn": "0006-3495", "publisher": "Biophysical Society", "publication": "Biophysical Journal", "publication_date": "2013-01-29", "series_number": "2", "volume": "104", "issue": "2", "pages": "2A" }, { "id": "authors:c6n4a-wc529", "collection": "authors", "collection_id": "c6n4a-wc529", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130111-105340383", "type": "article", "title": "Cell-Selective Biological Activity of Rhodium Metalloinsertors Correlates with Subcellular Localization", "author": [ { "family_name": "Komor", "given_name": "Alexis C.", "clpid": "Komor-A-C" }, { "family_name": "Schneider", "given_name": "Curtis J.", "clpid": "Schneider-C-J" }, { "family_name": "Weidmann", "given_name": "Alyson G.", "clpid": "Weidmann-A-G" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Deficiencies in the mismatch repair (MMR) pathway are associated with several types of cancers, as well as resistance to commonly used chemotherapeutics. Rhodium metalloinsertors have been found to bind DNA mismatches with high affinity and specificity in vitro, and also exhibit cell-selective cytotoxicity, targeting MMR-deficient cells over MMR-proficient cells. Ten distinct metalloinsertors with varying lipophilicities have been synthesized and their mismatch binding affinities and biological activities determined. Although DNA photocleavage experiments demonstrate that their binding affinities are quite similar, their cell-selective antiproliferative and cytotoxic activities vary significantly. Inductively coupled plasma mass spectrometry (ICP-MS) experiments have uncovered a relationship between the subcellular distribution of these metalloinsertors and their biological activities. Specifically, we find that all of our metalloinsertors localize in the nucleus at sufficient concentrations for binding to DNA mismatches. However, the metalloinsertors with high rhodium localization in the mitochondria show toxicity that is not selective for MMR-deficient cells, whereas metalloinsertors with less mitochondrial rhodium show activity that is highly selective for MMR-deficient versus proficient cells. This work supports the notion that specific targeting of the metalloinsertors to nuclear DNA gives rise to their cell-selective cytotoxic and antiproliferative activities. The selectivity in cellular targeting depends upon binding to mismatches in genomic DNA.", "doi": "10.1021/ja3090687", "pmcid": "PMC3740518", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2012-11-21", "series_number": "46", "volume": "134", "issue": "46", "pages": "19223-19233" }, { "id": "authors:swk2f-7rv79", "collection": "authors", "collection_id": "swk2f-7rv79", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130116-113416623", "type": "article", "title": "Luminescent Properties of Ruthenium(II) Complexes with Sterically Expansive Ligands Bound to DNA Defects", "author": [ { "family_name": "McConnell", "given_name": "Anna J.", "orcid": "0000-0001-7329-4319", "clpid": "McConnell-Anna-J" }, { "family_name": "Lim", "given_name": "Mi Hee", "clpid": "Lim-Mi-Hee" }, { "family_name": "Olmon", "given_name": "Eric D.", "clpid": "Olmon-E-D" }, { "family_name": "Song", "given_name": "Hang", "clpid": "Song-Hang" }, { "family_name": "Dervan", "given_name": "Elizabeth E.", "clpid": "Dervan-E-E" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "A new family of ruthenium(II) complexes with sterically expansive ligands for targeting DNA defects was prepared, and their luminescent responses to base pair mismatches and/or abasic sites were investigated. Design of the complexes sought to combine the mismatch specificity of sterically expansive metalloinsertors, such as [Rh(bpy)_2(chrysi)]^(3+) (chrysi = chrysene-5,6-quinone diimine), and the light switch behavior of [Ru(bpy)_2(dppz)]^(2+) (dppz = dipyrido[3,2-\u0251:2\u2032,3\u2032c]phenazine). In one approach, complexes bearing analogues of chrysi incorporating hydrogen-bonding functionality similar to dppz were synthesized. While the complexes show luminescence only at low temperatures (77 K), competition experiments with [Ru(bpy)_2(dppz)]^(2+) at ambient temperatures reveal that the chrysi derivatives preferentially bind DNA mismatches. In another approach, various substituents were introduced onto the dppz ligand to increase its steric bulk for mismatch binding while maintaining planarity. Steady state luminescence and luminescence lifetime measurements reveal that these dppz derivative complexes behave as DNA \"light switches\" but that the selectivity in binding and luminescence with mismatched/abasic versus well-matched DNA is not high. In all cases, luminescence depends sensitively upon structural perturbations to the dppz ligand.", "doi": "10.1021/ic3019524", "pmcid": "PMC3622160", "issn": "0020-1669", "publisher": "American Chemical Society", "publication": "Inorganic Chemistry", "publication_date": "2012-11-19", "series_number": "22", "volume": "51", "issue": "22", "pages": "12511-12520" }, { "id": "authors:xa8rd-n6b58", "collection": "authors", "collection_id": "xa8rd-n6b58", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120807-093450882", "type": "article", "title": "Solution, surface, and single molecule platforms for the study of DNA-mediated charge transport", "author": [ { "family_name": "Muren", "given_name": "Natalie B.", "clpid": "Muren-N-B" }, { "family_name": "Olmon", "given_name": "Eric D.", "clpid": "Olmon-E-D" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The structural core of DNA, a continuous stack of aromatic heterocycles, the base pairs, which extends down the helical axis, gives rise to the fascinating electronic properties of this molecule that is so critical for life. Our laboratory and others have developed diverse experimental platforms to investigate the capacity of DNA to conduct charge, termed DNA-mediated charge transport (DNA CT). Here, we present an overview of DNA CT experiments in solution, on surfaces, and with single molecules that collectively provide a broad and consistent perspective on the essential characteristics of this chemistry. DNA CT can proceed over long molecular distances but is remarkably sensitive to perturbations in base pair stacking. We discuss how this foundation, built with data from diverse platforms, can be used both to inform a mechanistic description of DNA CT and to inspire the next platforms for its study: living organisms and molecular electronics.", "doi": "10.1039/C2CP41602F", "pmcid": "PMC3478128", "issn": "1463-9076", "publisher": "Royal Society of Chemistry", "publication": "Physical Chemistry Chemical Physics", "publication_date": "2012-10-28", "series_number": "40", "volume": "14", "issue": "40", "pages": "13754-13771" }, { "id": "authors:y7b0n-x9c71", "collection": "authors", "collection_id": "y7b0n-x9c71", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20121116-100524704", "type": "article", "title": "DNA Charge Transport for Sensing and Signaling", "author": [ { "family_name": "Sontz", "given_name": "Pamela A.", "clpid": "Sontz-P-A" }, { "family_name": "Muren", "given_name": "Natalie B.", "clpid": "Muren-N-B" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The DNA duplex is an exquisite macromolecular array that stores genetic information to encode proteins and regulate pathways. Its unique structure also imparts chemical function that allows it also to mediate charge transport (CT). We have utilized diverse platforms to probe DNA CT, using spectroscopic, electrochemical, and even genetic methods. These studies have established powerful features of DNA CT chemistry. DNA CT can occur over long molecular distances as long as the bases are well stacked. The perturbations in base stacking that arise with single base mismatches, DNA lesions, and the binding of some proteins that kink the DNA all inhibit DNA CT. Significantly, single molecule studies of DNA CT show that ground state CT can occur over 34 nm if the duplex is well stacked; one single base mismatch inhibits CT. The DNA duplex is an effective sensor for the integrity of the base pair stack. Moreover, the efficiency of DNA CT is what one would expect for a stack of graphite sheets: equivalent to the stack of DNA base pairs and independent of the sugar-phosphate backbone.\n\nSince DNA CT offers a means to carry out redox chemistry from a distance, we have considered how this chemistry might be used for long range biological signaling. We have taken advantage of our chemical probes and platforms to characterize DNA CT in the context of the cell. CT can occur over long distances, perhaps funneling damage to particular sites and insulating others from oxidative stress. Significantly, transcription factors that activate the genome to respond to oxidative stress can also be activated from a distance through DNA CT. Numerous proteins maintain the integrity of the genome and an increasing number of them contain [4Fe-4S] clusters that do not appear to carry out either structural or enzymatic roles. Using electrochemical methods, we find that DNA binding shifts the redox potentials of the clusters, activating them towards oxidation at physiological potentials.\n\nWe have proposed a model that describes how repair proteins may utilize DNA CT to efficiently search the genome for lesions. Importantly, many of these proteins occur in low copy numbers within the cell, and thus a processive mechanism does not provide a sufficient explanation of how they find and repair lesions before the cell divides. Using atomic force microscopy and genetic assays, we show that repair proteins proficient at DNA CT can relocalize in the vicinity of DNA lesions and can cooperate in finding lesions within the cell. Conversely, proteins defective in DNA CT cannot relocalize in the vicinity of lesions and do not assist other proteins involved in repair within the cell. Moreover such genetic defects are associated with disease in human protein analogues. As we continue to unravel this chemistry and discover more proteins with redox cofactors involved in genome maintenance, we are learning more regarding opportunities for long range signaling and sensing, and more examples of DNA CT chemistry that may provide critical functions within the cell.", "doi": "10.1021/ar3001298", "pmcid": "PMC3495616", "issn": "0001-4842", "publisher": "American Chemical Society", "publication": "Accounts of Chemical Research", "publication_date": "2012-10-16", "series_number": "10", "volume": "45", "issue": "10", "pages": "1792-1800" }, { "id": "authors:n4r04-fdn21", "collection": "authors", "collection_id": "n4r04-fdn21", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120824-131018535", "type": "article", "title": "Crystal structure of \u0394-[Ru(bpy)_2dppz]^(2+) bound to mismatched DNA reveals side-by-side metalloinsertion and intercalation", "author": [ { "family_name": "Song", "given_name": "Hang", "clpid": "Song-Hang" }, { "family_name": "Kaiser", "given_name": "Jens T.", "orcid": "0000-0002-5948-5212", "clpid": "Kaiser-J-T" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "DNA mismatches represent a novel target in the development of diagnostics and therapeutics for cancer, because deficiencies in DNA mismatch repair are implicated in cancers, and cells that are repair-deficient show a high frequency of mismatches. Metal complexes with bulky intercalating ligands serve as probes for DNA mismatches. Here, we report the high-resolution (0.92 \u00c5) crystal structure of the ruthenium 'light switch' complex \u0394-[Ru(bpy)_(2)dppz]^(2+) (bpy = 2,2\u2032-bipyridine and dppz = dipyridophenazine), which is known to show luminescence on binding to duplex DNA, bound to both mismatched and well-matched sites in the oligonucleotide 5\u2032-(dCGGAAATTACCG)_(2)-3\u2032 (underline denotes AA mismatches). Two crystallographically independent views reveal that the complex binds mismatches through metalloinsertion, ejecting both mispaired adenosines. Additional ruthenium complexes are intercalated at well-matched sites, creating an array of complexes in the minor groove stabilized by stacking interactions between bpy ligands and extruded adenosines. This structure attests to the generality of metalloinsertion and metallointercalation as DNA binding modes.", "doi": "10.1038/nchem.1375", "pmcid": "PMC3478149", "issn": "1755-4330", "publisher": "Nature Publishing Group", "publication": "Nature Chemistry", "publication_date": "2012-08", "series_number": "8", "volume": "4", "issue": "8", "pages": "615-620" }, { "id": "authors:t6pav-59j44", "collection": "authors", "collection_id": "t6pav-59j44", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120810-143422701", "type": "article", "title": "DNA sensing by electrocatalysis with hemoglobin", "author": [ { "family_name": "Pheeney", "given_name": "Catrina G.", "clpid": "Pheeney-C-G" }, { "family_name": "Guerra", "given_name": "Luis F.", "clpid": "Guerra-L-F" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Electrocatalysis offers a means of electrochemical signal amplification, yet in DNA-based sensors, electrocatalysis has required high-density DNA films and strict assembly and passivation conditions. Here, we describe the use of hemoglobin as a robust and effective electron sink for electrocatalysis in DNA sensing on low-density DNA films. Protein shielding of the heme redox center minimizes direct reduction at the electrode surface and permits assays on low-density DNA films. Electrocatalysis with methylene blue that is covalently tethered to the DNA by a flexible alkyl chain linkage allows for efficient interactions with both the base stack and hemoglobin. Consistent suppression of the redox signal upon incorporation of a single cytosine-adenine (CA) mismatch in the DNA oligomer demonstrates that both the unamplified and the electrocatalytically amplified redox signals are generated through DNA-mediated charge transport. Electrocatalysis with hemoglobin is robust: It is stable to pH and temperature variations. The utility and applicability of electrocatalysis with hemoglobin is demonstrated through restriction enzyme detection, and an enhancement in sensitivity permits femtomole DNA sampling.", "doi": "10.1073/pnas.1201551109", "pmcid": "PMC3406877", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2012-07-17", "series_number": "29", "volume": "109", "issue": "29", "pages": "11528-11533" }, { "id": "authors:cwfmm-99q21", "collection": "authors", "collection_id": "cwfmm-99q21", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120521-152748382", "type": "article", "title": "DNA Electrochemistry with Tethered Methylene Blue", "author": [ { "family_name": "Pheeney", "given_name": "Catrina G.", "clpid": "Pheeney-C-G" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Methylene blue (MB\u2032), covalently attached to DNA through a flexible C_12 alkyl linker, provides a sensitive redox reporter in DNA electrochemistry measurements. Tethered, intercalated MB\u2032 is reduced through DNA-mediated charge transport; the incorporation of a single base mismatch at position 3, 10, or 14 of a 17-mer causes an attenuation of the signal to 62 \u00b1 3% of the well-matched DNA, irrespective of position in the duplex. The redox signal intensity for MB\u2032\u2013DNA is found to be least 3-fold larger than that of Nile blue (NB)\u2013DNA, indicating that MB\u2032 is even more strongly coupled to the \u03c0-stack. The signal attenuation due to an intervening mismatch does, however, depend on DNA film density and the backfilling agent used to passivate the surface. These results highlight two mechanisms for reduction of MB\u2032 on the DNA-modified electrode: reduction mediated by the DNA base pair stack and direct surface reduction of MB\u2032 at the electrode. These two mechanisms are distinguished by their rates of electron transfer that differ by 20-fold. The extent of direct reduction at the surface can be controlled by assembly and buffer conditions.", "doi": "10.1021/la300566x", "pmcid": "PMC3398613", "issn": "0743-7463", "publisher": "American Chemical Society", "publication": "Langmuir", "publication_date": "2012-05-01", "series_number": "17", "volume": "28", "issue": "17", "pages": "7063-7070" }, { "id": "authors:kymxs-fpg30", "collection": "authors", "collection_id": "kymxs-fpg30", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120228-100512207", "type": "article", "title": "DNA charge transport as a first step in coordinating the detection of lesions by repair proteins", "author": [ { "family_name": "Sontz", "given_name": "Pamela A.", "clpid": "Sontz-P-A" }, { "family_name": "Mui", "given_name": "Timothy P.", "clpid": "Mui-Timothy-P" }, { "family_name": "Fuss", "given_name": "Jill O.", "clpid": "Fuss-J-O" }, { "family_name": "Tainer", "given_name": "John A.", "clpid": "Tainer-J-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Damaged bases in DNA are known to lead to errors in replication and transcription, compromising the integrity of the genome. We have proposed a model where repair proteins containing redox-active [4Fe-4S] clusters utilize DNA charge transport (CT) as a first step in finding lesions. In this model, the population of sites to search is reduced by a localization of protein in the vicinity of lesions. Here, we examine this model using single-molecule atomic force microscopy (AFM). XPD, a 5\u2032-3\u2032 helicase involved in nucleotide excision repair, contains a [4Fe-4S] cluster and exhibits a DNA-bound redox potential that is physiologically relevant. In AFM studies, we observe the redistribution of XPD onto kilobase DNA strands containing a single base mismatch, which is not a specific substrate for XPD but, like a lesion, inhibits CT. We further provide evidence for DNA-mediated signaling between XPD and Endonuclease III (EndoIII), a base excision repair glycosylase that also contains a [4Fe-4S] cluster. When XPD and EndoIII are mixed together, they coordinate in relocalizing onto the mismatched strand. However, when a CT-deficient mutant of either repair protein is combined with the CT-proficient repair partner, no relocalization occurs. These data not only indicate a general link between the ability of a repair protein to carry out DNA CT and its ability to redistribute onto DNA strands near lesions but also provide evidence for coordinated DNA CT between different repair proteins in their search for damage in the genome.", "doi": "10.1073/pnas.1120063109", "pmcid": "PMC3277573", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2012-02-07", "series_number": "6", "volume": "109", "issue": "6", "pages": "1856-1861" }, { "id": "authors:ytpac-vcd48", "collection": "authors", "collection_id": "ytpac-vcd48", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120104-142531511", "type": "article", "title": "Transducing methyltransferase activity into electrical signals in a carbon nanotube\u2013DNA device", "author": [ { "family_name": "Wang", "given_name": "Hanfei", "clpid": "Wang-Hanfei" }, { "family_name": "Muren", "given_name": "Natalie B.", "clpid": "Muren-N-B" }, { "family_name": "Ordinario", "given_name": "David", "clpid": "Ordinario-D" }, { "family_name": "Gorodetsky", "given_name": "Alon A.", "orcid": "0000-0002-3811-552X", "clpid": "Gorodetsky-A-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Nuckolls", "given_name": "Colin", "clpid": "Nuckolls-C" } ], "abstract": "This study creates a device where the DNA is electronically integrated to serve as both the biological target and electrical transducer in a CNT\u2013DNA\u2013CNT device. We detect DNA binding and methylation by the methyltransferase M.SssI at the single molecule level. We demonstrate sequence-specific, reversible binding of M.SssI and protein-catalyzed methylation that alters the protein-binding affinity of the device. This device, which relies on the exquisite electrical sensitivity of DNA, represents a unique route for the specific, single molecule detection of enzymatic activity.", "doi": "10.1039/c1sc00772f", "pmcid": "PMC3399246", "issn": "2041-6520", "publisher": "Royal Society of Chemistry", "publication": "Chemical Science", "publication_date": "2012-01-01", "series_number": "1", "volume": "3", "issue": "1", "pages": "62-65" }, { "id": "authors:ter2z-ye677", "collection": "authors", "collection_id": "ter2z-ye677", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120124-084500760", "type": "article", "title": "Selective Cytotoxicity of Rhodium Metalloinsertors in Mismatch Repair-Deficient Cells", "author": [ { "family_name": "Ernst", "given_name": "Russell J.", "clpid": "Ernst-R-J" }, { "family_name": "Komor", "given_name": "Alexis C.", "clpid": "Komor-A-C" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Mismatches in DNA occur naturally during replication and as a result of endogenous DNA damaging agents, but the mismatch repair (MMR) pathway acts to correct mismatches before subsequent rounds of replication. Rhodium metalloinsertors bind to DNA mismatches with high affinity and specificity and represent a promising strategy to target mismatches in cells. Here we examine the biological fate of rhodium metalloinsertors bearing dipyridylamine ancillary ligands in cells deficient in MMR versus those that are MMR-proficient. These complexes are shown to exhibit accelerated cellular uptake which permits the observation of various cellular responses, including disruption of the cell cycle, monitored by flow cytometry assays, and induction of necrosis, monitored by dye exclusion and caspase inhibition assays, that occur preferentially in the MMR-deficient cell line. These cellular responses provide insight into the mechanisms underlying the selective activity of this novel class of targeted anticancer agents.", "doi": "10.1021/bi2015822", "pmcid": "PMC3364161", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "2011-12-20", "series_number": "50", "volume": "50", "issue": "50", "pages": "10919-10928" }, { "id": "authors:erwzj-w2a22", "collection": "authors", "collection_id": "erwzj-w2a22", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120113-114638971", "type": "article", "title": "Using Metal Complex Reduced States to Monitor the Oxidation of\n DNA", "author": [ { "family_name": "Olmon", "given_name": "Eric D.", "clpid": "Olmon-E-D" }, { "family_name": "Hill", "given_name": "Michael G.", "clpid": "Hill-M-G" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Metallointercalating photooxidants interact intimately with the base stack of double-stranded DNA and exhibit rich photophysical and electrochemical properties, making them ideal probes for the study of DNA-mediated charge transport (CT). The complexes [Rh(phi)_2(bpy\u2032)]^(3+) (phi = 9,10-phenanthrenequinone diimine; bpy\u2032 = 4-methyl-4\u2032-(butyric acid)-2,2\u2032-bipyridine), [Ir(ppy)_2(dppz\u2032)]^+ (ppy = 2-phenylpyridine; dppz\u2032 = 6-(dipyrido[3,2-a:2\u2032,3\u2032-c]phenazin-11-yl)hex-5-ynoic acid), and [Re(CO)_3(dppz)(py\u2032)]^+ (dppz = dipyrido[2,3-a:2\u2032,3\u2032-c]phenazine; py\u2032 = 3-(pyridin-4-yl)-propanoic acid) were each covalently tethered to DNA to compare their photooxidation efficiencies. Biochemical studies show that upon irradiation, the three complexes oxidize guanine by long-range DNA-mediated CT with the efficiency: Rh > Re > Ir. Comparison of spectra obtained by spectroelectrochemistry after bulk reduction of the free metal complexes with those obtained by transient absorption (TA) spectroscopy of the conjugates suggests that the reduced metal states form following excitation of the conjugates at 355 nm. Electrochemical experiments and kinetic analysis of the TA decays indicate that the thermodynamic driving force for CT, variations in the efficiency of back electron transfer, and coupling to DNA are the primary factors responsible for the trend observed in the guanine oxidation yields of the three complexes.", "doi": "10.1021/ic201511y", "pmcid": "PMC3277451", "issn": "0020-1669", "publisher": "American Chemical Society", "publication": "Inorganic Chemistry", "publication_date": "2011-12-05", "series_number": "23", "volume": "50", "issue": "23", "pages": "12034-12044" }, { "id": "authors:t9zfw-1xm39", "collection": "authors", "collection_id": "t9zfw-1xm39", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111116-102627735", "type": "article", "title": "ATP-Stimulated, DNA-Mediated Redox Signaling by XPD, a DNA\n Repair and Transcription Helicase", "author": [ { "family_name": "Mui", "given_name": "Timothy P.", "clpid": "Mui-Timothy-P" }, { "family_name": "Fuss", "given_name": "Jill O.", "clpid": "Fuss-J-O" }, { "family_name": "Ishida", "given_name": "Justin P.", "clpid": "Ishida-Justin-P" }, { "family_name": "Tainer", "given_name": "John A.", "clpid": "Tainer-J-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Using DNA-modified electrodes, we show DNA-mediated signaling by XPD, a helicase that contains a [4Fe-4S] cluster and is critical for nucleotide excision repair and transcription. The DNA-mediated redox signal resembles that of base excision repair proteins, with a DNA-bound redox potential of ~80 mV versus NHE. Significantly, this signal increases with ATP hydrolysis. Moreover, the redox signal is substrate-dependent, reports on the DNA conformational changes associated with enzymatic function, and may reflect a general biological role for DNA charge transport.", "doi": "10.1021/ja207222t", "pmcid": "PMC3234108", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2011-10-19", "series_number": "41", "volume": "133", "issue": "41", "pages": "16378-16381" }, { "id": "authors:6wsba-5sk84", "collection": "authors", "collection_id": "6wsba-5sk84", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111115-142739242", "type": "article", "title": "Charge Photoinjection in Intercalated and Covalently Bound [Re(CO)_(3)(dppz)(py)]^(+)\u2013DNA Constructs Monitored by Time-Resolved Visible and Infrared Spectroscopy", "author": [ { "family_name": "Olmon", "given_name": "Eric D.", "clpid": "Olmon-E-D" }, { "family_name": "Sontz", "given_name": "Pamela A.", "clpid": "Sontz-P-A" }, { "family_name": "Blanco-Rodr\u00edguez", "given_name": "Ana-Mar\u00eda", "clpid": "Blanco-Rodr\u00edguez-A-M" }, { "family_name": "Towrie", "given_name": "Michael", "clpid": "Towrie-M" }, { "family_name": "Clark", "given_name": "Ian P.", "clpid": "Clark-I-P" }, { "family_name": "Vl\u010dek", "given_name": "Anton\u00edn, Jr.", "clpid": "Vl\u010dek-A-Jr" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The complex [Re(CO)_(3)(dppz)(py\u2032-OR)]+ (dppz = dipyrido[3,2-a:2\u2032,3\u2032-c]phenazine; py\u2032-OR = 4-functionalized pyridine) offers IR sensitivity and can oxidize DNA directly from the excited state, making it a promising probe for the study of DNA-mediated charge transport (CT). The behavior of several covalent and noncovalent Re\u2013DNA constructs was monitored by time-resolved IR (TRIR) and UV/visible spectroscopies, as well as biochemical methods, confirming the long-range oxidation of DNA by the excited complex. Optical excitation of the complex leads to population of MLCT and at least two distinct intraligand states. Experimental observations that are consistent with charge injection from these excited states include similarity between long-time TRIR spectra and the reduced state spectrum observed by spectroelectrochemistry, the appearance of a guanine radical signal in TRIR spectra, and the eventual formation of permanent guanine oxidation products. The majority of reactivity occurs on the ultrafast time scale, although processes dependent on slower conformational motions of DNA, such as the accumulation of oxidative damage at guanine, are also observed. The ability to measure events on such disparate time scales, its superior selectivity in comparison to other spectroscopic techniques, and the ability to simultaneously monitor carbonyl ligand and DNA IR absorption bands make TRIR a valuable tool for the study of CT in DNA.", "doi": "10.1021/ja205568r", "pmcid": "PMC3227519", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2011-08-31", "series_number": "34", "volume": "133", "issue": "34", "pages": "13718-13730" }, { "id": "authors:stxnv-2sx90", "collection": "authors", "collection_id": "stxnv-2sx90", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110725-095427413", "type": "article", "title": "Mutants of the Base Excision Repair Glycosylase, Endonuclease III: DNA Charge Transport as a First Step in Lesion Detection", "author": [ { "family_name": "Romano", "given_name": "Christine A.", "clpid": "Romano-C-A" }, { "family_name": "Sontz", "given_name": "Pamela A.", "clpid": "Sontz-P-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Endonuclease III (EndoIII) is a base excision repair glycosylase that targets damaged pyrimidines and contains a [4Fe-4S] cluster. We have proposed a model where BER proteins that contain redox-active [4Fe-4S] clusters utilize DNA charge transport (CT) as a first step in the detection of DNA lesions. Here, several mutants of EndoIII were prepared to probe their efficiency of DNA/protein charge transport. Cyclic voltammetry experiments on DNA-modified electrodes show that aromatic residues F30, Y55, Y75, and Y82 help mediate charge transport between DNA and the [4Fe-4S] cluster. On the basis of circular dichroism studies to measure protein stability, mutations at residues W178 and Y185 are found to destabilize the protein; these residues may function to protect the [4Fe-4S] cluster. Atomic force microscopy studies furthermore reveal a correlation in the ability of mutants to carry out protein/DNA CT and their ability to relocalize onto DNA strands containing a single base mismatch; EndoIII mutants that are defective in carrying out DNA/protein CT do not redistribute onto mismatch-containing strands, consistent with our model. These results demonstrate a link between the ability of the repair protein to carry out DNA CT and its ability to relocalize near lesions, thus pointing to DNA CT as a key first step in the detection of base damage in the genome.", "doi": "10.1021/bi2003179", "pmcid": "PMC3134277", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "2011-07-12", "series_number": "27", "volume": "50", "issue": "27", "pages": "6133-6145" }, { "id": "authors:pkbjb-yra39", "collection": "authors", "collection_id": "pkbjb-yra39", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110506-101158648", "type": "article", "title": "Metal complexes for DNA-mediated charge transport", "author": [ { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Olmon", "given_name": "Eric D.", "clpid": "Olmon-E-D" }, { "family_name": "Sontz", "given_name": "Pamela A.", "clpid": "Sontz-P-A" } ], "abstract": "In all organisms, oxidation threatens the integrity of the genome. DNA-mediated charge transport (CT) may play an important role in the generation and repair of this oxidative damage. In studies involving long-range CT from intercalating Ru and Rh complexes to 5\u2032-GG-3\u2032 sites, we have examined the efficiency of CT as a function of distance, temperature, and the electronic coupling of metal oxidants bound to the base stack. Most striking is the shallow distance dependence and the sensitivity of DNA CT to how the metal complexes are stacked in the helix. Experiments with cyclopropylamine-modified bases have revealed that charge occupation occurs at all sites along the bridge. Using Ir complexes, we have seen that the process of DNA-mediated reduction is very similar to that of DNA-mediated oxidation. Studies involving metalloproteins have, furthermore, shown that their redox activity is DNA-dependent and can be DNA-mediated. Long range DNA-mediated CT can facilitate the oxidation of DNA-bound base excision repair proteins to initiate a redox-active search for DNA lesions. DNA CT can also activate the transcription factor SoxR, triggering a cellular response to oxidative stress. Indeed, these studies show that within the cell, redox-active proteins may utilize the same chemistry as that of synthetic metal complexes in vitro, and these proteins may harness DNA-mediated CT to reduce damage to the genome and regulate cellular processes.", "doi": "10.1016/j.ccr.2010.09.002", "pmcid": "PMC3105778", "issn": "0010-8545", "publisher": "Elsevier", "publication": "Coordination Chemistry Reviews", "publication_date": "2011-04", "series_number": "7-8", "volume": "255", "issue": "7-8", "pages": "619-634" }, { "id": "authors:rgy7p-qw730", "collection": "authors", "collection_id": "rgy7p-qw730", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110502-100301067", "type": "article", "title": "Single-Step Charge Transport through DNA over Long Distances", "author": [ { "family_name": "Genereux", "given_name": "Joseph C.", "orcid": "0000-0002-5093-7710", "clpid": "Genereux-J-C" }, { "family_name": "Wuerth", "given_name": "Stephanie M.", "clpid": "Wuerth-S-M" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Quantum yields for charge transport across adenine tracts of increasing length have been measured by monitoring hole transport in synthetic oligonucleotides between photoexcited 2-aminopurine, a fluorescent analogue of adenine, and N_2-cyclopropyl guanine. Using fluorescence quenching, a measure of hole injection, and hole trapping by the cyclopropyl guanine derivative, we separate the individual contributions of single- and multistep channels to DNA charge transport and find that with 7 or 8 intervening adenines the charge transport is a coherent, single-step process. Moreover, a transition occurs from multistep to single-step charge transport with increasing donor/acceptor separation, opposite to that generally observed in molecular wires. These results establish that coherent transport through DNA occurs preferentially across 10 base pairs, favored by delocalization over a full turn of the helix.", "doi": "10.1021/ja107033v", "pmcid": "PMC3079569", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2011-03-23", "series_number": "11", "volume": "133", "issue": "11", "pages": "3863-3868" }, { "id": "authors:yx4jt-e1158", "collection": "authors", "collection_id": "yx4jt-e1158", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110322-141743600", "type": "article", "title": "DNA charge transport over 34 nm", "author": [ { "family_name": "Slinker", "given_name": "Jason D.", "clpid": "Slinker-J-D" }, { "family_name": "Muren", "given_name": "Natalie B.", "clpid": "Muren-N-B" }, { "family_name": "Renfrew", "given_name": "Sara E.", "clpid": "Renfrew-S-E" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Molecular wires show promise in nanoscale electronics but the synthesis of uniform, long conductive molecules is a significant challenge. DNA of precise length, by contrast, is easily synthesized, but its conductivity has not been explored over the distances required for nanoscale devices. Here we demonstrate DNA charge transport (CT) over 34 nm in 100-mer monolayers on gold. Multiplexed gold electrodes modified with 100-mer DNA yield sizable electrochemical signals from a distal, covalent Nile Blue redox probe. Significant signal attenuation upon incorporation of a single base pair mismatch demonstrates that CT is DNA-mediated. Efficient cleavage of these 100-mers by a restriction enzyme indicates that the DNA adopts a native conformation that is accessible to protein binding. Similar electron transfer rates are measured through 100-mer and 17-mer monolayers, consistent with rate-limiting electron tunneling through the saturated carbon linker. This DNA-mediated CT distance of 34 nm surpasses most reports of molecular wires.", "doi": "10.1038/NCHEM.982", "pmcid": "PMC3079570", "issn": "1755-4330", "publisher": "Nature Publishing Group", "publication": "Nature Chemistry", "publication_date": "2011-03", "series_number": "3", "volume": "3", "issue": "3", "pages": "228-233" }, { "id": "authors:19401-6rx29", "collection": "authors", "collection_id": "19401-6rx29", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100602-153002681", "type": "article", "title": "Targeting a ruthenium complex to the nucleus with short peptides", "author": [ { "family_name": "Puckett", "given_name": "Cindy A.", "clpid": "Puckett-C-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "In an effort to develop octahedral metal complexes as chemotherapeutic and diagnostic agents targeted to DNA, it is critical to optimize the properties of their cellular uptake. Appending d-octaarginine has been found to improve both the uptake and nuclear localization efficiency of these complexes, but the increased positive charge interferes with selective DNA binding and hence activity. Herein, we evaluate the nuclear entry of a series of luminescent ruthenium peptide conjugates of shorter sequence and lower charge. As is the case for the d-octaarginine conjugate (Ru-D-R8), the tetrapeptide RrRK (where r = d-arginine) facilitates nuclear localization of the ruthenium complex above a threshold concentration, though the threshold is higher for this conjugate (Ru\u2013RrRK) than for Ru-D-R8. Furthermore, appended fluorescein, which lowers the threshold concentration for Ru-D-R8, does not improve nuclear entry of Ru\u2013RrRK, indicating that fluorescein conjugation is not a general strategy for modulating the distribution of cell-penetrating peptides. Similarly, the concentration required for nuclear entry of Ru\u2013RrRK is much higher than has been reported for a thiazole orange RrRK conjugate, demonstrating the influence of payload on the efficiency of uptake and localization of cell-penetrating peptides.", "doi": "10.1016/j.bmc.2010.03.081", "pmcid": "PMC2873839", "issn": "0960-894X", "publisher": "Elsevier", "publication": "Bioorganic and Medicinal Chemistry Letters", "publication_date": "2010-05-15", "series_number": "10", "volume": "18", "issue": "10", "pages": "3564-3569" }, { "id": "authors:5sfhf-r1121", "collection": "authors", "collection_id": "5sfhf-r1121", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100517-152102648", "type": "article", "title": "DNA-Mediated Electron Transfer in Naphthalene-Modified Oligonucleotides", "author": [ { "family_name": "Tanaka", "given_name": "Makiko", "clpid": "Tanaka-Makiko" }, { "family_name": "Elias", "given_name": "Benjamin", "orcid": "0000-0001-5037-3313", "clpid": "Elias-B" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Naphthalene-modified oligonucleotides have been synthesized and characterized with respect to electron transfer chemistry. Using the Sonogashira coupling reaction, naphthalene can be covalently anchored onto a modified uridine through an ethynyl linkage. This tethering allows for effective electronic coupling with the DNA bases, resulting in a significant red shift of the absorption bands of the naphthalenic chromophore. Modification with this chromophore does not appear to affect the overall stability and structure of the DNA. Upon selective irradiation of the naphthalene moiety at 340 nm, photoreduction of a distal electron trap, 5-bromouridine, embedded in the DNA base stack occurs. This DNA-mediated reduction from a distance was found to be significantly more efficient with substitution of 5-bromouridine toward the 5\u2032-end than toward the 3\u2032-end. These results support a general preference for electron transfer through DNA toward the 5\u2032-end, irrespective of the donor. In addition, differences in efficiency of photoreduction through intrastrand and interstrand pathways are observed. For DNA-mediated reduction, as with DNA-mediated oxidation, significant differences in the charge transfer reaction are apparent that depend upon subtle differences in coupling into the DNA base stack.", "doi": "10.1021/jo1000862", "pmcid": "PMC2879047", "issn": "0022-3263", "publisher": "American Chemical Society", "publication": "Journal of Organic Chemistry", "publication_date": "2010-04-16", "series_number": "8", "volume": "75", "issue": "8", "pages": "2423-2428" }, { "id": "authors:rpz24-wkn27", "collection": "authors", "collection_id": "rpz24-wkn27", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100324-111156290", "type": "article", "title": "Multiplexed DNA-Modified Electrodes", "author": [ { "family_name": "Slinker", "given_name": "Jason D.", "clpid": "Slinker-J-D" }, { "family_name": "Muren", "given_name": "Natalie B.", "clpid": "Muren-N-B" }, { "family_name": "Gorodetsky", "given_name": "Alon A.", "orcid": "0000-0002-3811-552X", "clpid": "Gorodetsky-A-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "We report the use of silicon chips with 16 DNA-modified electrodes (DME chips) utilizing DNA-mediated charge transport for multiplexed detection of DNA and DNA-binding protein targets. Four DNA sequences were simultaneously distinguished on a single DME chip with 4-fold redundancy, including one incorporating a single base mismatch. These chips also enabled investigation of the sequence-specific activity of the restriction enzyme Alu1. DME chips supported dense DNA monolayer formation with high reproducibility, as confirmed by statistical comparison to commercially available rod electrodes. The working electrode areas on the chips were reduced to 10 \u03bcm in diameter, revealing microelectrode behavior that is beneficial for high sensitivity and rapid kinetic analysis. These results illustrate how DME chips facilitate sensitive and selective detection of DNA and DNA-binding protein targets in a robust and internally standardized multiplexed format.", "doi": "10.1021/ja909915m", "pmcid": "PMC3334307", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2010-03-03", "series_number": "8", "volume": "132", "issue": "8", "pages": "2769-2774" }, { "id": "authors:avbxf-c8s75", "collection": "authors", "collection_id": "avbxf-c8s75", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100407-134557359", "type": "article", "title": "Mechanisms for DNA Charge Transport", "author": [ { "family_name": "Genereux", "given_name": "Joseph C.", "orcid": "0000-0002-5093-7710", "clpid": "Genereux-J-C" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "DNA charge transport (CT) chemistry has received considerable attention by scientific researchers over the past 15 years since our first provocative publication on long range CT in a DNA assembly.1,2 This interest, shared by physicists, chemists and biologists, reflects the potential of DNA CT to provide a sensitive route for signaling, whether in the construction of nanoscale biosensors or as an enzymatic tool to detect damage in the genome. Research into DNA CT chemistry began as a quest to determine whether the DNA double helix, a macromolecular assembly in solution with \u03c0-stacked base pairs, might share conductive characteristics with \u03c0-stacked solids. Physicists carried out sophisticated experiments to measure the conductivity of DNA samples, but the means to connect discrete DNA assemblies into the devices to gauge conductivity varied, as did the conditions under which conductivities were determined. Chemists constructed DNA assemblies to measure hole and electron transport in solution using a variety of hole and electron donors. Here, too, DNA CT was seen to depend upon the connections, or coupling, between donors and the DNA base pair stack. Importantly, these experiments have resolved the debate over whether DNA CT is possible. Moreover these studies have shown that DNA CT, irrespective of the oxidant or reductant used to initiate the chemistry, can occur over long molecular distances but can be exquisitely sensitive to perturbations in the base pair stack. \n\nHere we review some of the critical characteristics of DNA charge transport chemistry, taking examples from a range of systems, and consider these characteristics in the context of their mechanistic implications. This review is not intended to be exhaustive but instead to be illustrative. For instance, we describe studies involving measurements in solution using pendant photooxidants to inject holes, conductivity studies with covalently modified assemblies, and electrochemical studies on DNA-modified electrodes. We do not focus in detail on the differences amongst these constructs but instead on their similarities. It is the similarity among these various systems that allows us to consider different mechanisms to describe DNA CT. Thus we review also the various mechanisms for DNA CT that have been put forth and attempt to reconcile these mechanistic proposals with the many disparate measurements of DNA CT. Certainly the debate among researchers has shifted from \"is DNA CT possible?\" to \"how does it work?\". This review intends to explore this latter question in detail.", "doi": "10.1021/cr900228f", "pmcid": "PMC2879062", "issn": "0009-2665", "publisher": "American Chemical Society", "publication": "Chemical Reviews", "publication_date": "2010-03", "series_number": "3", "volume": "110", "issue": "3", "pages": "1642-1662" }, { "id": "authors:xykej-qc734", "collection": "authors", "collection_id": "xykej-qc734", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100216-153031939", "type": "article", "title": "Exploring the cellular accumulation of metal complexes", "author": [ { "family_name": "Puckett", "given_name": "Cindy A.", "clpid": "Puckett-C-A" }, { "family_name": "Ernst", "given_name": "Russell J.", "clpid": "Ernst-R-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Transition metal complexes offer great potential as diagnostic and therapeutic agents, and a growing number of biological applications have been explored. To be effective, these complexes must reach their intended target inside the cell. Here we review the cellular accumulation of metal complexes, including their uptake, localization, and efflux. Metal complexes are taken up inside cells through various mechanisms, including passive diffusion and entry through organic and metal transporters. Emphasis is placed on the methods used to examine cellular accumulation, to identify the mechanism(s) of uptake, and to monitor possible efflux. Conjugation strategies that have been employed to improve the cellular uptake characteristics of metal complexes are also described.", "doi": "10.1039/b922209j", "pmcid": "PMC2873847", "issn": "1477-9226", "publisher": "Royal Society of Chemistry", "publication": "Dalton Transactions", "publication_date": "2010-02-07", "series_number": "5", "volume": "39", "issue": "5", "pages": "1159-1170" }, { "id": "authors:80gwz-8ns84", "collection": "authors", "collection_id": "80gwz-8ns84", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100405-093806861", "type": "article", "title": "DNA-Mediated Charge Transport in Redox Sensing and Signaling", "author": [ { "family_name": "Genereux", "given_name": "Joseph C.", "orcid": "0000-0002-5093-7710", "clpid": "Genereux-J-C" }, { "family_name": "Boal", "given_name": "Amie K.", "orcid": "0000-0002-1234-8472", "clpid": "Boal-A-K" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The transport of charge through the DNA base-pair stack offers a route to carry out redox chemistry at a distance. Here we describe characteristics of this chemistry that have been elucidated and how this chemistry may be utilized within the cell. The shallow distance dependence associated with these redox reactions permits DNA-mediated signaling over long molecular distances in the genome and facilitates the activation of redox-sensitive transcription factors globally in response to oxidative stress. The long-range funneling of oxidative damage to sites of low oxidation potential in the genome also may provide a means of protection within the cell. Furthermore, the sensitivity of DNA charge transport to perturbations in base-pair stacking, as may arise with base lesions and mismatches, may be used as a route to scan the genome for damage as a first step in DNA repair. Thus, the ability of double-helical DNA in mediating redox chemistry at a distance provides a natural mechanism for redox sensing and signaling in the genome.", "doi": "10.1021/ja907669c", "pmcid": "PMC2902267", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2010-01-27", "series_number": "3", "volume": "132", "issue": "3", "pages": "891-905" }, { "id": "authors:w7cbm-08h76", "collection": "authors", "collection_id": "w7cbm-08h76", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090923-143133443", "type": "article", "title": "Redox signaling between DNA repair proteins for efficient lesion detection", "author": [ { "family_name": "Boal", "given_name": "Amie K.", "orcid": "0000-0002-1234-8472", "clpid": "Boal-A-K" }, { "family_name": "Genereux", "given_name": "Joseph C.", "orcid": "0000-0002-5093-7710", "clpid": "Genereux-J-C" }, { "family_name": "Sontz", "given_name": "Pamela A.", "clpid": "Sontz-P-A" }, { "family_name": "Gralnick", "given_name": "Jeffrey A.", "orcid": "0000-0001-9250-7770", "clpid": "Gralnick-J-A" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Base excision repair (BER) enzymes maintain the integrity of the genome, and in humans, BER mutations are associated with cancer. Given the remarkable sensitivity of DNA-mediated charge transport (CT) to mismatched and damaged base pairs, we have proposed that DNA repair glycosylases (EndoIII and MutY) containing a redox-active [4Fe4S] cluster could use DNA CT in signaling one another to search cooperatively for damage in the genome. Here, we examine this model, where we estimate that electron transfers over a few hundred base pairs are sufficient for rapid interrogation of the full genome. Using atomic force microscopy, we found a redistribution of repair proteins onto DNA strands containing a single base mismatch, consistent with our model for CT scanning. We also demonstrated in Escherichia coli a cooperativity between EndoIII and MutY that is predicted by the CT scanning model. This relationship does not require the enzymatic activity of the glycosylase. Y82A EndoIII, a mutation that renders the protein deficient in DNA-mediated CT, however, inhibits cooperativity between MutY and EndoIII. These results illustrate how repair proteins might efficiently locate DNA lesions and point to a biological role for DNA-mediated CT within the cell.", "doi": "10.1073/pnas.0908059106", "pmcid": "PMC2741234", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2009-09-08", "series_number": "36", "volume": "106", "issue": "36", "pages": "15237-15242" }, { "id": "authors:b22fd-rpe97", "collection": "authors", "collection_id": "b22fd-rpe97", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090828-231031224", "type": "article", "title": "DNA-mediated redox signaling for transcriptional activation of SoxR", "author": [ { "family_name": "Lee", "given_name": "Paul E.", "clpid": "Lee-P-E" }, { "family_name": "Demple", "given_name": "Bruce", "clpid": "Demple-B" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "In enteric bacteria, the cellular response to oxidative stress is activated by oxidation of the iron-sulfur clusters in SoxR, which then induces transcription of soxS, turning on a battery of defense genes. Here we demonstrate both in vitro and in cells that activation of SoxR can occur in a DNA-mediated reaction with guanine radicals, an early genomic signal of oxidative stress, serving as the oxidant. SoxR in its reduced form is found to inhibit guanine damage by repairing guanine radicals. Moreover, cells treated with a DNA-binding photooxidant, which generates guanine radicals, promotes the expression of soxS. In vitro, this photooxidant, tethered to DNA 80 bp from the soxS promoter, induces transcription by activating SoxR upon irradiation. Thus, transcription can be activated from a distance through DNA-mediated charge transport. This chemistry offers a general strategy for DNA-mediated signaling of oxidative stress.", "doi": "10.1073/pnas.0906429106", "pmcid": "PMC2726364", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2009-08-11", "series_number": "32", "volume": "106", "issue": "32", "pages": "13164-13168" }, { "id": "authors:j1zz6-p6479", "collection": "authors", "collection_id": "j1zz6-p6479", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090901-133357644", "type": "article", "title": "Fluorescein Redirects a Ruthenium\u2212Octaarginine Conjugate to the Nucleus", "author": [ { "family_name": "Puckett", "given_name": "Cindy A.", "clpid": "Puckett-C-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The cellular uptake and localization of a Ru\u2212octaarginine conjugate with and without an appended fluorescein are compared. The inherent luminescence of the Ru(II) dipyridophenazine complex allows observation of its uptake without the addition of a fluorophore. Ru\u2212octaarginine\u2212fluorescein stains the cytosol, nuclei, and nucleoli of HeLa cells under conditions where the Ru\u2212octaarginine conjugate without fluorescein shows only punctate cytoplasmic labeling. At higher concentrations, however, Ru\u2212octaarginine without the fluorescein tag does exhibit cytoplasmic, nuclear, and nucleolar staining. Attaching fluorescein to Ru\u2212octaarginine lowers the threshold concentration required for diffuse cytoplasmic labeling and nuclear entry. Hence, the localization of the fluorophore-bound peptide cannot serve as a proxy for that of the free peptide.", "doi": "10.1021/ja9025165", "pmcid": "PMC2747598", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2009-07-01", "series_number": "25", "volume": "131", "issue": "25", "pages": "8738-8739" }, { "id": "authors:phv8z-2zy62", "collection": "authors", "collection_id": "phv8z-2zy62", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090824-113601367", "type": "article", "title": "Sensitivity of Ru(bpy)_2dppz^(2+) Luminescence to DNA Defects", "author": [ { "family_name": "Lim", "given_name": "Mi Hee", "clpid": "Lim-Mi-Hee" }, { "family_name": "Song", "given_name": "Hang", "clpid": "Song-Hang" }, { "family_name": "Olmon", "given_name": "Eric D.", "clpid": "Olmon-E-D" }, { "family_name": "Dervan", "given_name": "Elizabeth E.", "clpid": "Dervan-E-E" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The luminescent characteristics of Ru(bpy)_2dppz^(2+) (dppz = dipyrido[3,2-a:2\u2032,3\u2032-c]phenazine), a DNA light switch, were investigated in the presence of oligonucleotides containing single base mismatches or an abasic site. In water, the ruthenium luminescence is quenched, but, bound to well matched duplex DNA, the Ru complex luminesces. Here we show that with DNAs containing a defect, rac-, \u0394-, and \u039b-Ru(bpy)_2dppz^(2+) exhibit significant luminescent enhancements above that with well matched DNA. In the presence of a single base mismatch, large luminescent enhancements are evident for the \u0394-Ru isomer; the \u039b-isomer shows particularly high luminescence bound to an oligonucleotide containing an abasic site. Similar increases are not evident with two common DNA-binding organic fluorophores, ethidium bromide and TO-PRO-3. Titrations with hairpin oligonucleotides containing a variable mismatch site show correlation between the level of luminescent enhancement and the thermodynamic destabilization associated with the mismatch. This correlation is reminiscent of that found earlier for a bulky rhodium complex that binds mismatched DNA sites through metalloinsertion, where the complex binds the DNA from the minor groove side, ejecting the mismatched bases into the major groove. Differential quenching studies with minor and major groove quenchers and time-resolved emission studies support this metalloinsertion mode for the dppz complex at the defect site. Certainly these data underscore the utility of Ru(bpy)_2dppz^(2+) as a sensitive luminescent reporter of DNA and its defects.", "doi": "10.1021/ic900407n", "pmcid": "PMC2747521", "issn": "0020-1669", "publisher": "American Chemical Society", "publication": "Inorganic Chemistry", "publication_date": "2009-06-15", "series_number": "12", "volume": "48", "issue": "12", "pages": "5392-5397" }, { "id": "authors:0hqp0-f6t20", "collection": "authors", "collection_id": "0hqp0-f6t20", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090903-144603520", "type": "article", "title": "A Bulky Rhodium Complex Bound to an Adenosine-Adenosine DNA Mismatch: General Architecture of the Metalloinsertion Binding Mode", "author": [ { "family_name": "Zeglis", "given_name": "Brian M.", "clpid": "Zeglis-B-M" }, { "family_name": "Pierre", "given_name": "Val\u00e9rie C.", "clpid": "Pierre-V-C" }, { "family_name": "Kaiser", "given_name": "Jens T.", "orcid": "0000-0002-5948-5212", "clpid": "Kaiser-J-T" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Two crystal structures of \u0394-Rh(bpy)_2(chrysi)^(3+) (chrysi is 5,6-chrysenequinone diimine) bound to the oligonucleotide duplex 5\u2032-CGGAAATTACCG-3\u2032 containing two adenosine-adenosine mismatches (italics) through metalloinsertion were determined. Diffraction quality crystals with two different space groups (P3_221 and P4_32_12) were obtained under very similar crystallization conditions. In both structures, the bulky rhodium complex inserts into the two mismatched sites from the minor groove side, ejecting the mismatched bases into the major groove. The conformational changes are localized to the mismatched site; the metal complex replaces the mismatched base pair without an increase in base pair rise. The expansive metal complex is accommodated in the duplex by a slight opening in the phosphodiester backbone; all sugars retain a C2\u2032-endo puckering, and flanking base pairs neither stretch nor shear. The structures differ, however, in that in one of the structures, an additional metal complex is bound by intercalation from the major groove at the central 5\u2032-AT-3\u2032 step. We conclude that this additional metal complex is intercalated into this central step because of crystal packing forces. The structures described here of \u0394-Rh(bpy)_2(chrysi)^(3+) bound to thermodynamically destabilized AA mismatches share critical features with binding by metalloinsertion in two other oligonucleotides containing different single-base mismatches. These results underscore the generality of metalloinsertion as a new mode of noncovalent binding by small molecules with a DNA duplex.", "doi": "10.1021/bi900194e", "pmcid": "PMC2747516", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "2009-05-26", "series_number": "20", "volume": "48", "issue": "20", "pages": "4247-4253" }, { "id": "authors:sxr23-s2482", "collection": "authors", "collection_id": "sxr23-s2482", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090828-231033057", "type": "article", "title": "Molecular electronics: DNA charges ahead", "author": [ { "family_name": "Genereux", "given_name": "Joseph C.", "orcid": "0000-0002-5093-7710", "clpid": "Genereux-J-C" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Some sequences of DNA conduct charge better than others. Replacing adenine with an analogue allows more sequences to transport charge effectively.", "doi": "10.1038/nchem.188", "issn": "1755-4330", "publisher": "Nature Publishing Group", "publication": "Nature Chemistry", "publication_date": "2009-05", "series_number": "2", "volume": "1", "issue": "2", "pages": "106-107" }, { "id": "authors:pga0g-jz577", "collection": "authors", "collection_id": "pga0g-jz577", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090601-115902054", "type": "article", "title": "DNA mismatch binding and antiproliferative activity of rhodium metalloinsertors", "author": [ { "family_name": "Ernst", "given_name": "Russell J.", "clpid": "Ernst-R-J" }, { "family_name": "Song", "given_name": "Hang", "clpid": "Song-Hang" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Deficiencies in mismatch repair (MMR) are associated with carcinogenesis. Rhodium metalloinsertors bind to DNA base mismatches with high specificity and inhibit cellular proliferation preferentially in MMR-deficient cells versus MMR-proficient cells. A family of chrysenequinone diimine complexes of rhodium with varying ancillary ligands that serve as DNA metalloinsertors has been synthesized, and both DNA mismatch binding affinities and antiproliferative activities against the human colorectal carcinoma cell lines HCT116N and HCT116O, an isogenic model system for MMR deficiency, have been determined. DNA photocleavage experiments reveal that all complexes bind to the mismatch sites with high specificities; DNA binding affinities to oligonucleotides containing single base CA and CC mismatches, obtained through photocleavage titration or competition, vary from 10^4 to 10^8 M^\u22121 for the series of complexes. Significantly, binding affinities are found to be inversely related to ancillary ligand size and directly related to differential inhibition of the HCT116 cell lines. The observed trend in binding affinity is consistent with the metalloinsertion mode where the complex binds from the minor groove with ejection of mismatched base pairs. The correlation between binding affinity and targeting of the MMR-deficient cell line suggests that rhodium metalloinsertors exert their selective biological effects on MMR-deficient cells through mismatch binding in vivo.", "doi": "10.1021/ja8081044", "pmcid": "PMC2747594", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2009-02-18", "series_number": "6", "volume": "131", "issue": "6", "pages": "2359-2366" }, { "id": "authors:4drjh-qer68", "collection": "authors", "collection_id": "4drjh-qer68", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090409-140710606", "type": "article", "title": "Recognition of abasic sites and single base bulges in DNA by a metalloinsertor", "author": [ { "family_name": "Zeglis", "given_name": "Brian M.", "clpid": "Zeglis-B-M" }, { "family_name": "Boland", "given_name": "Jennifer A.", "clpid": "Boland-J-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Abasic sites and single base bulges are thermodynamically destabilizing DNA defects that can lead to cancerous transformations if left unrepaired by the cell. Here we discuss the binding properties with abasic sites and single base bulges of Rh(bpy)_2(chrysi)^(3+), a complex previously shown to bind thermodynamically destabilized mismatch sites via metalloinsertion. Photocleavage experiments show that Rh(bpy)_2(chrysi)^(3+) selectively binds abasic sites with affinities of 1\u22124 \u00d7 10^6 M^(\u22121); specific binding is independent of unpaired base identity but is somewhat contingent on sequence context. Single base bulges are also selectively bound and cleaved, but in this case, the association constants are significantly lower (~10^5 M^(\u22121)), and the binding is dependent on both unpaired base identity and bulge sequence context. A wide variety of evidence, including strand scission asymmetry, binding enantiospecificity, and MALDI-TOF cleavage fragment analysis, suggests that Rh(bpy)_2(chrysi)^(3+) binds abasic sites, like mismatches, through insertion of the bulky chrysi ligand into the base pair stack from the minor groove side and ejection of the unpaired base. At single base bulge sites, a similar, though not identical, metalloinsertion mode is suggested. The recognition of abasic sites and single base bulges with bulky metalloinsertors holds promise for diagnostic and therapeutic applications.", "doi": "10.1021/bi801885w", "pmcid": "PMC2747346", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "2009-02-10", "series_number": "5", "volume": "48", "issue": "5", "pages": "839-849" }, { "id": "authors:7yt5n-8fb58", "collection": "authors", "collection_id": "7yt5n-8fb58", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090918-080256727", "type": "article", "title": "Common Mitochondrial DNA Mutations Generated through DNA-Mediated Charge Transport", "author": [ { "family_name": "Merino", "given_name": "Edward J.", "clpid": "Merino-E-J" }, { "family_name": "Davis", "given_name": "Molly L.", "clpid": "Davis-M-L" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Mutation sites that arise in human mitochondrial DNA as a result of oxidation by a rhodium photooxidant have been identified. HeLa cells were incubated with [Rh(phi)2bpy]Cl3 (phi is 9,10-phenanthrenequinone diimine), an intercalating photooxidant, to allow the complex to enter the cell and bind mitochondrial DNA. Photoexcitation of DNA-bound [Rh(phi)2bpy]3+ can promote the oxidation of guanine from a distance through DNA-mediated charge transport. After two rounds of photolysis and growth of cells incubated with the rhodium complex, DNA mutations in a portion of the mitochondrial genome were assessed via manual sequencing. The mutational pattern is consistent with dG to dT transversions in the repetitive guanine tracts. Significantly, the mutational pattern found overlaps oxidative damage hot spots seen previously. These mutations are found within conserved sequence block II, a critical regulatory element involved in DNA replication, and these have been identified as sites of low oxidation potential to which oxidative damage is funneled. On the basis of this mutational analysis and its correspondence to sites of long-range oxidative damage, we infer a critical role for DNA charge transport in generating these mutations and, thus, in regulating mitochondrial DNA replication under oxidative stress.", "doi": "10.1021/bi801570j", "pmcid": "PMC2668510", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "2009-02-03", "series_number": "4", "volume": "48", "issue": "4", "pages": "660-666" }, { "id": "authors:rtx91-v4b90", "collection": "authors", "collection_id": "rtx91-v4b90", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:GORbc08", "type": "article", "title": "DNA-Mediated Electrochemistry", "author": [ { "family_name": "Gorodetsky", "given_name": "Alon A.", "orcid": "0000-0002-3811-552X", "clpid": "Gorodetsky-A-A" }, { "family_name": "Buzzeo", "given_name": "Marisa C.", "clpid": "Buzzeo-M-C" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The base pair stack of DNA has been demonstrated as a medium for long-range charge transport chemistry both in solution and at DNA-modified surfaces. This chemistry is exquisitely sensitive to structural perturbations in the base pair stack as occur with lesions, single base mismatches, and protein binding. We have exploited this sensitivity for the development of reliable electrochemical assays based on DNA charge transport at self-assembled DNA monolayers. Here, we discuss the characteristic features, applications, and advantages of DNA-mediated electrochemistry.", "doi": "10.1021/bc8003149", "pmcid": "PMC2663395", "issn": "1043-1802", "publisher": "American Chemical Society", "publication": "Bioconjugate Chemistry", "publication_date": "2008-12-17", "series_number": "12", "volume": "19", "issue": "12", "pages": "2285-2296" }, { "id": "authors:84s5p-dbm29", "collection": "authors", "collection_id": "84s5p-dbm29", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:GORl08", "type": "article", "title": "Scanning Electrochemical Microscopy of DNA Monolayers Modified with Nile Blue", "author": [ { "family_name": "Gorodetsky", "given_name": "Alon A.", "orcid": "0000-0002-3811-552X", "clpid": "Gorodetsky-A-A" }, { "family_name": "Hammond", "given_name": "William J.", "clpid": "Hammond-W-J" }, { "family_name": "Hill", "given_name": "Michael G.", "clpid": "Hill-M-G" }, { "family_name": "Slowinski", "given_name": "Krzysztof", "clpid": "Slowinski-K" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Scanning electrochemical microscopy (SECM) is used to probe long-range charge transport (CT) through DNA monolayers containing the redox-active Nile Blue (NB) intercalator covalently affixed at a specific location in the DNA film. At substrate potentials negative of the formal potential of covalently attached NB, the electrocatalytic reduction of Fe(CN)63\u2212 generated at the SECM tip is observed only when NB is located at the DNA/solution interface; for DNA films containing NB in close proximity to the DNA/electrode interface, the electrocatalytic effect is absent. This behavior is consistent with both rapid DNA-mediated CT between the NB intercalator and the gold electrode as well as a rate-limiting electron transfer between NB and the solution phase Fe(CN)63\u2212. The DNA-mediated nature of the catalytic cycle is confirmed through sequence-specific and localized detection of attomoles of TATA-binding protein, a transcription factor that severely distorts DNA upon binding. Importantly, the strategy outlined here is general and allows for the local investigation of the surface characteristics of DNA monolayers both in the absence and in the presence of DNA binding proteins. These experiments highlight the utility of DNA-modified electrodes as versatile platforms for SECM detection schemes that take advantage of CT mediated by the DNA base pair stack.", "doi": "10.1021/la8029243", "pmcid": "PMC2668266", "issn": "0743-7463", "publisher": "American Chemical Society", "publication": "Langmuir", "publication_date": "2008-12-16", "series_number": "24", "volume": "24", "issue": "24", "pages": "14282-14288" }, { "id": "authors:vh6db-4wp83", "collection": "authors", "collection_id": "vh6db-4wp83", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:BUZbc08", "type": "article", "title": "Redmond Red as a Redox Probe for the DNA-Mediated Detection of Abasic Sites", "author": [ { "family_name": "Buzzeo", "given_name": "Marisa C.", "clpid": "Buzzeo-M-C" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Redmond Red, a fluoropore containing a redox-active phenoxazine core, has been explored as a new electrochemical probe for the detection of abasic sites in double-stranded DNA. The electrochemical behavior of Redmond Red-modified DNA at gold surfaces exhibits stable, quasi-reversible voltammetry with a midpoint potential centered around \u221250 mV versus NHE. Importantly, with Redmond Red positioned opposite an abasic site within the DNA duplex, the electrochemical response is significantly enhanced compared to Redmond Red positioned across from a base. Redmond Red, reporting only if well-stacked in the duplex, represents a sensitive probe to detect abasic sites electrochemically in a DNA-mediated reaction.", "doi": "10.1021/bc800339y", "pmcid": "PMC2747513", "issn": "1043-1802", "publisher": "American Chemical Society", "publication": "Bioconjugate Chemistry", "publication_date": "2008-11-19", "series_number": "11", "volume": "19", "issue": "11", "pages": "2110-2112" }, { "id": "authors:9f3jq-7bh30", "collection": "authors", "collection_id": "9f3jq-7bh30", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090504-093543546", "type": "article", "title": "Back-electron transfer suppresses the periodic length dependence of DNA-mediated charge transport across adenine tracts", "author": [ { "family_name": "Genereux", "given_name": "Joseph C.", "orcid": "0000-0002-5093-7710", "clpid": "Genereux-J-C" }, { "family_name": "Augustyn", "given_name": "Katherine E.", "clpid": "Augustyn-K-E" }, { "family_name": "Davis", "given_name": "Molly L.", "clpid": "Davis-M-L" }, { "family_name": "Shao", "given_name": "Fangwei", "orcid": "0000-0003-2007-3920", "clpid": "Shao-Fangwei" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "DNA-mediated charge transport (CT) is exquisitely sensitive to the integrity of the bridging \u03c0-stack and is characterized by a shallow distance dependence. These properties are obscured by poor coupling between the donor/acceptor pair and the DNA bridge, or by convolution with other processes. Previously, we found a surprising periodic length dependence for the rate of DNA-mediated CT across adenine tracts monitored by 2-aminopurine fluorescence. Here we report a similar periodicity by monitoring N2-cyclopropylguanosine decomposition by rhodium and anthraquinone photooxidants. Furthermore, we find that this periodicity is attenuated by consequent back-electron transfer (BET), as observed by direct comparison between sequences that allow and suppress BET. Thus, the periodicity can be controlled by engineering the extent of BET across the bridge. The periodic length dependence is not consistent with a periodicity predicted by molecular wire theory but is consistent with a model where multiples of four to five base pairs form an ideal CT-active length of a bridging adenine domain.", "doi": "10.1021/ja8052738", "pmcid": "PMC2663386", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2008-11-12", "series_number": "45", "volume": "130", "issue": "45", "pages": "15150-15156" }, { "id": "authors:y0j7j-stk95", "collection": "authors", "collection_id": "y0j7j-stk95", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:PUCb08", "type": "article", "title": "Mechanism of cellular uptake of a ruthenium polypyridyl complex", "author": [ { "family_name": "Puckett", "given_name": "Cindy A.", "clpid": "Puckett-C-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Transition metal complexes provide a promising avenue for the design of therapeutic and diagnostic agents, but the limited understanding of their cellular uptake is a roadblock to their effective application. Here, we examine the mechanism of cellular entry of a luminescent ruthenium(II) polypyridyl complex, Ru(DIP)2dppz2+ (where DIP = 4,7-diphenyl-1,10-phenanthroline and dppz = dipyridophenazine), into HeLa cells, with the extent of uptake measured by flow cytometry. No diminution of cellular uptake is observed under metabolic inhibition with deoxyglucose and oligomycin, indicating an energy-independent mode of entry. The presence of organic cation transporter inhibitors also does not significantly alter uptake. However, the cellular internalization of Ru(DIP)2dppz2+ is sensitive to the membrane potential. Uptake decreases when cells are depolarized with high potassium buffer and increases when cells are hyperpolarized with valinomycin. These results support passive diffusion of Ru(DIP)2dppz2+ into the cell.", "doi": "10.1021/bi800856t", "pmcid": "PMC2747514", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "2008-11-11", "series_number": "45", "volume": "47", "issue": "45", "pages": "11711-11716" }, { "id": "authors:10nfz-wvr87", "collection": "authors", "collection_id": "10nfz-wvr87", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:ELIac08", "type": "article", "title": "Ping-Pong Electron Transfer through DNA", "author": [ { "family_name": "Elias", "given_name": "Benjamin", "orcid": "0000-0001-5037-3313", "clpid": "Elias-B" }, { "family_name": "Genereux", "given_name": "Joseph C.", "orcid": "0000-0002-5093-7710", "clpid": "Genereux-J-C" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Herein we describe a novel Ir system that is able to promote the reduction of pyrimidine bases from a distance without the presence of an external quencher. Instead, DNA-mediated ET is triggered by DNA-mediated HT. Thus, photoactivation of these Ir assemblies results in both a forward and a reverse pattern for charge migration, which we term ping-pong electron transfer through DNA (Scheme 1).", "doi": "10.1002/anie.200803556", "pmcid": "PMC2748353", "issn": "1433-7851", "publisher": "Wiley", "publication": "Angewandte Chemie International Edition", "publication_date": "2008-11-10", "series_number": "47", "volume": "47", "issue": "47", "pages": "9067-9070" }, { "id": "authors:8bdds-19m60", "collection": "authors", "collection_id": "8bdds-19m60", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160229-073032218", "type": "article", "title": "Binding of Ru(bpy)_2(eilatin)^(2+)to Matched and Mismatched DNA", "author": [ { "family_name": "Zeglis", "given_name": "Brian M.", "clpid": "Zeglis-B-M" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The DNA-binding properties of Ru(bpy)_2(eilatin)^(2+) have been investigated to determine if the sterically expansive eilatin ligand confers specificity for destabilized single-base mismatches in DNA. Competitive DNA photocleavage experiments employing a sequence-neutral metallointercalator, Rh(bpy)_2(phi)^(3+)(phi = 9,10-phenanthrenequinonediimine), and a mismatch-specific metalloinsertor, Rh(bpy)_2(chrysi)^(3+) (chrysi = chrysene-5,6-quinonediimine), reveal that the eilatin complex binds to a CC mismatched site with an apparent binding constant of 2.2(2) \u00d7 10^6 M^(\u22121). Nonetheless, the selectivity in binding mismatched DNA is not high: competitive titrations with Rh(bpy)_2(phi)^(3+) show that the complex binds also to well-matched B-form sites. Thus, Ru(bpy)_2(eilatin)^(2+), despite containing the extremely expansive eilatin ligand, displays lower selectivity for the mismatch than does Rh(bpy)_2(chrysi)^(3+), a metalloinsertor containing the smaller, though still bulky, chrysene-5,6-quinonediimine ligand. In summary, the size and shape of the eilatin ligand allow stacking with both well-matched and mismatched DNA.", "doi": "10.1021/ic8006537", "pmcid": "PMC2747595", "issn": "0020-1669", "publisher": "American Chemical Society", "publication": "Inorganic Chemistry", "publication_date": "2008-07-21", "series_number": "14", "volume": "47", "issue": "14", "pages": "6452-6457" }, { "id": "authors:kksky-nj380", "collection": "authors", "collection_id": "kksky-nj380", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160226-135927342", "type": "article", "title": "Targeting Abasic Sites and Single Base Bulges in DNA with Metalloinsertors", "author": [ { "family_name": "Zeglis", "given_name": "Brian M.", "clpid": "Zeglis-B-M" }, { "family_name": "Boland", "given_name": "Jennifer A.", "clpid": "Boland-J-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The site-specific recognition of abasic sites and single base bulges in duplex DNA by sterically expansive rhodium metalloinsertors has been investigated. Through DNA photocleavage experiments, Rh(bpy)_2(chrysi)^(3+) is shown to bind both abasic sites and single base bulges site-specifically and, upon irradiation, to cleave the backbone of the defect-containing DNA. Photocleavage titrations reveal that the metal complex binds DNA containing an abasic site with high affinity (2.6(5) \u00d7 10^6 M^(\u22121)), comparably to the metalloinsertor and a CC mismatch. The complex binds single base bulge sites with lower affinity (\u223c10^5 M^(\u22121)). Analysis of cleavage products and the correlation of affinities with helix destabilization suggest that Rh(bpy)_2(chrysi)^(3+) binds both lesions via metalloinsertion, as observed for Rh binding at mismatched sites, a binding mode in which the mismatched or unpaired bases are extruded from the helix and replaced in the base stack by the sterically expansive ligand of the metalloinsertor.", "doi": "10.1021/ja801479y", "pmcid": "PMC2759749", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2008-06-18", "series_number": "24", "volume": "130", "issue": "24", "pages": "7530-7531" }, { "id": "authors:r6zp6-sap87", "collection": "authors", "collection_id": "r6zp6-sap87", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160127-111127271", "type": "article", "title": "Biological contexts for DNA charge transport chemistry", "author": [ { "family_name": "Merino", "given_name": "Edward J.", "clpid": "Merino-E-J" }, { "family_name": "Boal", "given_name": "Amie K.", "orcid": "0000-0002-1234-8472", "clpid": "Boal-A-K" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Many experiments have now shown that double helical DNA can serve as a conduit for efficient charge transport (CT) reactions over long distances in vitro. These results prompt the consideration of biological roles for DNA-mediated CT. DNA CT has been demonstrated to occur in biologically relevant environments such as within the mitochondria and nuclei of HeLa cells as well as in isolated nucleosomes. In mitochondria, DNA damage that results from CT is funneled to a crucial regulatory element. Thus, DNA CT provides a strategy to funnel damage to particular sites in the genome. DNA CT might also be important in long-range signaling to DNA-bound proteins. Both DNA repair proteins, containing Fe-S clusters, and the transcription factor, p53, which is regulated through thiol-disulfide switches, can be oxidized from a distance through DNA-mediated CT. These observations highlight a means through which oxidative stress may be chemically signaled in the genome over long distances through CT from guanine radicals to DNA-bound proteins. Moreover, DNA-mediated CT may also play a role in signaling among DNA-binding proteins, as has been proposed as a mechanism for how DNA repair glycosylases more efficiently detect lesions inside the cell.", "doi": "10.1016/j.cbpa.2008.01.046", "pmcid": "PMC3227530", "issn": "1367-5931", "publisher": "Elsevier", "publication": "Current Opinion in Chemical Biology", "publication_date": "2008-04", "series_number": "2", "volume": "12", "issue": "2", "pages": "229-237" }, { "id": "authors:jgjr9-2b412", "collection": "authors", "collection_id": "jgjr9-2b412", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160226-135927612", "type": "article", "title": "Electrical Detection of TATA Binding Protein at DNA-Modified Microelectrodes", "author": [ { "family_name": "Gorodetsky", "given_name": "Alon A.", "orcid": "0000-0002-3811-552X", "clpid": "Gorodetsky-A-A" }, { "family_name": "Ebrahim", "given_name": "Ali", "clpid": "Ebrahim-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "A simple method for the electrochemical detection of TATA-binding protein is demonstrated at DNA-modified microelectrodes. The assay is general and based on the interruption of DNA-mediated charge transport to Nile Blue, a redox-active probe covalently attached to the DNA base pair stack. Nanomolar quantities of TATA binding protein can be detected on the microelectrodes even in the presence of micromolar amounts of bovine serum albumin, EndonucleaseIII, or Bam HI methyltransferase. The scheme outlined provides a basis for the sensitive electrical detection of numerous proteins on a single DNA chip.", "doi": "10.1021/ja7106756", "pmcid": "PMC2747583", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2008-03-12", "series_number": "10", "volume": "130", "issue": "10", "pages": "2924-2925" }, { "id": "authors:fn2h6-cm306", "collection": "authors", "collection_id": "fn2h6-cm306", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:GORpnas08", "type": "article", "title": "DNA binding shifts the redox potential of the transcription factor SoxR", "author": [ { "family_name": "Gorodetsky", "given_name": "Alon A.", "orcid": "0000-0002-3811-552X", "clpid": "Gorodetsky-A-A" }, { "family_name": "Dietrich", "given_name": "Lars E. P.", "clpid": "Dietrich-L-E-P" }, { "family_name": "Lee", "given_name": "Paul E.", "clpid": "Lee-P-E" }, { "family_name": "Demple", "given_name": "Bruce", "clpid": "Demple-B" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Electrochemistry measurements on DNA-modified electrodes are used to probe the effects of binding to DNA on the redox potential of SoxR, a transcription factor that contains a [2Fe-2S] cluster and is activated through oxidation. A DNA-bound potential of +200 mV versus NHE (normal hydrogen electrode) is found for SoxR isolated from Escherichia coli and Pseudomonas aeruginosa. This potential value corresponds to a dramatic shift of +490 mV versus values found in the absence of DNA. Using Redmond red as a covalently bound redox reporter affixed above the SoxR binding site, we also see, associated with SoxR binding, an attenuation in the Redmond red signal compared with that for Redmond red attached below the SoxR binding site. This observation is consistent with a SoxR-binding-induced structural distortion in the DNA base stack that inhibits DNA-mediated charge transport to the Redmond red probe. The dramatic shift in potential for DNA-bound SoxR compared with the free form is thus reconciled based on a high-energy conformational change in the SoxR\u2013DNA complex. The substantial positive shift in potential for DNA-bound SoxR furthermore indicates that, in the reducing intracellular environment, DNA-bound SoxR is primarily in the reduced form; the activation of DNA-bound SoxR would then be limited to strong oxidants, making SoxR an effective sensor for oxidative stress. These results more generally underscore the importance of using DNA electrochemistry to determine DNA-bound potentials for redox-sensitive transcription factors because such binding can dramatically affect this key protein property.", "doi": "10.1073/pnas.0800093105", "pmcid": "PMC2268809", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2008-03-11", "series_number": "10", "volume": "105", "issue": "10", "pages": "3684-3689" }, { "id": "authors:bv1xz-fbn53", "collection": "authors", "collection_id": "bv1xz-fbn53", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160210-161130692", "type": "article", "title": "Conductivity of a single DNA duplex bridging a carbon nanotube gap", "author": [ { "family_name": "Guo", "given_name": "Xuefeng", "clpid": "Guo-Xuefeng" }, { "family_name": "Gorodetsky", "given_name": "Alon A.", "orcid": "0000-0002-3811-552X", "clpid": "Gorodetsky-A-A" }, { "family_name": "Hone", "given_name": "James", "orcid": "0000-0002-8084-3301", "clpid": "Hone-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Nuckolls", "given_name": "Colin", "clpid": "Nuckolls-C" } ], "abstract": "We describe a general method to integrate DNA strands between single-walled carbon nanotube electrodes and to measure their electrical properties. We modified DNA sequences with amines on either the 5' terminus or both the 3' and 5' termini and coupled these to the single-walled carbon nanotube electrodes through amide linkages, enabling the electrical properties of complementary and mismatched strands to be measured. Well-matched duplex DNA in the gap between the electrodes exhibits a resistance on the order of 1 M\u03a9. A single GT or CA mismatch in a DNA 15-mer increases the resistance of the duplex approx300-fold relative to a well-matched one. Certain DNA sequences oriented within this gap are substrates for Alu I, a blunt end restriction enzyme. This enzyme cuts the DNA and eliminates the conductive path, supporting the supposition that the DNA is in its native conformation when bridging the ends of the single-walled carbon nanotubes.", "doi": "10.1038/nnano.2008.4", "pmcid": "PMC2747584", "issn": "1748-3387", "publisher": "Nature Publishing Group", "publication": "Nature Nanotechnology", "publication_date": "2008-03", "series_number": "3", "volume": "3", "issue": "3", "pages": "163-167" }, { "id": "authors:bbb0k-bkx69", "collection": "authors", "collection_id": "bbb0k-bkx69", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160229-120833212", "type": "article", "title": "DNA Oxidation by Charge Transport in Mitochondria", "author": [ { "family_name": "Merino", "given_name": "Edward J.", "clpid": "Merino-E-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Sites of oxidative DNA damage in functioning mitochondria have been identified using a rhodium photooxidant as a probe. Here we show that a primer extension reaction can be used to monitor oxidative DNA damage directly in functioning mitochondria after photoreaction with a rhodium intercalator that penetrates the intact mitochondrial membrane. The complex [Rh(phi)_2bpy]Cl_3 (phi = 9,10-phenanthrenequinonediimine) binds to DNA within the mitochondria and, upon irradiation, initiates DNA oxidation reactions. Significantly, piperidine treatment of the mitochondria leads to protein-dependent primer extension stops spaced every \u223c20 base pairs. Hence, within the mitochondria, the DNA is well covered and packaged by proteins. Photolysis of the mitochondria containing [Rh(phi)_2bpy]^(3+) leads to oxidative DNA damage at positions 260 and 298; both are mutational hot spots associated with cancers. The latter position is the 5'-nucleotide of conserved sequence block II and is critical to replication of the mitochondrial DNA. The oxidative damage is found to be DNA-mediated, utilizing a charge transport mechanism, as the Rh binding sites are spatially separated from the oxidation-prone regions. This long-range DNA-mediated oxidation occurs despite protein association. Indeed, the oxidation of the mitochondrial DNA leads not only to specific oxidative lesions, but also to a corresponding change in the protein-induced stops in the primer extension. Mitochondrial DNA damage promotes specific changes in protein\u2212DNA contacts and is thus sensed by the mitochondrial protein machinery.", "doi": "10.1021/bi701775s", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "2008-02-12", "series_number": "6", "volume": "47", "issue": "6", "pages": "1511-1517" }, { "id": "authors:rr44x-ta292", "collection": "authors", "collection_id": "rr44x-ta292", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160226-135926234", "type": "article", "title": "Charge Migration along the DNA Duplex: Hole versus Electron Transport", "author": [ { "family_name": "Elias", "given_name": "Benjamin", "orcid": "0000-0001-5037-3313", "clpid": "Elias-B" }, { "family_name": "Shao", "given_name": "Fangwei", "orcid": "0000-0003-2007-3920", "clpid": "Shao-Fangwei" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Cyclometalated Ir(III) complexes tethered to 18-mer oligonucleotides through a functionalized dipyridophenazine ligand have been used to study the distance dependence profile of hole and electron transport along DNA. These DNA assemblies allow a direct comparison of hole and electron transport with a single donor coupled into the base stack. Interestingly, both processes, monitored with modified bases as hole or electron kinetic traps incorporated in the strands, appear to have similarly shallow dependences in their reactions with distance. As with hole transport, perturbations to the base stack also attenuate electron transport.", "doi": "10.1021/ja710358p", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2008-01-30", "series_number": "4", "volume": "130", "issue": "4", "pages": "1152-1153" }, { "id": "authors:q321x-kfb91", "collection": "authors", "collection_id": "q321x-kfb91", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:ZEGcc07", "type": "article", "title": "Metallo-intercalators and metallo-insertors", "author": [ { "family_name": "Zeglis", "given_name": "Brian M.", "clpid": "Zeglis-B-M" }, { "family_name": "Pierre", "given_name": "Valerie C.", "clpid": "Pierre-V-C" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Since the elucidation of the structure of double helical DNA, the construction of small molecules that recognize and react at specific DNA sites has been an area of considerable interest. In particular, the study of transition metal complexes that bind DNA with specificity has been a burgeoning field. This growth has been due in large part to the useful properties of metal complexes, which possess a wide array of photophysical attributes and allow for the modular assembly of an ensemble of recognition elements. Here we review recent experiments in our laboratory aimed at the design and study of octahedral metal complexes that bind DNA non-covalently and target reactions to specific sites. Emphasis is placed both on the variety of methods employed to confer site-specificity and upon the many applications for these complexes. Particular attention is given to the family of complexes recently designed that target single base mismatches in duplex DNA through metallo-insertion.", "doi": "10.1039/b710949k", "pmcid": "PMC2790054", "issn": "1359-7345", "publisher": "Royal Society of Chemistry", "publication": "Chemical Communications", "publication_date": "2007-11-28", "series_number": "44", "volume": "2007", "issue": "44", "pages": "4565-4579" }, { "id": "authors:xrvt7-fyk77", "collection": "authors", "collection_id": "xrvt7-fyk77", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160226-135927080", "type": "article", "title": "Long-Range Electron and Hole Transport through DNA with Tethered Cyclometalated Iridium(III) Complexes", "author": [ { "family_name": "Shao", "given_name": "Fangwei", "orcid": "0000-0003-2007-3920", "clpid": "Shao-Fangwei" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "A cyclometalated complex of Ir(III) is covalently tethered to DNA oligonucleotides and serves as both a photooxidant and photoreductant in the study of DNA-mediated hole transport (HT) and electron transport (ET). Spectroscopic and melting temperature studies support intercalation of the tethered complex into the DNA duplex through the functionalized dppz ligand. Using these tethered assemblies, ET and HT is initiated in DNA by the same photoredox probe. Cyclopropylamine substituted bases, N_4-cyclopropylcytosine (^(CP)C) and N_2-cyclopropylguanine (^(CP)G) are used as kinetically fast electron and hole traps to probe the resulting electron migration processes after direct irradiation of the tethered Ir assembly. Oxidation of ^(CP)G and ^(CP)C is promoted efficiently by HT from photoexcited Ir(III) when the modified bases are positioned in the purine strands of the A-tract. In contrast, when CPC is embedded in a pyrimidine tract, ET to yield reductive decomposition is observed. Thus, the Ir(III)-tethered DNA assembly containing cyclopropyl-modified bases provides a unique model system to explore the two DNA-mediated electron migration processes using the same photoredox probe and the same DNA bridge.", "doi": "10.1021/ja0752437", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2007-11-28", "series_number": "47", "volume": "129", "issue": "47", "pages": "14733-14738" }, { "id": "authors:vtc24-mrn44", "collection": "authors", "collection_id": "vtc24-mrn44", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:AUGpnas07", "type": "article", "title": "A role for DNA-mediated charge transport in regulating p53: Oxidation of the DNA-bound protein from a distance", "author": [ { "family_name": "Augustyn", "given_name": "Katherine E.", "clpid": "Augustyn-K-E" }, { "family_name": "Merino", "given_name": "Edward J.", "clpid": "Merino-E-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Charge transport (CT) through the DNA base pairs provides a means to promote redox reactions at a remote site and potentially to effect signaling between molecules bound to DNA. Here we describe the oxidation of a cell-cycle regulatory protein, p53, from a distance through DNA-mediated CT. A consensus p53 binding site as well as three DNA promoters regulated by p53 were synthesized containing a tethered DNA photooxidant, anthraquinone. Photoinduced oxidation of the protein occurs from a distance; introduction of an intervening CA mismatch, which inhibits DNA-mediated CT, prevents oxidation of p53. DNA-mediated oxidation is shown to promote dissociation of p53 from only some promoters, and this sequence-selectivity in oxidative dissociation correlates with the biological regulation of p53. Under severe oxidative stress, effected here through oxidation at long range, p53 dissociates from a promoter that activates DNA repair as well as the promoter for the negative regulator of p53, Mdm2, but not from a promoter activating cell-cycle arrest. Mass spectrometry results are consistent with disulfide bond formation in p53 upon DNA-mediated oxidation. Furthermore, DNA-bound p53 oxidation is shown in vivo by up-regulation of p53 and subsequent irradiation in the presence of a rhodium photooxidant to give a new p53 adduct that can be reversed with thiol treatment. This DNA-mediated oxidation of p53 parallels that seen by treating cells with hydrogen peroxide. These results indicate a unique mechanism using DNA-mediated CT chemistry by which p53 activity on different promoters may be controlled globally under conditions of oxidative stress.", "doi": "10.1073/pnas.0709326104", "pmcid": "PMC2141881", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2007-11-27", "series_number": "48", "volume": "104", "issue": "48", "pages": "18907-18912" }, { "id": "authors:261na-a1v75", "collection": "authors", "collection_id": "261na-a1v75", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160229-073228331", "type": "article", "title": "Synthesis and Characterization of Iridium(III) Cyclometalated Complexes with Oligonucleotides: Insights into Redox Reactions with DNA", "author": [ { "family_name": "Shao", "given_name": "Fangwei", "orcid": "0000-0003-2007-3920", "clpid": "Shao-Fangwei" }, { "family_name": "Elias", "given_name": "Benjamin", "orcid": "0000-0001-5037-3313", "clpid": "Elias-B" }, { "family_name": "Lu", "given_name": "Wei", "clpid": "Lu-Wei" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Heteroleptic cyclometalated complexes of Ir(III) containing the dipyridophenazine ligand are synthesized through the direct introduction of a functionalized dipyridophenazine ligand onto a bis(dichloro)-bridged Ir(III) precusor and characterized by ^1H NMR, mass spectrometry, as well as spectroscopic and electrochemical properties. The excited state of the Ir(III) complexes have sufficient driving force to oxidize purines and to reduce pyrimidine nucleobases. Luminescence and EPR measurements of the Ir(III) complex with an unmodified dppz bound to DNA show the formation of a guanine radical upon irradiation, resulting from an oxidative photoinduced electron-transfer process. Evidence is also obtained indirectly for reductive photoinduced electron transfer from the excited complex to the thymine base in DNA. We have also utilized cyclopropylamine-substituted nucleosides as ultrafast kinetic traps to report transient charge occupancy in oligonucleotides when DNA is irradiated in the presence of noncovalently bound complexes. These experiments establish that the derivatized Ir(III) complexes, with photoactivation, can trigger the oxidation of guanine and the reduction of cytosine.", "doi": "10.1021/ic7014012", "issn": "0020-1669", "publisher": "American Chemical Society", "publication": "Inorganic Chemistry", "publication_date": "2007-11-26", "series_number": "24", "volume": "46", "issue": "24", "pages": "10187-10199" }, { "id": "authors:fxn65-spp27", "collection": "authors", "collection_id": "fxn65-spp27", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160302-071129473", "type": "article", "title": "DNA Strand Cleavage near a CC Mismatch Directed by a Metalloinsertor", "author": [ { "family_name": "Lim", "given_name": "Mi Hee", "clpid": "Lim-Mi-Hee" }, { "family_name": "Lau", "given_name": "Irvin H.", "clpid": "Lau-Irvin-H" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Reagents for recognition and efficient cleavage of mismatched DNA without photoactivation were designed. They contain a combination of a mismatch-directing metalloinsertor, [Rh(bpy)_2(chrysi)]^(3+) (bpy = 2,2'-bipyridyl, chrysi = 5,6-chrysenequinone diimine), and an oxidative cleavage functionality, [Cu(phen)_2]^+ (Cu). Both unconjugated (Rh+Cu) and conjugated (Rh\u2212Cu) frameworks of the Rh insertor and Cu were prepared. Compared to Cu, both constructs Rh+Cu and Rh\u2212Cu exhibit efficient site-specific DNA scission only with mismatched DNA, confirmed by experiments with ^(32)P-labeled oligonucleotides. Furthermore, these studies indicate that DNA cleavage occurs near the mismatch in the minor groove and on both strands. Interestingly, the order of reactivity of the three systems with a CC mismatch is Rh+Cu > Rh\u2212Cu \u226b Cu. Rh binding appears to direct Cu reactivity with or without tethering. These results illustrate advantages and disadvantages in bifunctional conjugation.", "doi": "10.1021/ic701598k", "pmcid": "PMC2747586", "issn": "0020-1669", "publisher": "American Chemical Society", "publication": "Inorganic Chemistry", "publication_date": "2007-11-12", "series_number": "23", "volume": "46", "issue": "23", "pages": "9528-9530" }, { "id": "authors:w6bmx-ymc25", "collection": "authors", "collection_id": "w6bmx-ymc25", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160127-111126513", "type": "article", "title": "DNA repair glycosylases with a [4Fe\u20134S] cluster: A redox cofactor for DNA-mediated charge transport?", "author": [ { "family_name": "Boal", "given_name": "Amie K.", "orcid": "0000-0002-1234-8472", "clpid": "Boal-A-K" }, { "family_name": "Yavin", "given_name": "Eylon", "clpid": "Yavin-E" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The [4Fe\u20134S] cluster is ubiquitous to a class of base excision repair enzymes in organisms ranging from bacteria to man and was first considered as a structural element, owing to its redox stability under physiological conditions. When studied bound to DNA, two of these repair proteins (MutY and Endonuclease III from Escherichia coli) display DNA-dependent reversible electron transfer with characteristics typical of high potential iron proteins. These results have inspired a reexamination of the role of the [4Fe\u20134S] cluster in this class of enzymes. Might the [4Fe\u20134S] cluster be used as a redox cofactor to search for damaged sites using DNA-mediated charge transport, a process well known to be highly sensitive to lesions and mismatched bases? Described here are experiments demonstrating the utility of DNA-mediated charge transport in characterizing these DNA-binding metalloproteins, as well as efforts to elucidate this new function for DNA as an electronic signaling medium among the proteins.", "doi": "10.1016/j.jinorgbio.2007.05.001", "pmcid": "PMC2094209", "issn": "0162-0134", "publisher": "Elsevier", "publication": "Journal of Inorganic Biochemistry", "publication_date": "2007-11", "series_number": "11-12", "volume": "101", "issue": "11-12", "pages": "1913-1921" }, { "id": "authors:q5f8r-mdz30", "collection": "authors", "collection_id": "q5f8r-mdz30", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160302-071129129", "type": "article", "title": "Charge Separation in a Ruthenium-Quencher Conjugate Bound to DNA", "author": [ { "family_name": "Augustyn", "given_name": "Katherine E.", "clpid": "Augustyn-K-E" }, { "family_name": "Stemp", "given_name": "E. D. A.", "orcid": "0000-0003-2098-4214", "clpid": "Stemp-E-D-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "A novel tris heteroleptic dipyridophenazine complex of ruthenium(II), [{Ru(phen)(dppz)(bpy'-his)}{Ru(NH_3)_5}]^(5+), containing a covalently tethered ruthenium pentammine quencher coordinated through a bridging histidine has been synthesized and characterized spectroscopically and biochemically in a DNA environment and in organic solvent. Steady-state and time-resolved luminescence measurements indicate that the tethered Ru complex is quenched relative to the parent complexes [Ru(phen)(dppz)(bpy')]^(2+) and [Ru(phen)(dppz)(bpy'-his)]^(2+) in DNA and acetonitrile, consistent with intramolecular photoinduced electron transfer. Intercalated into guanine-containing DNA, [{Ru(phen)(dppz)(bpy'-his)}{Ru(NH_3)_5}]^(5+), upon excitation and intramolecular quenching, is capable of injecting charge into the duplex based upon the EPR detection of guanine radicals. DNA-mediated charge transport is also indicated using a kinetically fast cyclopropylamine-substituted base as an electron hole trap. Guanine damage is not observed, however, in measurements using the guanine radical as the kinetically slower hole trap, indicating that back electron-transfer reactions are competitive with guanine oxidation. Moreover, transient absorption measurements reveal a novel photophysical reaction pathway for [{Ru(phen)(dppz)(bpy'-his)}{Ru(NH_3)_5}]^(5+) in the presence of DNA that is competitive with the intramolecular flash-quench process. These results illustrate the remarkably rich redox chemistry that can occur within a bimolecular ruthenium complex intercalated in duplex DNA.", "doi": "10.1021/ic701276t", "issn": "0020-1669", "publisher": "American Chemical Society", "publication": "Inorganic Chemistry", "publication_date": "2007-10-29", "series_number": "22", "volume": "46", "issue": "22", "pages": "9337-9350" }, { "id": "authors:n67gy-df741", "collection": "authors", "collection_id": "n67gy-df741", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160226-135926826", "type": "article", "title": "Insertion of a Bulky Rhodium Complex into a DNA Cytosine\u2212Cytosine Mismatch: An NMR Solution Study", "author": [ { "family_name": "Cordier", "given_name": "Christine", "clpid": "Cordier-C" }, { "family_name": "Pierre", "given_name": "Val\u00e9rie C.", "clpid": "Pierre-V-C" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The bulky octahedral complex Rh(bpy)_2chrysi^(3+) (chrysi = 5,6-chrysenequinonediimine) binds single-base mismatches in a DNA duplex with micromolar binding affinities and high selectivity. Here we present an NMR solution study to characterize the binding mode of this bulky metal complex with its target CC mismatch in the oligonucleotide duplex (5'-CGGACTCCG-3')_2. Both NOESY and COSY studies indicate that Rh(bpy)_2chrysi^(3+) inserts deeply in the DNA at the mismatch site via the minor groove and with ejection of both destabilized cytosines into the opposite major groove. The insertion only minimally distorts the conformation of the oligonucleotide local to the binding site. Both flanking, well-matched base pairs remain tightly hydrogen-bonded to each other, and 2D DQF-COSY experiments indicate that all sugars maintain their original C_2'-endo conformation. Remarkably, ^(31)P NMR reveals that opening of the phosphate angles from a B_I to a B_(II) conformation is sufficient for insertion of the bulky metal complex. These results corroborate those obtained crystallographically and, importantly, provide structural evidence for this specific insertion mode in solution.", "doi": "10.1021/ja0739436", "pmcid": "PMC2748819", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2007-10-10", "series_number": "40", "volume": "129", "issue": "40", "pages": "12287-12295" }, { "id": "authors:kmcn5-m6810", "collection": "authors", "collection_id": "kmcn5-m6810", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160229-103205895", "type": "article", "title": "Coupling into the Base Pair Stack Is Necessary for DNA-Mediated Electrochemistry", "author": [ { "family_name": "Gorodetsky", "given_name": "Alon A.", "orcid": "0000-0002-3811-552X", "clpid": "Gorodetsky-A-A" }, { "family_name": "Green", "given_name": "Omar", "clpid": "Green-O" }, { "family_name": "Yavin", "given_name": "Eylon", "clpid": "Yavin-E" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The electrochemistry of DNA films modified with different redox probes linked to DNA through saturated and conjugated tethers was investigated. Experiments feature two redox probes bound to DNA on two surfaces:\u2009 anthraquinone (AQ)-modified uridines incorporated into thiolated DNA on gold (Au) and 2,2,6,6-tetramethylpiperidine 1-oxyl (TEMPO)-modified uridines in pyrene-labeled DNA on highly oriented pyrolytic graphite (HOPG). The electrochemistry of these labels when incorporated into DNA has been examined in DNA films containing both well matched and mismatched DNA. DNA-mediated electrochemistry is found to be effective for the TEMPO probe linked with an acetylene linker but not for a saturated TEMPO connected through an ethylenediamine linker. For the AQ probe, DNA-mediated electrochemistry is found with an acetylene linker to uridine but not with an alkyl chain to the 5' terminus of the oligonucleotide. Large electrochemical signals and effective discrimination of intervening base mismatches are achieved for the probes connected through the acetylene linkages, while probes connected through saturated linkages exhibit small electrochemical signals associated only with direct surface to probe charge transfer and poor mismatch discrimination. Thus DNA electrochemistry with these probes is dramatically influenced by the chemical nature of their linkage to DNA. These results highlight the importance of effective coupling into the \u03c0-stack for long-range DNA-mediated electrochemistry.", "doi": "10.1021/bc0700483", "issn": "1043-1802", "publisher": "American Chemical Society", "publication": "Bioconjugate Chemistry", "publication_date": "2007-09", "series_number": "5", "volume": "18", "issue": "5", "pages": "1434-1441" }, { "id": "authors:w4tgb-m6r13", "collection": "authors", "collection_id": "w4tgb-m6r13", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160210-145408316", "type": "article", "title": "Distance-Independent DNA Charge Transport across an Adenine Tract", "author": [ { "family_name": "Augustyn", "given_name": "Katherine E.", "clpid": "Augustyn-K-E" }, { "family_name": "Genereux", "given_name": "Joseph C.", "orcid": "0000-0002-5093-7710", "clpid": "Genereux-J-C" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Charging along: DNA-mediated charge transport across adenine tracts is monitored by using a probe interior to the bridge (N^6-cyclopropyladenine (^(CP)A), shown in red). This trap was incorporated serially across the bridge and could be oxidized by a distal rhodium photooxidant without significant attenuation in yield over a distance of 5\u2005nm. These results are consistent with complete delocalization of charge across the DNA bridge.", "doi": "10.1002/anie.200701522", "issn": "1433-7851", "publisher": "Wiley", "publication": "Angewandte Chemie International Edition", "publication_date": "2007-07-23", "series_number": "30", "volume": "46", "issue": "30", "pages": "5731-5733" }, { "id": "authors:fyncs-e3a80", "collection": "authors", "collection_id": "fyncs-e3a80", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160226-135926560", "type": "article", "title": "Inorganic\u2212Organic Hybrid Luminescent Binary Probe for DNA Detection Based on Spin-Forbidden Resonance Energy Transfer", "author": [ { "family_name": "Mart\u00ed", "given_name": "Angel A.", "clpid": "Mart\u00ed-A-A" }, { "family_name": "Puckett", "given_name": "Cindy A.", "clpid": "Puckett-C-A" }, { "family_name": "Dyer", "given_name": "Joanne", "clpid": "Dyer-J" }, { "family_name": "Stevens", "given_name": "Nathan", "clpid": "Stevens-N" }, { "family_name": "Jockusch", "given_name": "Steffen", "clpid": "Jockusch-S" }, { "family_name": "Ju", "given_name": "Jingyue", "clpid": "Ju-Jingyue" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Turro", "given_name": "Nicholas J.", "clpid": "Turro-N-J" } ], "abstract": "We describe the design of new fluorescent binary probe sensors for DNA detection based on spin-forbidden resonance energy transfer (SF-RET). Binary probes consist of a donor and acceptor fluorophores that are attached to two different oligonucleotides and serve as a resonance energy transfer (RET) donor\u2212acceptor pair when hybridized to adjacent sites of a target sequence. In the absence of target, excitation of the donor results in fluorescence only from the donor, but when the probes hybridize to the target, the fluorophores are brought into close proximity favoring RET, yielding fluorescence mainly from the acceptor fluorophore. These new binary probes use the metal complex Ru(bpy')(DIP)_2^(2+) as the energy donor and an organic fluorophore (Cy5) as the energy acceptor. Energy transfer from the MLCT state of the Ru complex to singlet Cy5 is spin forbidden and produces a delayed fluorescence of Cy5. This paper demonstrates that fluorescence delay of Cy5 can be used to time resolve the emission of the probe from the intense fluorescence background of a model system for cellular background; this provides the reported system to overcome intense autofluorescence, an important and general advantage over \"classical\" spin-allowed steady-state probes.", "doi": "10.1021/ja0717257", "pmcid": "PMC2747585", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2007-07-18", "series_number": "28", "volume": "129", "issue": "28", "pages": "8680-8681" }, { "id": "authors:4pw2w-5wz82", "collection": "authors", "collection_id": "4pw2w-5wz82", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160229-085218437", "type": "article", "title": "DNA-Mediated Electrochemistry of Disulfides on Graphite", "author": [ { "family_name": "Gorodetsky", "given_name": "Alon A.", "orcid": "0000-0002-3811-552X", "clpid": "Gorodetsky-A-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The electrochemistry of disulfides incorporated into the sugar\u2212phosphate backbone of pyrene-modified DNA has been examined on highly oriented pyrolytic graphite (HOPG). Two signals, one irreversible, one reversible, are observed at \u2212160 and \u2212290 mV versus normal hydrogen electrode, respectively. The inclusion of a single base mismatch in the DNA duplex below the location of the disulfide leads to a significant attenuation in the electrochemical signal, while the inclusion of a mismatch above the disulfide has little effect on the electrochemistry observed. Thus disulfide reduction in the DNA backbone appears to be DNA-mediated. The redox couples found show a strong pH dependence consistent with formation of a disulfide radical anion or 2e- reduction of the disulfide to the two thiols. These data demonstrate that DNA electrochemistry can be utilized to promote disulfide reduction at a distance mediated by the DNA duplex.", "doi": "10.1021/ja071006s", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2007-05-16", "series_number": "19", "volume": "129", "issue": "19", "pages": "6074-6075" }, { "id": "authors:5zj06-c7k94", "collection": "authors", "collection_id": "5zj06-c7k94", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160217-105103863", "type": "article", "title": "Oxidation by DNA Charge Transport Damages Conserved Sequence Block II, a Regulatory Element in Mitochondrial DNA", "author": [ { "family_name": "Merino", "given_name": "Edward J.", "clpid": "Merino-E-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Sites of oxidative damage in mitochondrial DNA have been identified on the basis of DNA-mediated charge transport. Our goal is to understand which sites in mitochondrial DNA are prone to oxidation at long range and whether such oxidative damage correlates with cancerous transformation. Here we show that a primer extension reaction can be used to monitor directly oxidative damage to authentic mitochondrial DNA through photoreactions with a rhodium intercalator. The complex [Rh(phi)_2bpy]Cl_3 (phi = 9,10-phenanthrenequinone diimine) binds to DNA without sequence specificity and, upon photoactivation, either promotes strand breaks directly at the binding site or promotes one-electron oxidative damage; comparing the sites of base oxidation to direct strand breaks reveals the oxidative damage that arises from a distance through DNA-mediated charge transport. Significantly, base oxidation by charge transport overlaps with known mutational hot spots associated with cancers at nucleotides surrounding positions 263 and 303; the latter is known as conserved sequence block II and is vital to DNA replication. Since DNA base oxidation at conserved sequence block II should weaken the ability of damaged mitochondrial genomes to be replicated, DNA-mediated charge transport may provide a protection mechanism for excluding damaged DNA.", "doi": "10.1021/bi062024+", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "2007-03-13", "series_number": "10", "volume": "46", "issue": "10", "pages": "2805-2811" }, { "id": "authors:fmaw0-e3r03", "collection": "authors", "collection_id": "fmaw0-e3r03", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141117-130951144", "type": "article", "title": "DNA base mismatch detection with bulky rhodium intercalators: synthesis and applications", "author": [ { "family_name": "Zeglis", "given_name": "Brian M.", "clpid": "Zeglis-B-M" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "This protocol describes the syntheses and applications of two metallointercalators, Rh(bpy)_2(chrysi)^(3+) and Rh(bpy)_2(phzi)^(3+), that target single base mismatches in DNA. The complexes bind mismatched DNA sites specifically and, upon photoactivation, promote strand scission neighboring the mismatch. Owing to their high specificity and sequence context independence, targeting mismatches\nwith these complexes offers an attractive alternative to current mismatch- and SNP-detection methodologies. This protocol also describes the synthesis of these complexes and their use in marking mismatched sites. Irradiation of 32P-labeled duplex DNA with either intercalator followed by denaturing PAGE allows the detection of mismatches in oligonucleotides. The protocol also outlines a method for efficient detection of single nucleotide polymorphisms (SNPs) in larger genes or plasmids. Pooled genes are denatured and re-annealed to form heteroduplexes; they are then incubated with either complex, irradiated and analyzed using capillary electrophoresis to probe for mismatches (SNP sites). The synthesis of the metallointercalators requires approximately 5\u20137 d. The mismatch- and SNP-detection experiments each require approximately 3 d.", "doi": "10.1038/nprot.2007.22", "pmcid": "PMC2754800", "issn": "1754-2189", "publisher": "Nature Publishing Group", "publication": "Nature Protocols", "publication_date": "2007-03-08", "series_number": "2", "volume": "2", "issue": "2", "pages": "357-371" }, { "id": "authors:sc43r-vrx56", "collection": "authors", "collection_id": "sc43r-vrx56", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160226-135928097", "type": "article", "title": "Differential Ionic Permeation of DNA-Modified Electrodes", "author": [ { "family_name": "Ceres", "given_name": "Donato M.", "clpid": "Ceres-D-M" }, { "family_name": "Udit", "given_name": "Andrew K.", "clpid": "Udit-A-K" }, { "family_name": "Hill", "given_name": "Haley D.", "clpid": "Hill-H-D" }, { "family_name": "Hill", "given_name": "Michael G.", "clpid": "Hill-M-G" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Ionic permselectivity of DNA films has been investigated by the analysis of the electrochemical response of methylene blue (MB) as a function of pH and ionic strength on DNA-modified electrodes in aqueous p-nitrophenol (p-NP) and phosphate buffers. We have observed a linear Pourbaix diagram in p-NP buffer indicating that the reduction of MB occurs with a two-electron plus one-proton reaction. Interestingly, in phosphate buffer the Pourbaix diagram is curved and this suggests that the thermodynamics of MB incorporated in the film depend also on the ratio of mono- versus divalent anions in the bulk. This result indicates that DNA films do not behave as pure ion-exclusion films, but instead there is a differential permselectivity that depends on the identity of the anions. Based on this consideration of the ionic distribution in the films, we provide a new method for the analysis of the DNA surface coverage based on AC impedance of an anionic species, ferricyanide. The methodology is of particular value in analyzing DNA hybridization and dehybridization. This approach presents an advantage compared to standard ruthenium hexammine assays since our methodology is insensitive to film morphology, and is highly sensitive to the amount of negative charge on the surface.", "doi": "10.1021/jp066324c", "issn": "1520-6106", "publisher": "American Chemical Society", "publication": "Journal of Physical Chemistry B", "publication_date": "2007-01-25", "series_number": "3", "volume": "111", "issue": "3", "pages": "663-668" }, { "id": "authors:whb6r-hxn36", "collection": "authors", "collection_id": "whb6r-hxn36", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160229-085221379", "type": "article", "title": "Methods to Explore Cellular Uptake of Ruthenium Complexes", "author": [ { "family_name": "Puckett", "given_name": "Cindy A.", "clpid": "Puckett-C-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The cellular uptake of a series of dipyridophenazine (dppz) complexes of Ru(II) was examined by flow cytometry. The complexes, owing to their facile synthesis, stability, and luminescence, provide a route to compare and contrast systematically factors governing cellular entry. Substituting the ancillary ligands in the dppz complexes of Ru(II) permits variation in the overall complex charge, size, and hydrophobicity. In HeLa cells, cellular uptake appears to be facilitated by the lipophilic 4,7-diphenyl-1,10-phenanthroline (DIP) ligand. Despite the large size of Ru(DIP)_2dppz^(2+) (20 \u00c5 diameter), this complex is readily transported inside the cell compared to smaller and more hydrophilic complexes, such as Ru(bpy)_2dppz^(2+). Accumulation in the cellular interior is confirmed by confocal microscopy.", "doi": "10.1021/ja0677564", "pmcid": "PMC2747593", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2007-01-10", "series_number": "1", "volume": "129", "issue": "1", "pages": "46-47" }, { "id": "authors:bj9ys-6rn84", "collection": "authors", "collection_id": "bj9ys-6rn84", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:PIEpnas07", "type": "article", "title": "Insights into finding a mismatch through the structure of a mispaired DNA bound by a rhodium intercalator", "author": [ { "family_name": "Pierre", "given_name": "Valerie C.", "clpid": "Pierre-V-C" }, { "family_name": "Kaiser", "given_name": "Jens T.", "orcid": "0000-0002-5948-5212", "clpid": "Kaiser-J-T" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "We report the 1.1-\u00c5 resolution crystal structure of a bulky rhodium complex bound to two different DNA sites, mismatched and matched in the oligonucleotide 5'-(dCGGAAATTCCCG)2-3'. At the AC mismatch site, the structure reveals ligand insertion from the minor groove with ejection of both mismatched bases and elucidates how destabilized mispairs in DNA may be recognized. This unique binding mode contrasts with major groove intercalation, observed at a matched site, where doubling of the base pair rise accommodates stacking of the intercalator. Mass spectral analysis reveals different photocleavage products associated with the two binding modes in the crystal, with only products characteristic of mismatch binding in solution. This structure, illustrating two clearly distinct binding modes for a molecule with DNA, provides a rationale for the interrogation and detection of mismatches.", "doi": "10.1073/pnas.0610170104", "pmcid": "PMC1766401", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2007-01-09", "series_number": "2", "volume": "104", "issue": "2", "pages": "429-434" }, { "id": "authors:e2zj2-jps79", "collection": "authors", "collection_id": "e2zj2-jps79", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:HARpnas06", "type": "article", "title": "DNA mismatch-specific targeting and hypersensitivity of mismatch-repair-deficient cells to bulky rhodium(III) intercalators", "author": [ { "family_name": "Hart", "given_name": "Jonathan R.", "clpid": "Hart-J-R" }, { "family_name": "Glebov", "given_name": "Oleg", "clpid": "Glebov-O" }, { "family_name": "Ernst", "given_name": "Russell J.", "clpid": "Ernst-R-J" }, { "family_name": "Kirsch", "given_name": "Ilan R.", "clpid": "Kirsch-I-R" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Mismatch repair (MMR) is critical to maintaining the integrity of the genome, and deficiencies in MMR are correlated with cancerous transformations. Bulky rhodium intercalators target DNA base mismatches with high specificity. Here we describe the application of bulky rhodium intercalators to inhibit cellular proliferation differentially in MMR-deficient cells compared with cells that are MMR-proficient. Preferential inhibition by the rhodium complexes associated with MMR deficiency is seen both in a human colon cancer cell line and in normal mouse fibroblast cells; the inhibition of cellular proliferation depends strictly on the MMR deficiency of the cell. Furthermore, our assay of cellular proliferation is found to correlate with DNA mismatch targeting by the bulky metallointercalators. It is the {Delta}-isomer that is active both in targeting base mismatches and in inhibiting DNA synthesis. Additionally, the rhodium intercalators promote strand cleavage at the mismatch site with photoactivation, and we observe that the cellular response is enhanced with photoactivation. Targeting DNA mismatches may therefore provide a cell-selective strategy for chemotherapeutic design.", "doi": "10.1073/pnas.0607576103", "pmcid": "PMC1622828", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2006-10-17", "series_number": "42", "volume": "103", "issue": "42", "pages": "15359-15363" }, { "id": "authors:zkjh2-50f41", "collection": "authors", "collection_id": "zkjh2-50f41", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160229-103206591", "type": "article", "title": "Targeting DNA Mismatches with Rhodium Intercalators Functionalized with a Cell-Penetrating Peptide", "author": [ { "family_name": "Brunner", "given_name": "Jens", "clpid": "Brunner-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Cell-penetrating peptides are widely used to deliver cargo molecules into cells. Here we describe the synthesis, characterization, DNA binding, and cellular uptake studies of a series of metal\u2212peptide conjugates containing oligoarginine as a cell-penetrating peptide. d-Octaarginine units are appended onto a rhodium intercalator containing the sterically expansive chrysenequinone diimine (chrysi) ligand to form Rh(chrysi)(phen)(bpy)^(3+)-tethered oligoarginine conjugates, where the peptide is attached to the ancillary bpy ligand; some conjugates also include a fluorescein or thiazole orange tag. These complexes bind and with photoactivation selectively cleave DNA neighboring single-base mismatches. The presence of the oligoarginines is found to increase the nonspecific binding affinity of the complexes for both matched and mismatched DNA, but for these conjugates, photocleavage remains selective for the mismatched site, as assayed using both gel electrophoresis and mass spectrometry experiments. Significantly, the rhodium complex does not interfere with the delivery properties of the cell-penetrating peptide. Confocal microscopy experiments show rapid nuclear localization of the metal\u2212peptide conjugates containing the tethered fluorescein. Mass spectrometry experiments confirm the association of the rhodium with the HeLa cells. These results provide a strategy for targeting mismatch-selective metal complexes inside cell nuclei.", "doi": "10.1021/bi061198o", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "2006-10-10", "series_number": "40", "volume": "45", "issue": "40", "pages": "12295-12302" }, { "id": "authors:gktg8-grw79", "collection": "authors", "collection_id": "gktg8-grw79", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160209-124711381", "type": "article", "title": "Direct Electrochemistry of Endonuclease III in the Presence and Absence of DNA", "author": [ { "family_name": "Gorodetsky", "given_name": "Alon A.", "orcid": "0000-0002-3811-552X", "clpid": "Gorodetsky-A-A" }, { "family_name": "Boal", "given_name": "Amie K.", "orcid": "0000-0002-1234-8472", "clpid": "Boal-A-K" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The electrochemistry of the base excision repair enzyme Endonuclease III (Endo III) in the presence and absence of DNA has been examined on highly oriented pyrolytic graphite (HOPG). At the surface modified with pyrenated DNA, a reversible signal is observed at 20 mV versus NHE for the [4Fe\u22124S]^(3+/2+) couple of Endo III, similar to Au. Without DNA modification, oxidative and reductive signals for the [4Fe\u22124S] cluster of Endo III are found on bare HOPG, allowing a direct comparison between DNA-bound and free redox potentials. These data indicate a shift of approximately \u2212200 mV in the 3+/2+ couple upon binding of Endo III to DNA. This potential shift reflects a difference in affinity for DNA of more than 3 orders of magnitude between the oxidized 3+ and reduced 2+ protein and provides quantitative support for our model utilizing DNA-mediated charge transport to redistribute base excision repair enzymes in the vicinity of damaged DNA.", "doi": "10.1021/ja064784d", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2006-09-01", "series_number": "37", "volume": "128", "issue": "37", "pages": "12082-12083" }, { "id": "authors:psp03-mt764", "collection": "authors", "collection_id": "psp03-mt764", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160229-085222529", "type": "article", "title": "Electrochemistry Using Self-Assembled DNA Monolayers on Highly Oriented Pyrolytic Graphite", "author": [ { "family_name": "Gorodetsky", "given_name": "Alon A.", "orcid": "0000-0002-3811-552X", "clpid": "Gorodetsky-A-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Duplex DNA functionalized with pyrene has been utilized to fabricate DNA-modified electrodes on highly oriented pyrolytic graphite (HOPG). Films have been characterized using AFM and radioactive labeling as well as electrochemically. The data obtained are consistent with a close-packed structure in the film with helices oriented in a nearly upright orientation, as seen earlier with the fabrication of thiol-tethered duplexes on gold. Also as on gold, we observe the reduction of DNA-bound intercalators in a DNA-mediated reaction. The reduction of the intercalator is attenuated in the presence of the single-base mismatches, CA and GT, independent of the sequence composition of the oligonucleotide. This sensitivity to single-base mismatches is enhanced when methylene blue reduction is coupled in an electrocatalytic cycle with ferricyanide. The extended potential range afforded by the HOPG surface has allowed us also to investigate the electrochemistry of previously inaccessible metallointercalators, Ru(bpy)_2dppz^(2+) and Os(phen)_2dppz^(2+), at the DNA-modified HOPG surface. These results support the application of DNA-modified HOPG as a convenient and reproducible surface for electrochemical DNA sensors using DNA-mediated charge transport.", "doi": "10.1021/la0611054", "issn": "0743-7463", "publisher": "American Chemical Society", "publication": "Langmuir", "publication_date": "2006-08-29", "series_number": "18", "volume": "22", "issue": "18", "pages": "7917-7922" }, { "id": "authors:c1scb-dzw25", "collection": "authors", "collection_id": "c1scb-dzw25", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160229-085221075", "type": "article", "title": "Site-Specific DNA Photocleavage by Rhodium Intercalators Analyzed by MALDI-TOF Mass Spectrometry", "author": [ { "family_name": "Brunner", "given_name": "Jens", "clpid": "Brunner-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The DNA photocleavage reaction of mismatch-selective Rh complexes has been analyzed by MALDI-TOF mass spectrometry as well as gel electrophoresis analysis of radioactively tagged oligonucleotides. Analogous results are obtained with these two techniques showing site-specific cleavage neighboring the mismatch to yield primarily 5'- and 3'-phosphate termini. Additional intermediates and products are observed, however, using MALDI-TOF analysis. MALDI-TOF mass spectrometry is seen to be particularly powerful in the analysis of DNA cleavage by site-specific molecules. The method requires no radioactive labeling, only little material, and analysis can be accomplished within minutes. Moreover, this mass spectral analysis of DNA cleavage yields direct information regarding products rather than simply the base pair site of cleavage.", "doi": "10.1021/ja0612753", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2006-05-31", "series_number": "21", "volume": "128", "issue": "21", "pages": "6772-6773" }, { "id": "authors:bzzxj-6r184", "collection": "authors", "collection_id": "bzzxj-6r184", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160209-124007376", "type": "article", "title": "A Mismatch-Selective Bifunctional Rhodium\u2212Oregon Green Conjugate: A Fluorescent Probe for Mismatched DNA", "author": [ { "family_name": "Zeglis", "given_name": "Brian M.", "clpid": "Zeglis-B-M" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "A fluorescent metallointercalator conjugate that selectively targets DNA base mismatches has been synthesized by coupling an organic fluorophore to a bulky Rh intercalator containing the chrysenequinone diimine ligand. Ion pairing between the cationic Rh and anionic fluorophore moieties dramatically quenches the fluorescence of the conjugate in solution and in the presence of matched DNA. However, in the presence of mismatched DNA, the fluorescence of the conjugate is increased >300%. This increase in fluorescence is attributed to the loss in intramolecular quenching associated with DNA binding; intercalation of the Rh moiety into the mismatched site can lead to electrostatic repulsion of the anionic fluorophore away from the DNA phosphate backbone and Rh. Denaturing PAGE experiments with ^(32)P-labeled oligonucleotides indicate that the conjugate selectively binds the mismatched DNA with a binding affinity of 6 \u00d7 10^5 M^(-1) and, upon irradiation, cleaves the DNA backbone neighboring the mismatched site.", "doi": "10.1021/ja061409c", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2006-05-01", "series_number": "17", "volume": "128", "issue": "17", "pages": "5654-5655" }, { "id": "authors:tz815-9fs64", "collection": "authors", "collection_id": "tz815-9fs64", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:YAVpnas06", "type": "article", "title": "Electron trap for DNA-bound repair enzymes: A strategy for DNA-mediated signaling", "author": [ { "family_name": "Yavin", "given_name": "Eylon", "clpid": "Yavin-Eylon" }, { "family_name": "Stemp", "given_name": "Eric D. A.", "orcid": "0000-0003-2098-4214", "clpid": "Stemp-Eric-D-A" }, { "family_name": "O'Shea", "given_name": "Valerie L.", "clpid": "O'Shea-Valerie-L" }, { "family_name": "David", "given_name": "Sheila S.", "orcid": "0000-0001-5873-7935", "clpid": "David-Sheila-S" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Despite a low copy number within the cell, base excision repair (BER) enzymes readily detect DNA base lesions and mismatches. These enzymes also contain [Fe4S4] clusters, yet a redox role for these iron cofactors had been unclear. Here, we provide evidence that BER proteins may use DNA-mediated redox chemistry as part of a signaling mechanism to detect base lesions. By using chemically modified bases, we show electron trapping on DNA in solution with bound BER enzymes by electron paramagnetic resonance (EPR) spectroscopy. We demonstrate electron transfer from two BER proteins, Endonuclease III (EndoIII) and MutY, to modified bases in DNA containing oxidized nitroxyl radical EPR probes. Electron trapping requires that the modified base is coupled to the DNA {pi}-stack, and trapping efficiency is increased when a noncleavable MutY substrate analogue is located distally to the trap. These results are consistent with DNA binding leading to the activation of the repair proteins toward oxidation. Significantly, these results support a mechanism for DNA repair that involves DNA-mediated charge transport.", "doi": "10.1073/pnas.0600239103", "pmcid": "PMC1450131", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2006-03-07", "series_number": "10", "volume": "103", "issue": "10", "pages": "3610-3614" }, { "id": "authors:m92ew-hcs68", "collection": "authors", "collection_id": "m92ew-hcs68", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160229-085222275", "type": "article", "title": "Sequence Dependence of Charge Transport through DNA Domains", "author": [ { "family_name": "Shao", "given_name": "Fangwei", "orcid": "0000-0003-2007-3920", "clpid": "Shao-Fangwei" }, { "family_name": "Augustyn", "given_name": "Katherine", "clpid": "Augustyn-K-E" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Here we examine the photooxidation of two kinetically fast electron hole traps, N_4-cyclopropylcytosine (^(CP)C) and N_2-cyclopropylamine-guanosine (CPG), incorporated in DNA duplexes of various sequence using different photooxidants. DNA oxidation studies are carried out either with noncovalently bound [Ru(phen)(dppz)(bpy')]^(3+) (dppz = dipyridophenazine) and [Rh(phi)_2(bpy)]^(3+) (phi = phenanthrenequinone diimine) or with anthraquinone tethered to DNA. Because the cyclopropylamine-substituted bases decompose rapidly upon oxidation, their efficiency of decomposition provides a measure of relative hole localization. Consistent with a higher oxidation potential for ^(CP)C versus ^(CP)G in DNA, ^(CP)C decomposes with photooxidation by [Rh(phi)_2(bpy)]^(3+), while CPG undergoes ring-opening both with photoexcited [Rh(phi)_2(bpy)]^(3+) and with [Ru(phen)(dppz)(bpy')]^(3+). Anthraquinone-modified DNA assemblies of identical base composition but different base sequence are also probed. Single and double base substitutions within adenine tracts modulate ^(CP)C decomposition. In fact, the entire sequence within the DNA assembly is seen to govern ^(CP)C oxidation, not simply the bases intervening between ^(CP)C and the tethered photooxidant. These data are reconciled in the context of a mechanistic model of conformationally gated charge transport through delocalized DNA domains. Photooxidations of anthraquinone-modified DNA assemblies containing both ^(CP)C and ^(CP)G, but with varied distances separating the modified bases, point to a domain size of at least three bases. Our model for DNA charge transport is distinguished from polaron models. In our model, delocalized domains within the base pair stack form transiently based upon sequence-dependent DNA structure and dynamics. Given these results, DNA charge transport is indeed remarkably sensitive to DNA sequence and structure.", "doi": "10.1021/ja0563399", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2005-12-14", "series_number": "49", "volume": "127", "issue": "49", "pages": "17445-17452" }, { "id": "authors:mnrdc-4km03", "collection": "authors", "collection_id": "mnrdc-4km03", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160129-163937195", "type": "article", "title": "Reductive and Oxidative DNA Damage by Photoactive Platinum(II) Intercalators", "author": [ { "family_name": "Lu", "given_name": "Wei", "clpid": "Lu-Wei" }, { "family_name": "Vicic", "given_name": "David A.", "clpid": "Vicic-D-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Several photoactive platinum R-diimine intercalators have been prepared to develop new probes of DNA oxidation and reduction chemistry. Five water-soluble bis(mes')Pt(II) complexes (mes') N,N,N,3,5-pentamethylaniline) with various aromatic \u03b1-diimine ligands (dppz= dipyridophenazine, np = naphtha[2,3-f][1,\u03c9]phenanthroline, CN-np = naphtho[2,3-f][1,10]phenanthroline-9-carbonitrile, CN_2-np = naphtho[2,3-f][1,10]phenanthroline-9,14-dicarbonitrile, and bp = benzo-[f][1,10]phenanthroline) were synthesized. The complex [(np)Pt(mes')_2]Cl_2 was also characterized by X-ray crystallography, and the crystal structure shows that the ortho-methyl groups of the mes' ligands conveniently block substitution at the vacant sites of platinum without overlapping with the intercalating \u03b1-diimine ligand. The Pt(II) complexes were found to have excited-state oxidation and reduction potentials of -0.6 to -1.0 and 1.0 to 1.5 V versus NHE, respectively, making them potent photoreductants as well as photooxidants. Many of the complexes are found to promote the photooxidation of N^2-cyclopropyldeoxyguanosine (d^(Cp)G). Photoexcited [(dppz)Pt(mes')_2]^(2+) is found to be most efficient in this photooxidation, as well as in the photoreduction of N^4-cyclopropylcytidine (^(Cp)C); these modified nucleosides rapidly decompose in a ring-opening reaction upon oxidation or reduction. Photoexcited [(dppz)Pt(mes')_2]Cl_2, upon intercalation into the DNA \u03c0 stack, is found, in addition, to promote reductive and oxidative damage within the DNA duplex, as is also probed using the kinetically fast electron and hole traps, ^(Cp)C and ^(Cp)G. These Pt complexes may therefore offer useful reactive tools to compare and contrast directly reductive and oxidative chemistry in double helical DNA.", "doi": "10.1021/ic051124l", "issn": "0020-1669", "publisher": "American Chemical Society", "publication": "Inorganic Chemistry", "publication_date": "2005-10-31", "series_number": "22", "volume": "44", "issue": "22", "pages": "7970-7980" }, { "id": "authors:mer6j-0e782", "collection": "authors", "collection_id": "mer6j-0e782", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160209-123604635", "type": "article", "title": "DNA Charge Transport Leading to Disulfide Bond Formation", "author": [ { "family_name": "Takada", "given_name": "Tadao", "clpid": "Takada-Tadao" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Here, we show that DNA-mediated charge transport (CT) can lead to the oxidation of thiols to form disulfide bonds in DNA. DNA assemblies were prepared possessing anthraquinone (AQ) as a photooxidant spatially separated on the duplex from two SH groups incorporated into the DNA backbone. Upon AQ irradiation, HPLC analysis reveals DNA ligated through a disulfide. The reaction efficiency is seen to vary in assemblies containing intervening DNA mismatches, confirming that the reaction is DNA-mediated. Interestingly, one intervening mismatch near the thiols promotes an increase in efficiency, which we attribute to increased base dynamics. Hence, here, where the reaction is on the backbone rather than within the base stack, stacking perturbations do not necessarily lead to an inhibitory effect on DNA CT.", "doi": "10.1021/ja054306n", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2005-09-01", "series_number": "35", "volume": "127", "issue": "35", "pages": "12204-12205" }, { "id": "authors:shrcz-rtn21", "collection": "authors", "collection_id": "shrcz-rtn21", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:DERpnas05", "type": "article", "title": "Electrically monitoring DNA repair by photolyase", "author": [ { "family_name": "DeRosa", "given_name": "Maria C.", "clpid": "DeRosa-M-C" }, { "family_name": "Sancar", "given_name": "Aziz", "clpid": "Sancar-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Cyclobutane pyrimidine dimers are the major DNA photoproducts produced upon exposure to UV radiation. If left unrepaired, these lesions can lead to replication errors, mutation, and cell death. Photolyase is a light-activated flavoenzyme that binds to pyrimidine dimers in DNA and repairs them in a reaction triggered by electron transfer from the photoexcited flavin cofactor to the dimer. Using gold electrodes modified with DNA duplexes containing a cyclobutane thymine dimer (T <> T), here we probe the electrochemistry of the flavin cofactor in Escherichia coli photolyase. Cyclic and square-wave voltammograms of photolyase deposited on these electrodes show a redox signal at 40 mV versus normal hydrogen electrode, consistent with electron transfer to and from the flavin in the DNA-bound protein. This signal is dramatically attenuated on surfaces where the pi-stacking of the DNA bases is perturbed by the presence of an abasic site below the T <> T, an indication that the redox pathway is DNA-mediated. DNA repair can, moreover, be monitored electrically. Exposure of photolyase on T <> T-damaged DNA films to near-UV/blue light leads to changes in the flavin signal consistent with repair, as confirmed by parallel HPLC experiments. These results demonstrate the exquisite sensitivity of DNA electrochemistry to perturbations in base pair stacking and the applicability of this chemistry to probe reactions of proteins with DNA.", "doi": "10.1073/pnas.0503527102", "pmcid": "PMC1182438", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2005-08-02", "series_number": "31", "volume": "102", "issue": "31", "pages": "10788-10792" }, { "id": "authors:0wna2-45617", "collection": "authors", "collection_id": "0wna2-45617", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160209-123230374", "type": "article", "title": "DNA Electrochemistry through the Base Pairs Not the Sugar\u2212Phosphate Backbone", "author": [ { "family_name": "Liu", "given_name": "Tao", "clpid": "Liu-Tao" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Using intercalated, covalently bound daunomycin as a redox probe, ground state charge transport in DNA films with a perturbation in base pair stacking was examined in comparison with breaks in the sugar\u2212phosphate backbone. While the introduction of one or even two nicks in the sugar\u2212phosphate backbone yields no detectable effect on electron transfer, a CA mismatch significantly attenuates the electron transfer yield. These results confirm that the base pair stack is the pathway for DNA-mediated charge transfer, not the sugar\u2212phosphate backbone.", "doi": "10.1021/ja053025c", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2005-07-01", "series_number": "29", "volume": "127", "issue": "29", "pages": "10160-10161" }, { "id": "authors:74kne-ff823", "collection": "authors", "collection_id": "74kne-ff823", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160229-103206847", "type": "article", "title": "DNA-Bound Redox Activity of DNA Repair Glycosylases Containing [4Fe-4S] Clusters", "author": [ { "family_name": "Boal", "given_name": "Amie K.", "orcid": "0000-0002-1234-8472", "clpid": "Boal-Amie-K" }, { "family_name": "Yavin", "given_name": "Eylon", "clpid": "Yavin-Eylon" }, { "family_name": "Lukianova", "given_name": "Olga A.", "clpid": "Lukianova-Olga-A" }, { "family_name": "O'Shea", "given_name": "Valerie L.", "clpid": "O'Shea-Valerie-L" }, { "family_name": "David", "given_name": "Sheila S.", "orcid": "0000-0001-5873-7935", "clpid": "David-Sheila-S" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "MutY and endonuclease III, two DNA glycosylases from Escherichia coli, and AfUDG, a uracil DNA glycosylase from Archeoglobus fulgidus, are all base excision repair enzymes that contain the [4Fe-4S]\u00b2\u207a cofactor. Here we demonstrate that, when bound to DNA, these repair enzymes become redox-active; binding to DNA shifts the redox potential of the [4Fe-4S]^(3+/2+) couple to the range characteristic of high-potential iron proteins and activates the proteins toward oxidation. Electrochemistry on DNA-modified electrodes reveals potentials for Endo III and AfUDG of 58 and 95 mV versus NHE, respectively, comparable to 90 mV for MutY bound to DNA. In the absence of DNA modification of the electrode, no redox activity can be detected, and on electrodes modified with DNA containing an abasic site, the redox signals are dramatically attenuated; these observations show that the DNA base pair stack mediates electron transfer to the protein, and the potentials determined are for the DNA-bound protein. In EPR experiments at 10 K, redox activation upon DNA binding is also evident to yield the oxidized [4Fe-4S]\u00b3\u207a cluster and the partially degraded [3Fe-4S]1+ cluster. EPR signals at g = 2.02 and 1.99 for MutY and g = 2.03 and 2.01 for Endo III are seen upon oxidation of these proteins by Co(phen)_3\u00b3\u207a in the presence of DNA and are characteristic of [3Fe-4S]\u00b9\u207a clusters, while oxidation of AfUDG bound to DNA yields EPR signals at g = 2.13, 2.04, and 2.02, indicative of both [4Fe-4S]\u00b3\u207a and [3Fe-4S]\u00b9\u207a clusters. On the basis of this DNA-dependent redox activity, we propose a model for the rapid detection of DNA lesions using DNA-mediated electron transfer among these repair enzymes; redox activation upon DNA binding and charge transfer through well-matched DNA to an alternate bound repair protein can lead to the rapid redistribution of proteins onto genome sites in the vicinity of DNA lesions. This redox activation furthermore establishes a functional role for the ubiquitous [4Fe-4S] clusters in DNA repair enzymes that involves redox chemistry and provides a means to consider DNA-mediated signaling within the cell.", "doi": "10.1021/bi047494n", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "2005-06-14", "series_number": "23", "volume": "44", "issue": "23", "pages": "8397-8407" }, { "id": "authors:fc5r6-kdp76", "collection": "authors", "collection_id": "fc5r6-kdp76", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:YAVpnas05", "type": "article", "title": "Protein-DNA charge transport: Redox activation of a DNA repair protein by guanine radical", "author": [ { "family_name": "Yavin", "given_name": "Eylon", "clpid": "Yavin-Eylon" }, { "family_name": "Boal", "given_name": "Amie K.", "orcid": "0000-0002-1234-8472", "clpid": "Boal-Amie-K" }, { "family_name": "Stemp", "given_name": "Eric D. A.", "orcid": "0000-0003-2098-4214", "clpid": "Stemp-Eric-D-A" }, { "family_name": "Boon", "given_name": "Elizabeth M.", "orcid": "0000-0003-1891-839X", "clpid": "Boon-Elizabeth-M" }, { "family_name": "Livingston", "given_name": "Alison L.", "clpid": "Livingston-Alison-L" }, { "family_name": "O'Shea", "given_name": "Valerie L.", "clpid": "O'Shea-Valerie-L" }, { "family_name": "David", "given_name": "Sheila S.", "orcid": "0000-0001-5873-7935", "clpid": "David-Sheila-S" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "DNA charge transport (CT) chemistry provides a route to carry out oxidative DNA damage from a distance in a reaction that is sensitive to DNA mismatches and lesions. Here, DNA-mediated CT also leads to oxidation of a DNA-bound base excision repair enzyme, MutY. DNA-bound Ru(III), generated through a flash/quench technique, is found to promote oxidation of the [4Fe-4S](2+) cluster of MutY to [4Fe-4S](3+) and its decomposition product [3Fe-4S](1+). Flash/quench experiments monitored by EPR spectroscopy reveal spectra with g = 2.08, 2.06, and 2.02, characteristic of the oxidized clusters. Transient absorption spectra of poly(dGC) and [Ru(phen)(2)dppz](3+) (dppz = dipyridophenazine), generated in situ, show an absorption characteristic of the guanine radical that is depleted in the presence of MutY with formation instead of a long-lived species with an absorption at 405 nm; we attribute this absorption also to formation of the oxidized [4Fe-4S](3+) and [3Fe4S](1+) clusters. In ruthenium-tethered DNA assemblies, oxidative damage to the 5'-G of a 5'-GG-3' doublet is generated from a distance but this irreversible damage is inhibited by MutY and instead EPR experiments reveal cluster oxidation. With ruthenium-tethered assemblies containing duplex versus single-stranded regions, MutY oxidation is found to be mediated by the DNA duplex, with guanine radical as an intermediate oxidant; guanine radical formation facilitates MutY oxidation. A model is proposed for the redox activation of DNA repair proteins through DNA CT, with guanine radicals, the first product under oxidative stress, in oxidizing the DNA-bound repair proteins, providing the signal to stimulate DNA repair.", "doi": "10.1073/pnas.0409410102", "pmcid": "PMC553321", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2005-03-08", "series_number": "10", "volume": "102", "issue": "10", "pages": "3546-3551" }, { "id": "authors:x5gy8-gpb79", "collection": "authors", "collection_id": "x5gy8-gpb79", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160226-120946590", "type": "article", "title": "Electrochemical Detection of Lesions in DNA", "author": [ { "family_name": "Boal", "given_name": "Amie K.", "orcid": "0000-0002-1234-8472", "clpid": "Boal-A-K" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Electrochemical DNA-based sensors that exploit the inherent sensitivity of DNA-mediated charge transport (CT) to base pair stacking perturbations are capable of detecting base pair mismatches and some common base damage products. Here, using DNA-modified gold electrodes, monitoring the electrocatalytic reduction of DNA-bound methylene blue, we examine a wide range of base analogues and DNA damage products. Among those detected are base damage products O4-methyl-thymine, O6-methyl-guanine, 8-oxo-guanine, and 5-hydroxy-cytosine, as well as a therapeutic base, nebularine. The efficiency of DNA-mediated CT is found not to depend on the thermodynamic stability of the helix. However, general trends in how base modifications affect CT efficiency are apparent. Modifications to the hydrogen bonding interface in Watson\u2212Crick base pairs yields a substantial loss in CT efficiency, as does added steric bulk. Base structure modifications that may induce base conformational changes also appear to attenuate CT in DNA as do those that bury hydrophilic groups within the DNA helix. Addition and subtraction of methyl groups that do not disrupt hydrogen bonding interactions do not have a large effect on CT efficiency. This sensitive detection methodology based upon DNA-mediated CT may have utility in diagnostic applications and implicates DNA-mediated CT as a possible damage detection mechanism for DNA repair enzymes.", "doi": "10.1021/bc0497362", "issn": "1043-1802", "publisher": "American Chemical Society", "publication": "Bioconjugate Chemistry", "publication_date": "2005-03", "series_number": "2", "volume": "16", "issue": "2", "pages": "312-321" }, { "id": "authors:gf0mf-39375", "collection": "authors", "collection_id": "gf0mf-39375", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:SHApnas04", "type": "article", "title": "Long-range oxidative damage to cytosines in duplex DNA", "author": [ { "family_name": "Shao", "given_name": "Fangwei", "orcid": "0000-0003-2007-3920", "clpid": "Shao-Fangwei" }, { "family_name": "O'Neill", "given_name": "Melanie A.", "clpid": "O'Neill-M-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Charge transport (CT) through DNA has been found to occur over long molecular distances in a reaction that is sensitive to intervening structure. The process has been described mechanistically as involving diffusive charge-hopping among low-energy guanine sites. Using a kinetically fast electron hole trap, N-4-cyclopropylcytosine (C-CP), here we show that hole migration must involve also the higher-energy pyrimidine bases. In DNA assemblies containing either [Rh(phi)(2)(bpy')](3+) or an anthraquinone derivative, two high-energy photooxidants, appreciable oxidative damage at a distant C-CP is observed. The damage yield is modulated by lower-energy guanine sites on the same or complementary strand. Significantly, the efficiency in trapping at C-CP is equivalent to that at N-2-cyclopropylguanosine ((CP)G). Indeed, even when (CP)G and C-CP are incorporated as neighboring bases on the same strand, their efficiency of photodecomposition is comparable. Thus, CT is not simply a function of the relative energies of the isolated bases but instead may require orbital mixing among the bases. We propose that charge migration through DNA involves occupation of all of the DNA bases with radical delocalization within transient structure-dependent domains. These delocalized domains may form and break up transiently, facilitating and limiting CT. This dynamic delocalized model for DNA CT accounts for the sensitivity of the process to sequence-dependent DNA structure and provides a basis to reconcile and exploit DNA CT chemistry and physics.", "doi": "10.1073/pnas.0408128101", "pmcid": "PMC539793", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2004-12-28", "series_number": "52", "volume": "101", "issue": "52", "pages": "17914-17919" }, { "id": "authors:gp2kr-b0b24", "collection": "authors", "collection_id": "gp2kr-b0b24", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160209-121156848", "type": "article", "title": "Tuning the DNA Reactivity of cis-Platinum: Conjugation to a Mismatch-Specific Metallointercalator", "author": [ { "family_name": "Petitjean", "given_name": "Anne", "clpid": "Petitjean-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "A novel bimetallic conjugate combining a rhodium intercalator that selectively binds DNA mismatches and a reactive cis-platinum analogue that targets DNA by coordination has been prepared. The site-selectivity of the bimetallic complex in forming coordination adducts is examined using mismatched and well-matched oligonucleotides of different sequences. The results indicate that through the bifunctional complex, the platinum center can be targeted near mismatched sites. Interestingly, with mismatched, DNA both intrastrand and the less common interstrand cross-linked adducts are formed. The recognition of a DNA mismatch by the bulky Rh intercalator appears to direct the Pt unit, depending upon steric constraints, to react preferentially with mismatched DNA at a site that may or may not be the preferred site of Pt coordination. Thus, the presence of a permanent link to a site-specific intercalator is able to tune the reactivity of the cis-platinum analogue.", "doi": "10.1021/ja047235l", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2004-11-01", "series_number": "45", "volume": "126", "issue": "45", "pages": "14728-14729" }, { "id": "authors:c483h-gkf41", "collection": "authors", "collection_id": "c483h-gkf41", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160209-120729202", "type": "article", "title": "Electron Transfer Rates in DNA Films as a Function of Tether Length", "author": [ { "family_name": "Drummond", "given_name": "T. Gregory", "clpid": "Drummond-T-G" }, { "family_name": "Hill", "given_name": "Michael G.", "clpid": "Hill-M-G" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "A homologous series of DNA-modified electrodes has been investigated in which the molecular tether length varies. Using intercalated, covalently bound daunomycin as a redox probe, an exponential dependence of electron transfer rates on the number of intervening methylene groups in the \u03c3-bonded tether is observed. In contrast, variation in DM position within DNA yields no detectable change in rate. These data confirm that overall electron transfer rates in DNA films are limited by the tether, not the DNA.", "doi": "10.1021/ja044910i", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2004-11-01", "series_number": "46", "volume": "126", "issue": "46", "pages": "15010-15011" }, { "id": "authors:w2c27-xpe12", "collection": "authors", "collection_id": "w2c27-xpe12", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170421-084130900", "type": "article", "title": "DNA-Mediated Charge Transport Requires Conformational Motion of the DNA Bases: Elimination of Charge Transport in Rigid Glasses at 77 K", "author": [ { "family_name": "O'Neill", "given_name": "Melanie A.", "clpid": "O'Neill-M-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "We have proposed that DNA-mediated charge transport (CT) is gated by base motions, with only certain base conformations being CT-active; a CT-active conformation can be described as a domain, a transiently extended \u03c0-orbital defined dynamically by DNA sequence. Here, to explore these CT-active conformations, we examine the yield of base-base CT between photoexcited 2-aminopurine (Ap*) and guanine in DNA in rigid LiCl glasses at 77 K, where conformational rearrangement is effectively eliminated. Duplex DNA assemblies (35-mers) were constructed containing adenine bridges Ap(A)_nG (n = 0\u22124). The yield of CT was monitored through fluorescence quenching of Ap* by G. We find, first, that the emission intensity of Ap* in all DNA duplexes increases dramatically upon cooling and becomes comparable to free Ap*. This indicates that all quenching of Ap* in duplex DNA is a dynamic process that requires conformational motion of the DNA bases. Second, DNA-mediated CT between Ap* and G is not observed at 77 K; rather than hindering the ability of DNA to transport charge, conformational motion is required. Moreover, the lack of DNA-mediated CT at 77 K, even through the shortest bridge, suggests that the static structures adopted upon cooling do not represent optimum CT-active conformations. These observations are consistent with our model of conformationally gated CT. Through conformational motion of the DNA bases, CT-active domains form and break-up transiently, both facilitating and limiting CT.", "doi": "10.1021/ja0455897", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2004-10-20", "series_number": "41", "volume": "126", "issue": "41", "pages": "13234-13235" }, { "id": "authors:efqmz-eja90", "collection": "authors", "collection_id": "efqmz-eja90", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:HARpnas04", "type": "article", "title": "Single-nucleotide polymorphism discovery by targeted DNA photocleavage", "author": [ { "family_name": "Hart", "given_name": "Jonathan R.", "clpid": "Hart-J-R" }, { "family_name": "Johnson", "given_name": "Martin D.", "orcid": "0000-0002-4120-3029", "clpid": "Johnson-M-D" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Single-nucleotide polymorphisms are the largest source of genetic variation in humans. We report a method for the discovery of single-nucleotide polymorphisms within genomic DNA. Pooled genomic samples are amplified, denatured, and annealed to generate mismatches at polymorphic DNA sites. Upon photoactivation, these DNA mismatches are then cleaved site-specifically by using a small molecular probe, a bulky metallointercalator, Rhchrysi or Rhphzi. Fluorescent labeling of the cleaved products and separation by capillary electrophoresis permits rapid identification with single-base resolution of the single-nucleotide polymorphism site. This method is remarkably sensitive and minor allele frequencies as low as 5% can be readily detected.", "doi": "10.1073/pnas.0406169101", "pmcid": "PMC521117", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2004-09-28", "series_number": "39", "volume": "101", "issue": "39", "pages": "14040-14044" }, { "id": "authors:39y3p-xy220", "collection": "authors", "collection_id": "39y3p-xy220", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160209-122044703", "type": "article", "title": "DNA Charge Transport: Conformationally Gated Hopping through Stacked Domains", "author": [ { "family_name": "O'Neill", "given_name": "Melanie A.", "clpid": "O'Neill-M-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The role of base motions in delocalization and propagation of charge through double helical DNA must be established experimentally and incorporated into mechanistic descriptions of DNA-mediated charge transport (CT). Here, we address these fundamental issues by examining the temperature dependence of the yield of CT between photoexcited 2-aminopurine (Ap*) and G through DNA bridges of varied length and sequence. DNA assemblies (35-mers) were constructed containing adenine bridges Ap(A)_nG (n = 0\u22129, 3.4\u221234 \u00c5) and mixed bridges, ApAAIAG and ApATATG. CT was monitored through fluorescence quenching of Ap* by G and through HPLC analysis of photolyzed DNA assemblies containing Ap and the modified guanine, N_2-cyclopropylguanosine (^(CP)G); upon oxidation, the ^(CP)G radical cation undergoes rapid ring opening. First, we find that below the duplex melting temperature (\u223c60 \u00b0C), the yield of CT through duplex DNA increases with increasing temperature governed by the length and sequence of the DNA bridge. Second, the distance dependence of CT is regulated by temperature; enhanced DNA base fluctuations within duplex DNA extend CT to significantly longer distances, here up to 34 \u00c5 in <10 ns. Third, at all temperatures the yield of CT does not exhibit a simple distance dependence; an oscillatory component, with a period of \u223c4\u22125 base pairs, is evident. These data cannot be rationalized by superexchange, hopping of a localized charge injected into the DNA bridge, a temperature-induced transition from superexchange to thermally induced hopping, or by phonon-assisted polaron hopping. Instead, we propose that CT occurs within DNA assemblies possessing specific, well-coupled conformations of the DNA bases, CT-active domains, accessed through base motion. CT through DNA is described as conformationally gated hopping among stacked domains. Enhanced DNA base motions lead to longer range CT with a complex distance dependence that reflects the roles of coherent dynamics and charge delocalization through transient domains. Consequently, DNA CT is not a simple function of distance but is intimately related to the dynamical structure of the DNA bridge.", "doi": "10.1021/ja048956n", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2004-09-01", "series_number": "37", "volume": "126", "issue": "37", "pages": "11471-11483" }, { "id": "authors:8eq4r-0yx87", "collection": "authors", "collection_id": "8eq4r-0yx87", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160229-120833802", "type": "article", "title": "[Ru(bpy)_2(L)]Cl_2: Luminescent Metal Complexes That Bind DNA Base Mismatches", "author": [ { "family_name": "Ruba", "given_name": "Eva", "clpid": "Ruba-E" }, { "family_name": "Hart", "given_name": "Jonathan R.", "clpid": "Hart-J-R" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Here we report the synthesis of luminescent ruthenium complexes that bind DNA base pair mismatches. [Ru(bpy)_2(tpqp)]Cl_2 (tpqp = 7,8,13,14-tetrahydro-6-phenylquino[8,7-k][1,8]phenanthroline), [Ru(bpy)_2(pqp)]Cl_2 (pqp = 6-phenylquino[8,7-k][1,8]phenanthroline), and [Ru(bpy)_2(tactp)]Cl_2 [tactp = 4,5,9,18-tetraazachryseno[9,10-b]triphenylene] have been synthesized, and their spectroscopic properties in the absence and presence of DNA have been examined. While [Ru(bpy)_2(pqp)]^(2+) shows no detectable luminescence, [Ru(bpy)_2(tpqp)]^(2+) is luminescent in the absence and presence of DNA with an excited-state lifetime of 10 ns and a quantum yield of 0.002. Although no increase in emission intensity is associated with binding to mismatch-containing DNA, luminescence quenching experiments and measurements of steady-state fluorescence polarization provide evidence for preferential binding to oligonucleotides containing a CC mismatch. Furthermore, by marking the site of binding through singlet oxygen sensitized damage, the complex has been shown to target a CC mismatch site directly with a specific binding affinity, K_b = 4 \u00d7 10^6 M^(-1). [Ru(bpy)_2(tactp)]^(2+), an analogue of [Ru(bpy)_2(dppz)]^(2+) containing a bulky intercalating ligand, is luminescent in aqueous solution at micromolar concentrations and exhibits a 12-fold enhancement in luminescence in the presence of DNA. The complex, however, tends to aggregate in aqueous solution; we find a dimerization constant of 9.8 \u00d7 10^5 M^(-1). Again, by singlet oxygen sensitization it is apparent that [Ru(bpy)_2(tactp)]^(2+) binds preferentially to a CC mismatch; using a DNase I footprinting assay, a binding constant to a CC mismatch of 8 \u00d7 10^5 M^(-1) is found. Hence results with these novel luminescent complexes support the concept of using a structurally demanding ligand to obtain selectivity in targeting single base mismatches in DNA. The challenge is coupling the differential binding we can obtain to differential luminescence.", "doi": "10.1021/ic0499291", "issn": "0020-1669", "publisher": "American Chemical Society", "publication": "Inorganic Chemistry", "publication_date": "2004-07-26", "series_number": "15", "volume": "43", "issue": "15", "pages": "4570-4578" }, { "id": "authors:ypdx9-ch905", "collection": "authors", "collection_id": "ypdx9-ch905", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:DELpnas04", "type": "article", "title": "Charge equilibration between two distinct sites in double helical DNA", "author": [ { "family_name": "Delaney", "given_name": "Sarah", "clpid": "Delaney-S" }, { "family_name": "Yoo", "given_name": "Jae", "clpid": "Yoo-Jae" }, { "family_name": "Stemp", "given_name": "Eric D. A.", "orcid": "0000-0003-2098-4214", "clpid": "Stemp-E-D-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "DNA assemblies containing a pendant dipyridophenazine complex of Ru(II) along with two oxidative traps, a site containing the nucleoside analog methylindole (5'-GMG-3') and a 5'-GGG-3' site, have been constructed to explore long-range charge transport through the base pair stack. With these chemically well defined assemblies, in combination with the flash/quench technique, formation of the methylindole cation radical and the neutral guanine radical is monitored directly by using transient absorption spectroscopy, and yields of oxidative damage are quantitated biochemically by gel electrophoresis. In these assemblies the base radicals form with a rate of \u2265107 s\u20131. The rate of base radical formation does not change upon the addition of a second radical trap, the 5'-GGG-3' site; however, the yield of methylindole oxidation is significantly lower. This observation indicates that the 5'-GGG-3' site is effective in competing for the migrating charge and provides a second trapping site. Switching the orientation of the two trapping sites does not affect the yield of oxidized products at either site. Therefore, in DNA both forward and reverse charge transport occur so as to provide equilibration across the duplex on a timescale that is fast compared with trapping at a particular site. Further evidence of charge equilibration results from incorporating an intervening base-stacking perturbation and monitoring the fate of the injected charge. These experiments underscore the dynamic nature of DNA charge transport and reveal the importance of considering radical propagation in both directions along the DNA duplex.", "doi": "10.1073/pnas.0403791101", "pmcid": "PMC489968", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2004-07-20", "series_number": "29", "volume": "101", "issue": "29", "pages": "10511-10516" }, { "id": "authors:d8ybj-2em28", "collection": "authors", "collection_id": "d8ybj-2em28", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160209-121614706", "type": "article", "title": "Bifunctional Rhodium Intercalator Conjugates as Mismatch-Directing DNA Alkylating Agents", "author": [ { "family_name": "Schatzschneider", "given_name": "Ulrich", "clpid": "Schatzschneider-U" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "A conjugate of a DNA mismatch-specific rhodium intercalator, containing the bulky chrysenediimine ligand, and an aniline mustard has been prepared, and targeting of mismatches in DNA by this conjugate has been examined. The preferential alkylation of mismatched over fully matched DNA is found by a mobility shift assay at concentrations where untethered organic mustards show little reaction. The binding site of the Rh intercalator was determined by DNA photocleavage, and the position of covalent modification was established on the basis of the enhanced depurination associated with N-alkylation. The site-selective alkylation at mismatched DNA renders these conjugates useful tools for the covalent tagging of DNA base pair mismatches and new chemotherapeutic design.", "doi": "10.1021/ja048543m", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2004-07-01", "series_number": "28", "volume": "126", "issue": "28", "pages": "8630-8631" }, { "id": "authors:e611e-cz155", "collection": "authors", "collection_id": "e611e-cz155", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160209-122559989", "type": "article", "title": "Effects of the Photooxidant on DNA-Mediated Charge Transport", "author": [ { "family_name": "Williams", "given_name": "Tashica T.", "clpid": "Williams-T-T" }, { "family_name": "Dohno", "given_name": "Chikara", "clpid": "Dohno-C" }, { "family_name": "Stemp", "given_name": "Eric D. A.", "orcid": "0000-0003-2098-4214", "clpid": "Stemp-E-D-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "A direct comparison of DNA charge transport (CT) with different photooxidants has been made. Photooxidants tested include the two metallointercalators, Rh(phi)_2(bpy')^(3+) and Ru(phen)(bpy')(dppz)^(2+), and three organic intercalators, ethidium (Et), thionine (Th), and anthraquinone (AQ). CT has been examined through a DNA duplex containing an A_6-tract intervening between two 5'-CGGC-3' sites with each of the photooxidants covalently tethered to one end of the DNA duplex. CT is assayed both through determination of the yield of oxidative guanine damage and, in derivative DNA assemblies, by analysis of the yield of a faster oxidative trapping reaction, ring opening of N^2-cyclopropylguanine (d^(CP)G) within the DNA duplex. We find clear differences in oxidative damage ratios at the distal versus proximal 5'-CGGC-3' sites depending upon the photooxidant employed. Importantly, nondenaturing gel electrophoresis data demonstrate the absence of any DNA aggregation by the DNA-bound intercalators. Hence, differences seen with assemblies containing various photooxidants cannot be attributed to differential aggregation. Comparisons in assemblies using different photooxidants thus reveal characteristics of the photooxidant as well as characteristics of the DNA assembly. In the series examined, the lowest distal/proximal DNA damage ratios are obtained with Ru and AQ, while, for both Rh and Et, high distal/proximal damage ratios are found. The oxidative damage yields vary in the order Ru > AQ > Rh > Et, and photooxidants that produce higher distal/proximal damage ratios have lower yields. While no oxidative DNA damage is detected using thionine as a photooxidant, oxidation is evident using the faster cyclopropylguanosine trap; here, a complex distance dependence is found. Differences observed among photooxidants as well as the complex distance dependence are attributed to differences in rates of back electron transfer (BET). Such differences are important to consider in developing mechanistic models for DNA CT.", "doi": "10.1021/ja049869y", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2004-07-01", "series_number": "26", "volume": "126", "issue": "26", "pages": "8148-8158" }, { "id": "authors:w0s5f-q4595", "collection": "authors", "collection_id": "w0s5f-q4595", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160208-163052817", "type": "article", "title": "Direct Chemical Evidence for Charge Transfer between Photoexcited 2-Aminopurine and Guanine in Duplex DNA", "author": [ { "family_name": "O'Neill", "given_name": "Melanie A.", "clpid": "O'Neill-M-A" }, { "family_name": "Dohno", "given_name": "Chikara", "clpid": "Dohno-C" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Photoexcited 2-aminopurine (Ap*) is extensively exploited as a fluorescent base analogue in the study of DNA structure and dynamics. Quenching of Ap* in DNA is often attributed to stacking interactions between Ap* and DNA bases, despite compelling evidence indicating that charge transfer (CT) between Ap* and DNA bases contributes to quenching. Here we present direct chemical evidence that Ap* undergoes CT with guanine residues in duplex DNA, generating oxidative damage at a distance. Irradiation of Ap in DNA containing the modified guanine, cyclopropylguanosine (^(CP)G), initiates hole transfer from Ap* followed by rapid ring opening of the ^(CP)G radical cation. Ring opening accelerates hole trapping to a much shorter time regime than for guanine radicals in DNA; consequently, trapping effectively competes with back electron transfer (BET) leading to permanent CT chemistry. Significantly, BET remains competitive, even with this much faster trapping reaction, consistent with measured kinetics of DNA-mediated CT. The distance dependence of BET is sharper than that of forward CT, leading to an inverted dependence of product yield on distance; at short distances product yield is inhibited by BET, while at longer distances trapping dominates, leading to permanent products. The distance dependence of product yield is distinct from forward CT, or charge injection. As with photoinduced charge transfer in other chemical and biological systems, rapid kinetics for charge injection into DNA need not be associated with a high yield of DNA damage products.", "doi": "10.1021/ja037802p", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2004-02-01", "series_number": "5", "volume": "126", "issue": "5", "pages": "1316-1317" }, { "id": "authors:1szrb-1v585", "collection": "authors", "collection_id": "1szrb-1v585", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160229-120833527", "type": "article", "title": "^1H NMR Studies of Nickel(II) Complexes Bound to Oligonucleotides: A Novel Technique for Distinguishing the Binding Locations of Metal Complexes in DNA", "author": [ { "family_name": "Bhattacharya", "given_name": "Pratip K.", "clpid": "Bhattacharya-P-K" }, { "family_name": "Lawson", "given_name": "Holly J.", "clpid": "Lawson-H-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The selective paramagnetic relaxation of oligonucleotide proton resonances of d(GTCGAC)_2 and d(GTGCAC)_2 by Ni(phen)_2(L)^(2+) where L = dipyridophenazine (dppz), dipyrido[3,2-d:2',3'-f]quinoxaline (dpq), and phenanthrenequinone (phi) has been examined to obtain structural insight into the noncovalent binding of these metal complexes to DNA. In the oligonucleotide d(GTCGAC)_2, preferential broadening of the G1H8, G4H8, T2H6, and C3H6 proton resonances was observed with Ni(phen)_2(dppz)^(2+), Ni(phen)_2(dpq)^(2+), and Ni(phen)_2(phi)^(2+). In the case of the sequence d(GTGCAC)_2, where the central two bases are juxtaposed from the previous one, preferential broadening was observed instead for the A5H2 proton resonance. Thus, a subtle change in the sequence of the oligonucleotide can cause significant change in the binding location of the metal complex in the oligonucleotide. Owing to comparable changes for all metal complexes and sequences in broadening of the thymine methyl proton resonances, we attribute the switch in preferential broadening to a change in site location within the oligomer rather than to an alteration of groove location. Therefore, even for DNA-binding complexes of low sequence-specificity, distinct variations in binding as a function of sequence are apparent.", "doi": "10.1021/ic0348291", "issn": "0020-1669", "publisher": "American Chemical Society", "publication": "Inorganic Chemistry", "publication_date": "2003-12-29", "series_number": "26", "volume": "42", "issue": "26", "pages": "8811-8817" }, { "id": "authors:qh32c-z8h74", "collection": "authors", "collection_id": "qh32c-z8h74", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160229-085221665", "type": "article", "title": "In Situ Scanning Tunneling Microscopy of DNA-Modified Gold Surfaces: Bias and Mismatch Dependence", "author": [ { "family_name": "Ceres", "given_name": "Donato M.", "clpid": "Ceres-D-M" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "In situ scanning tunneling microscopy has been performed on DNA-modified gold surfaces under physiological conditions. The STM images of DNA-modified gold surfaces are strongly dependent on the applied potential and percentage of DNA duplexes containing a single base mismatch. At negative surface potentials we observe reproducible features that are attributed to DNA agglomerates where the DNA duplexes are in the upright orientation; at positive potentials, when DNA molecules lie down on the surface, the film is transparent, and only the gold surface is distinguishable. These observations indicate that DNA possesses a non-negligible local density of states which can be probed when the DNA duplex is in the upright orientation. By varying the percentage of DNA duplexes containing a single base mismatch, we have observed a dramatic change in the image contrast as a result of the perturbation induced by the mismatch on the electronic pathway inside the DNA. These results emphasize the central role of the integrity of the \u03c0-stack for DNA charge transport. Duplex DNA is a promising candidate in molecular electronics, but only in arrangements where the orbitals can efficiently overlap with the electronic states of the electrodes and the environment does not constrain the DNA in non-native, poorly stacked conformations.", "doi": "10.1021/ja0384476", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2003-12-10", "series_number": "49", "volume": "125", "issue": "49", "pages": "14964-14965" }, { "id": "authors:zb7v4-0z611", "collection": "authors", "collection_id": "zb7v4-0z611", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160229-112429045", "type": "article", "title": "Charge Transport in DNA Duplex/Quadruplex Conjugates", "author": [ { "family_name": "Delaney", "given_name": "Sarah", "clpid": "Delaney-S" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "DNA conjugates containing adjacent duplex and guanine quadruplex assemblies have been designed to explore charge transport into quadruplex architectures. The quadruplex assemblies have been characterized structurally using circular dichroism and by assaying for chemical protection. Using an intercalating rhodium photooxidant, noncovalently bound or tethered to the duplex end, oxidizing radicals are found to be trapped in the folded quadruplex. Damage is observed almost exclusively at the external tetrads of the quadruplex. Little damage of the center tetrad is observed, due most likely to lowered efficiency of radical trapping within the quadruplex core. This pattern of damage is distinct from that observed for repetitive G sequences within duplex DNA. The data indicate, furthermore, that in the conjugates examined, the guanine quadruplex provides a more effective trap than a 5'-GG-3' guanine doublet within duplex DNA. Within these assemblies, sufficient base\u2212base overlap must exist at the duplex/quadruplex junction to allow for charge migration. This funneling of damage to the quadruplex, as well as the unique pattern of damage within the quadruplex, requires consideration with respect to the analysis of oxidative DNA damage within the cell.", "doi": "10.1021/bi0351965", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "2003-12-09", "series_number": "48", "volume": "42", "issue": "48", "pages": "14159-14165" }, { "id": "authors:b0hvh-d6253", "collection": "authors", "collection_id": "b0hvh-d6253", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160212-080416474", "type": "article", "title": "Ultrafast Dynamics in DNA-Mediated Electron Transfer: Base Gating and the Role of Temperature", "author": [ { "family_name": "O'Neill", "given_name": "Melanie A.", "clpid": "O'Neill-M-A" }, { "family_name": "Becker", "given_name": "Hans-Christian", "clpid": "Becker-H-C" }, { "family_name": "Wan", "given_name": "Chaozhi", "clpid": "Wan-Chaozhi" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Zewail", "given_name": "Ahmed H.", "clpid": "Zewail-A-H" } ], "abstract": "The ultrafast dynamics of electron transfer (ET) between bases in DNA have been determined to elucidate the critical role of base-pair gating on the timescale of the electron transport and the temperature dependence of the rates. ET occurs only through DNA duplexes that adopt a specific, well-coupled alignment of bases (ET-active; see picture). Descriptions of ET dynamics must include fluctuations of DNA bases.", "doi": "10.1002/anie.200352831", "issn": "1433-7851", "publisher": "Wiley", "publication": "Angewandte Chemie International Edition", "publication_date": "2003-12-08", "series_number": "47", "volume": "42", "issue": "47", "pages": "5896-5900" }, { "id": "authors:k527a-mx064", "collection": "authors", "collection_id": "k527a-mx064", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170427-100416986", "type": "article", "title": "Reduction of Ferricyanide by Methylene Blue at a DNA-Modified Rotating-Disk Electrode", "author": [ { "family_name": "Boon", "given_name": "Elizabeth M.", "orcid": "0000-0003-1891-839X", "clpid": "Boon-E-M" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Bhagat", "given_name": "Vipin", "clpid": "Bhagat-V" }, { "family_name": "Nersissian", "given_name": "Migran", "clpid": "Nersissian-M" }, { "family_name": "Wang", "given_name": "Weidong", "clpid": "Wang-Weidong" }, { "family_name": "Hill", "given_name": "Michael G.", "clpid": "Hill-M-G" } ], "abstract": "The electrocatalytic reduction of ferricyanide mediated by methylene blue (MB) at a DNA-modified electrode was investigated by linear-sweep voltammetry at a rotating-gold-disk electrode (RDE). Electrodes were modified with thiol-terminated double-stranded oligonucleotides (sequence:\u2009 5'-SH-AGTACAGTCATCCGC-3') to form densely packed DNA films that blocked the electrochemical reduction of millimolar solutions of ferricyanide at overpotentials greater than 0.5 V. Addition of micromolar concentrations of MB to these solutions, however, resulted in the rapid appearance of catalytic currents as long as the potential was held negative of the formal potential of MB within the DNA film (\u22120.30 V vs SCE). MB binds reversibly to these DNA-modified surfaces, and the adsorption kinetics of MB were determined by a coulometric assay. These data fit a simple Langmuir model with k_1 (adsorption) = 7.5(6) \u00d7 10^5 M^(-1) s^(-1) and k_(-1) (desorption) = 0.043(8) s^(-1). Interestingly, linear-sweep RDE voltammograms recorded in the presence of MB revealed \"peaked\"-shaped i\u2212V traces, which took several seconds to reach their steady-state values. Moreover, the steady-state current density for reduction of Fe(CN)_6^(3-) was found to depend on the bulk concentration of MB in solution. A model is proposed to account for these data in which Fe(CN)_6^(3-) turnover is limited ultimately by the kinetics of MB crossing into and out of the film, and the chemical reaction between Fe(CN)_6^(3-) and reduced MB occurs at the film/solution interface.", "doi": "10.1021/la030266u", "issn": "0743-7463", "publisher": "American Chemical Society", "publication": "Langmuir", "publication_date": "2003-10-28", "series_number": "22", "volume": "19", "issue": "22", "pages": "9255-9259" }, { "id": "authors:03990-yw390", "collection": "authors", "collection_id": "03990-yw390", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:BOOpnas03", "type": "article", "title": "DNA-mediated charge transport for DNA repair", "author": [ { "family_name": "Boon", "given_name": "Elizabeth M.", "orcid": "0000-0003-1891-839X", "clpid": "Boon-E-M" }, { "family_name": "Livingston", "given_name": "Alison L.", "clpid": "Livingston-A-L" }, { "family_name": "Chmiel", "given_name": "Nikolas H.", "clpid": "Chmiel-N-H" }, { "family_name": "David", "given_name": "Sheila S.", "orcid": "0000-0001-5873-7935", "clpid": "David-S-S" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "MutY, like many DNA base excision repair enzymes, contains a [4Fe4S](2+) cluster of undetermined function. Electrochemical studies of MutY bound to a DNA-modified gold electrode demonstrate that the [4Fe4S] cluster of MutY can be accessed in a DNA-mediated redox reaction. Although not detectable without DNA, the redox potential of DNA-bound MutY is approximate to275 mV versus NHE, which is characteristic of HiPiP iron proteins. Binding to DNA is thus associated with a change in [4Fe4S](3+/2+) potential, activating the cluster toward oxidation. Given that DNA charge transport chemistry is exquisitely sensitive to perturbations in base pair structure, such as mismatches, we propose that this redox process of MutY bound to DNA exploits DNA charge transport and provides a DNA signaling mechanism to scan for mismatches and lesions in vivo.", "doi": "10.1073/pnas.2035257100", "pmcid": "PMC240652", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2003-10-28", "series_number": "22", "volume": "100", "issue": "22", "pages": "12543-12547" }, { "id": "authors:k27k9-hak46", "collection": "authors", "collection_id": "k27k9-hak46", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160219-115028115", "type": "article", "title": "DNA Electrochemistry as a Probe of Base Pair Stacking in A-, B-, and Z-Form DNA", "author": [ { "family_name": "Boon", "given_name": "Elizabeth M.", "orcid": "0000-0003-1891-839X", "clpid": "Boon-E-M" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "DNA-mediated charge transport (CT) chemistry is sensitive to DNA structure and base pair stacking. In an electrochemical assay based upon DNA CT, DNA-modified electrode surfaces are used to examine the electrochemical reduction of methylene blue (MB), a small molecule that binds to the DNA film by intercalation. Here electrochemically we probe CT in the three primary conformations of double-stranded nucleic acids, A-, B-, and Z-form DNA. The A-form is examined in the context of a DNA/RNA hybrid duplex and Z-DNA, in duplexes containing d(^(m)CG)_8 sequences at high Mg^(2+) concentrations. We find that both A- and B-DNA support efficient DNA CT as measured by MB reduction in the DNA film; a lower level of reduction is evident with the Z-form film. Furthermore, mismatches incorporated into A-form duplexes, as in B-form duplexes, disrupt MB reduction, thus providing a strategy for mutation detection through testing of RNA transcripts at DNA electrodes.", "doi": "10.1021/bc034139l", "issn": "1043-1802", "publisher": "American Chemical Society", "publication": "Bioconjugate Chemistry", "publication_date": "2003-10-24", "series_number": "6", "volume": "14", "issue": "6", "pages": "1140-1147" }, { "id": "authors:kk2rv-1h804", "collection": "authors", "collection_id": "kk2rv-1h804", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170523-145321462", "type": "article", "title": "Intercalative Stacking: A Critical Feature of DNA Charge-Transport Electrochemistry", "author": [ { "family_name": "Boon", "given_name": "Elizabeth M.", "orcid": "0000-0003-1891-839X", "clpid": "Boon-E-M" }, { "family_name": "Jackson", "given_name": "Nicole M.", "clpid": "Jackson-N-M" }, { "family_name": "Wightman", "given_name": "Matthew D.", "clpid": "Wightman-M-D" }, { "family_name": "Kelley", "given_name": "Shana O.", "orcid": "0000-0003-3360-5359", "clpid": "Kelley-S-O" }, { "family_name": "Hill", "given_name": "Michael G.", "clpid": "Hill-M-G" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "In electrochemistry experiments on DNA-modified electrodes, features of the redox probe that determine efficient charge transport through DNA-modified surfaces have been explored using methylene blue (MB^+) and Ru(NH_3)_6^(3+) as DNA-binding redox probes. The electrochemistry of these molecules is studied as a function of ionic strength to determine the necessity of tight binding to DNA and the number of electrons involved in the redox reaction; on the DNA surface, MB^+ displays 2e^-/1H^+ electrochemistry (pH 7) and Ru(NH^3)_6^(3+) displays 1e^- electrochemistry. We examine also the effect of electrode surface passivation and the effect of the mode (intercalation or electrostatic) of MB^+ and Ru(NH_3)_6^(3+) binding to DNA to highlight the importance of intercalation for reduction by a DNA-mediated charge-transport pathway. Furthermore, in experiments in which MB^+ is covalently linked to the DNA through a \u03c3-bonded tether and the ionic strength is varied, it is demonstrated that intercalative stacking rather than covalent \u03c3-bonding is essential for efficient reduction of MB^+. The results presented here therefore establish that efficient charge transport to the DNA-binding moiety in DNA films requires intercalative stacking and is mediated by the DNA base pair array.", "doi": "10.1021/jp030753i", "issn": "1520-6106", "publisher": "American Chemical Society", "publication": "Journal of Physical Chemistry B", "publication_date": "2003-10-23", "series_number": "42", "volume": "107", "issue": "42", "pages": "11805-11812" }, { "id": "authors:3hq0z-r5c93", "collection": "authors", "collection_id": "3hq0z-r5c93", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150325-155341855", "type": "article", "title": "Electrochemical DNA sensors", "author": [ { "family_name": "Drummond", "given_name": "T. Gregory", "clpid": "Drummond-T-G" }, { "family_name": "Hill", "given_name": "Michael G.", "clpid": "Hill-M-G" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Electrochemistry-based sensors offer sensitivity, selectivity and low cost for the detection of selected DNA sequences or mutated genes associated with human disease. DNA-based electrochemical sensors exploit a range of different chemistries, but all take advantage of nanoscale interactions between the target in solution, the recognition layer and a solid electrode surface. Numerous approaches to electrochemical detection have been developed, including direct electrochemistry of DNA, electrochemistry at polymer-modified electrodes, electrochemistry of DNA-specific redox reporters, electrochemical amplifications with nanoparticles, and electrochemical devices based on DNA-mediated charge transport chemistry.", "doi": "10.1038/nbt873", "issn": "1087-0156", "publisher": "Nature Publishing Group", "publication": "Nature Biotechnology", "publication_date": "2003-10", "series_number": "10", "volume": "21", "issue": "10", "pages": "1192-1199" }, { "id": "authors:r91dv-q9h80", "collection": "authors", "collection_id": "r91dv-q9h80", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160226-135927857", "type": "article", "title": "Long-Range DNA Charge Transport", "author": [ { "family_name": "Delaney", "given_name": "Sarah", "clpid": "Delaney-S" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The stack of base pairs within double helical DNA has been shown to mediate charge transport reactions. Charge transport through DNA can result in chemistry at a distance, yielding oxidative DNA damage at a site remote from the bound oxidant. Since DNA charge transport chemistry depends on coupling within the stacked base pair array, this chemistry is remarkably sensitive to sequence-dependent DNA structure and dynamics. Here, we discuss different features of DNA charge transport chemistry, including applications as well as possible biological consequences and opportunities.", "doi": "10.1021/jo030095y", "issn": "0022-3263", "publisher": "American Chemical Society", "publication": "Journal of Organic Chemistry", "publication_date": "2003-08-22", "series_number": "17", "volume": "68", "issue": "17", "pages": "6475-6483" }, { "id": "authors:pb4v8-77n67", "collection": "authors", "collection_id": "pb4v8-77n67", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160208-162638030", "type": "article", "title": "Fast Back Electron Transfer Prevents Guanine Damage by Photoexcited Thionine Bound to DNA", "author": [ { "family_name": "Dohno", "given_name": "Chikara", "clpid": "Dohno-C" }, { "family_name": "Stemp", "given_name": "Eric D. A.", "orcid": "0000-0003-2098-4214", "clpid": "Stemp-E-D-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The phenothiazinium dye thionine has a high excited state reduction potential and is quenched by guanine on the femtosecond time scale. Here, we show by gel electrophoresis that irradiation of thionine with 599 nm light in the presence of an oligonucleotide duplex does not produce permanent DNA damage. Upon photoexcitation of thionine weakly associated with guanosine-5'-monophosphate, the reduced protonated thionine radical and neutral guanine radical are detected by transient absorption spectroscopy, indicating that the quenching of thionine by guanine occurs via an electron-transfer mechanism. The observation of radical formation without permanent guanine damage indicates that fast back electron transfer plays a critical role in governing the yield of damage by DNA-binding molecules.", "doi": "10.1021/ja036397z", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2003-08-01", "series_number": "32", "volume": "125", "issue": "32", "pages": "9586-9587" }, { "id": "authors:g5k2y-n6j28", "collection": "authors", "collection_id": "g5k2y-n6j28", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160208-152837570", "type": "article", "title": "Rapid Radical Formation by DNA Charge Transport through Sequences Lacking Intervening Guanines", "author": [ { "family_name": "Yoo", "given_name": "Jae", "clpid": "Yoo-Jae" }, { "family_name": "Delaney", "given_name": "Sarah", "clpid": "Delaney-S" }, { "family_name": "Stemp", "given_name": "Eric D. A.", "orcid": "0000-0003-2098-4214", "clpid": "Stemp-E-D-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Using the flash-quench technique to probe DNA charge transport in assemblies containing a tethered ruthenium intercalator, the kinetics and yield of methylindole radical formation as a function of DNA sequence were studied by laser spectroscopy and biochemical methods. In these assemblies, the methylindole moiety serves as an artificial base of low oxidation potential. Hole injection and subsequent formation of the methylindole radical cation were observed at a distance of over 30 \u00c5 at rates \u226510^7 s^(-1) in assemblies containing no guanine bases intervening the ruthenium intercalator and GMG oxidation site. Radical yield was, however, strikingly sensitive to an intervening base mismatch; no significant methylindole radical formation was evident with an intervening AA mismatch. Also critical is the sequence at the injection site; this sequence determines initial hole localization and hence the probability of hole propagation. With guanine rather than inosine near the site of hole injection, decreased yields of radicals and long-range oxidative damage are observed. The presence of the low-energy guanine site in this case serves to localize the hole and therefore diminish charge transport through the base pair stack.", "doi": "10.1021/ja034326u", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2003-06-01", "series_number": "22", "volume": "125", "issue": "22", "pages": "6640-6641" }, { "id": "authors:0g602-r9t36", "collection": "authors", "collection_id": "0g602-r9t36", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:JUNpnas03", "type": "article", "title": "A rhodium(III) complex for high-affinity DNA base-pair mismatch recognition", "author": [ { "family_name": "Junicke", "given_name": "Henrik", "clpid": "Junicke-H" }, { "family_name": "Hart", "given_name": "Jonathan R.", "clpid": "Hart-J-R" }, { "family_name": "Kisko", "given_name": "Jennifer", "clpid": "Kisko-J" }, { "family_name": "Glebov", "given_name": "Oleg", "clpid": "Glebov-O" }, { "family_name": "Kirsch", "given_name": "Ilan R.", "clpid": "Kirsch-I-R" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "A rhodium(III) complex, rac-[Rh(bpy)(2)phzi](3+) (bpy, 2,2'-bipyridine; phzi, benzo[a]phenazine-5,6-quinone diimine) has been designed as a sterically demanding intercalator targeted to destabilized mismatched sites in double-helical DNA. The complex is readily synthesized by condensation of the phenazine quinone with the corresponding diammine complex. Upon photoactivation, the complex promotes direct strand scission at single-base mismatch sites within the DNA duplex. As with the parent mismatch-specific reagent, [Rh(bpy)(2)(chrysi)](3+) [chrysene-5,6-quinone diimine (chrysi)], mismatch selectivity depends on the helix destabilization associated with mispairing. Unlike the parent chrysi complex, the phzi analogue binds and cleaves with high affinity and efficiency. The specific binding constants for CA, CC, and CT mismatches within a 31-mer oligonucleotide duplex are 0.3, 1, and 6 x 10(7) M-1, respectively; site-specific photocleavage is evident at nanomolar concentrations. Moreover, the specificity, defined as the ratio in binding affinities for mispaired vs. well paired sites, is maintained. The increase in affinity is attributed to greater stability in the mismatched site associated with stacking by the heterocyclic aromatic ligand. The high-affinity complex is also applied in the differential cleavage of DNA obtained from cell lines deficient in mismatch repair vs. those proficient in mismatch repair. Agreement is found between photocleavage by the mismatch-specific probes and deficiency in mismatch repair. This mismatch-specific targeting, therefore, offers a potential strategy for new chemotherapeutic design.", "doi": "10.1073/pnas.0537194100", "pmcid": "PMC152991", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2003-04-01", "series_number": "7", "volume": "100", "issue": "7", "pages": "3737-3742" }, { "id": "authors:yxw13-gax31", "collection": "authors", "collection_id": "yxw13-gax31", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:ONEpnas02", "type": "article", "title": "Effects of strand and directional asymmetry on base-base coupling and charge transfer in double-helical DNA", "author": [ { "family_name": "O'Neill", "given_name": "Melanie A.", "clpid": "O'Neill-M-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Mechanistic models of charge transfer (CT) in macromolecules often focus on CT energetics and distance as the chief parameters governing CT rates and efficiencies. However, in DNA, features unique to the DNA molecule, in particular, the structure and dynamics of the DNA base stack, also have a dramatic impact on CT. Here we probe the influence of subtle structural variations on base-base CT within a DNA duplex by examining photoinduced quenching of 2-aminopurine (Ap) as a result of hole transfer (HT) to guanine (G). Photoexcited Ap is used as a dual reporter of variations in base stacking and CT efficiency. Significantly, the unique features of DNA, including the strandedness and directional asymmetry of the double helix, play a defining role in CT efficiency. For an (AT)(n) bridge, the orientation of the base pairs is critical; the yield of intrastrand HT is markedly higher through (A)n compared with (T)(n) bridges, whereas HT via intrastrand pathways is more efficient than through interstrand pathways. Remarkably, for reactions through the same DNA bridge, over the same distance, and with the same driving force, HT from photoexcited Ap to G in the 5' to 3' direction is more efficient and less dependent on distance than HT from 3' to 5'. We attribute these differences in HT efficiency to variations in base-base coupling within the DNA assemblies. Thus base-base coupling is a critical parameter in DNA CT and strongly depends on subtle structural nuances of duplex DNA.", "doi": "10.1073/pnas.012669599", "pmcid": "PMC139180", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2002-12-24", "series_number": "26", "volume": "99", "issue": "26", "pages": "16543-16550" }, { "id": "authors:a58dz-38t89", "collection": "authors", "collection_id": "a58dz-38t89", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160229-085221976", "type": "article", "title": "2-Aminopurine: A Probe of Structural Dynamics and Charge Transfer in DNA and DNA:RNA Hybrids", "author": [ { "family_name": "O'Neill", "given_name": "Melanie A.", "clpid": "O'Neill-M-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Spectroscopic techniques are employed to probe relationships between structural dynamics and charge transfer (CT) efficiency in DNA duplexes and DNA:RNA hybrids containing photoexcited 2-aminopurine (Ap*). To better understand the variety of interactions and reactions, including CT, between Ap* and DNA, the fluorescence behavior of Ap* is investigated in a full series of redox-inactive as well as redox-active assemblies. Thus, Ap* is developed as a dual reporter of structural dynamics and base\u2212base CT reactions in nucleic acid duplexes. CD, NMR, and thermal denaturation profiles are consistent with the family of DNA duplexes adopting a distinct conformation versus the DNA:RNA hybrids. Fluorescence measurements establish that the d(A)\u2212r(U) tract of the DNA:RNA hybrid exhibits enhanced structural flexibility relative to that of the d(A)\u2212d(T) tract of the DNA duplexes. The yield of CT from either G or 7-deazaguanine (Z) to Ap* in the assemblies was determined by comparing Ap* emission in redox-active G- or Z-containing duplexes to otherwise identical duplexes in which the G or Z is replaced by inosine (I), the redox-inactive nucleoside analogue. Investigations of CT not only demonstrate efficient intrastrand base\u2212base CT in the DNA:RNA hybrids but also reveal a distance dependence of CT yield that is more shallow through the d(A)\u2212r(U) bridge of the A-form DNA:RNA hybrids than through the d(A)\u2212d(T) bridge of the B-form DNA duplexes. The shallow distance dependence of intrastrand CT in DNA:RNA hybrids correlates with the increased conformational flexibility of bases within the hybrid duplexes. Measurements of interstrand base\u2212base CT provide another means to distinguish between the A- and B-form helices. Significantly, in the A-form DNA:RNA hybrids, a similar distance dependence is obtained for inter- and intrastrand reactions, while, in B-DNA, a more shallow distance dependence is evident with interstrand CT reactions. These observations are consistent with evaluations of intra- and interstrand base overlap in A- versus B-form duplexes. Overall, these data underscore the sensitivity of CT chemistry to nucleic acid structure and structural dynamics.", "doi": "10.1021/ja0208198", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2002-11-06", "series_number": "44", "volume": "124", "issue": "44", "pages": "13053-13066" }, { "id": "authors:dnfxd-eew66", "collection": "authors", "collection_id": "dnfxd-eew66", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:BHAnar02", "type": "article", "title": "1H NMR determination of base-pair lifetimes in oligonucleotides containing single base mismatches", "author": [ { "family_name": "Bhattacharya", "given_name": "Pratip K.", "clpid": "Bhattacharya-P-K" }, { "family_name": "Cha", "given_name": "Julie", "clpid": "Cha-Julie" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Proton nuclear magnetic resonance (NMR) spectroscopy is employed to characterize the kinetics of base-pair opening in a series of 9mer duplexes containing different single base mismatches. The imino protons from the different mismatched, as well as fully matched, duplexes are assigned from the imino-imino region in the WATERGATE NOESY spectra. The exchange kinetics of the imino protons are measured from selective longitudinal relaxation times. In the limit of infinite exchange catalyst concentration, the exchange times of the mismatch imino protons extrapolate to much shorter lifetimes than are commonly observed for an isolated GC base pair. Different mismatches exhibit different orders of base-pair lifetimes, e.g. a TT mismatch has a shorter base-pair lifetime than a GG mismatch. The effect of the mismatch was observed up to a distance of two neighboring base pairs. This indicates that disruption in the duplex caused by the mismatch is quite localized. The overall order of base-pair lifetimes in the selected sequence context of the base pair is GC > GG > AA > CC > AT > TT. Interestingly, the fully matched AT base pair has a shorter base-pair lifetime relative to many of the mismatches. Thus, in any given base pair, the exchange lifetime can exhibit a strong dependence on sequence context. These findings may be relevant to the way mismatch recognition is accomplished by proteins and small molecules.", "doi": "10.1093/nar/gkf601", "pmcid": "PMC135820", "issn": "0305-1048", "publisher": "Oxford University Press", "publication": "Nucleic Acids Research", "publication_date": "2002-11-01", "series_number": "21", "volume": "30", "issue": "21", "pages": "4740-4750" }, { "id": "authors:ptgee-n7111", "collection": "authors", "collection_id": "ptgee-n7111", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160210-155329163", "type": "article", "title": "DNA Cross-Linking with Metallointercalator\u2212Peptide Conjugates", "author": [ { "family_name": "Copeland", "given_name": "Kimberly D.", "clpid": "Copeland-K-D" }, { "family_name": "Lueras", "given_name": "Alexis M. K.", "clpid": "Lueras-A-M-K" }, { "family_name": "Stemp", "given_name": "Eric D. A.", "orcid": "0000-0003-2098-4214", "clpid": "Stemp-E-D-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Short peptides have been tethered to a DNA\u2212intercalating ruthenium complex to create a photoactivated cross-linking reagent. The ruthenium complex, [Ru(phen)(bpy')(dppz)]^(2+) (phen = 1,10-phenanthroline, bpy' = 4-(butyric acid)-4'-methyl-2,2'-bipyridine, and dppz = dipyridophenazine), delivers the peptide to DNA and initiates the cross-linking reaction by oxidizing DNA upon irradiation in the presence of an oxidative quencher. The tethered peptide, only five to six residues in length, forms cross-links with the oxidized site in DNA. Cross-linking was detected and studied by gel electrophoresis and through spectroscopic measurements. The ruthenium\u2212peptide complex is luminescent when bound to DNA, and the binding constants for several intercalator\u2212peptide conjugates were determined by luminescence titration. The composition of the peptide affects both binding affinity and the extent of cross-linking. The greatest amounts of cross-linking were observed with tethered peptides that contained positively charged residues, either lysine or arginine. To test the impact of individual residues on cross-linking, the central residue in a 5-mer peptide was substituted with seven different amino acids. Though mutation of this position had only a small effect on the extent of cross-linking, it was discovered that peptides containing Trp or Tyr gave a distinctive pattern of products in gels. In experiments using the untethered peptide and ruthenium complex, it was determined that delivery of the peptide by the ruthenium intercalator is not essential for cross-linking; peptide attachment to the metal complex can constrain cross-linking. Importantly, the cross-linking adducts produced with ruthenium\u2212peptide conjugates are luminescent and thus provide a luminescent cross-linking probe for DNA.", "doi": "10.1021/bi020407b", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "2002-10-01", "series_number": "42", "volume": "41", "issue": "42", "pages": "12785-12797" }, { "id": "authors:e3ksh-sgy19", "collection": "authors", "collection_id": "e3ksh-sgy19", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160210-154230344", "type": "article", "title": "An Electrochemical Probe of DNA Stacking in an Antisense Oligonucleotide Containing a C3'-endo-Locked Sugar", "author": [ { "family_name": "Boon", "given_name": "Elizabeth M.", "orcid": "0000-0003-1891-839X", "clpid": "Boon-E-M" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Pradeepkumar", "given_name": "Pushpangadan I.", "clpid": "Pradeepkumar-P-I" }, { "family_name": "Isaksson", "given_name": "Johan", "clpid": "Isaksson-J" }, { "family_name": "Petit", "given_name": "Catherine", "clpid": "Petit-C" }, { "family_name": "Chattopadhyaya", "given_name": "Jyoti", "clpid": "Chattopadhyaya-J" } ], "abstract": "The preferred base-stacking orientation of a conformationally constrained nucleotide (3\u2032-endo-locked) within DNA/DNA and DNA/RNA duplexes (see picture) was probed by charge transport through DNA-modified gold electrode surfaces. The conformation of the sugar is seen to sensitively determine the local stacking of the duplex. These results illustrate the utility of DNA-mediated charge transport through DNA-modified surfaces in characterizing small perturbations in DNA stacking and structure.", "doi": "10.1002/1521-3773(20020916)41:18<3402::AID-ANIE3402>3.0.CO;2-6", "issn": "1433-7851", "publisher": "Wiley", "publication": "Angewandte Chemie International Edition", "publication_date": "2002-09-16", "series_number": "18", "volume": "41", "issue": "18", "pages": "3402-3405" }, { "id": "authors:scvxf-3e780", "collection": "authors", "collection_id": "scvxf-3e780", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160210-155947915", "type": "article", "title": "DNA Mediated Charge Transport: Characterization of a DNA Radical Localized at an Artificial Nucleic Acid Base", "author": [ { "family_name": "Pascaly", "given_name": "Matthias", "clpid": "Pascaly-M" }, { "family_name": "Yoo", "given_name": "Jae", "clpid": "Yoo-Jae" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "DNA assemblies containing 4-methylindole incorporated as an artificial base provide a chemically well-defined system in which to explore the oxidative charge transport process in DNA. Using this artificial base, we have combined transient absorption and EPR spectroscopies as well as biochemical methods to test experimentally current mechanisms for DNA charge transport. The 4-methylindole radical cation intermediate has been identified using both EPR and transient absorption spectroscopies in oxidative flash-quench studies using a dipyridophenazine complex of ruthenium as the intercalating oxidant. The 4-methylindole radical cation intermediate is particularly amenable to study given its strong absorptivity at 600 nm and EPR signal measured at 77 K with g = 2.0065. Both transient absorption and EPR spectroscopies show that the 4-methylindole is well incorporated in the duplex; the data also indicate no evidence of guanine radicals, given the low oxidation potential of 4-methylindole relative to the nucleic acid bases. Biochemical studies further support the irreversible oxidation of the indole moiety and allow the determination of yields of irreversible product formation. The construction of these assemblies containing 4-methylindole as an artificial base is also applied in examining long-range charge transport mediated by the DNA base pair stack as a function of intervening distance and sequence. The rate of formation of the indole radical cation is \u2265107 s-1 for different assemblies with the ruthenium positioned 17\u221237 \u00c5 away from the methylindole and with intervening A\u2212T base pairs primarily composing the bridge. In these assemblies, methylindole radical formation at a distance is essentially coincident with quenching of the ruthenium excited state to form the Ru(III) oxidant; charge transport is not rate limiting over this distance regime. The measurements here of rates of radical cation formation establish that a model of G-hopping and AT-tunneling is not sufficient to account for DNA charge transport. Instead, these data are viewed mechanistically as charge transport through the DNA duplex primarily through hopping among well stacked domains of the helix defined by DNA sequence and dynamics.", "doi": "10.1021/ja0202210", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2002-08-01", "series_number": "31", "volume": "124", "issue": "31", "pages": "9083-9092" }, { "id": "authors:qs3vy-k1s68", "collection": "authors", "collection_id": "qs3vy-k1s68", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160210-160315353", "type": "article", "title": "DNA-Mediated Charge Transport as a Probe of MutY/DNA Interaction", "author": [ { "family_name": "Boon", "given_name": "Elizabeth M.", "orcid": "0000-0003-1891-839X", "clpid": "Boon-E-M" }, { "family_name": "Pope", "given_name": "Mary Ann", "clpid": "Pope-M-A" }, { "family_name": "Williams", "given_name": "Scott D.", "clpid": "Williams-S-D" }, { "family_name": "David", "given_name": "Sheila S.", "orcid": "0000-0001-5873-7935", "clpid": "David-S-S" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "MutY is an Escherichia coli DNA repair enzyme that binds to 8-oxo-G:A and G:A mismatches and catalyzes the deglycosylation of the mismatched 2'-deoxyadenosine. We have applied DNA-mediated charge transport to probe the interaction of MutY with its DNA substrate. Oligonucleotides synthesized with a tethered rhodium intercalator and guanine doublets placed before and after the MutY binding site are used to assay for base flipping activity by MutY. On the basis of this assay, we find no evidence that MutY uses progressive base flipping as a means to find its binding site; protein binding does not perturb long-range DNA charge transport. DNA-mediated charge transport can be utilized to promote protein\u2212DNA cross-linking from a distance. Long-range oxidation of 8-oxo-G within the MutY binding site using tethered rhodium intercalators promoted cross-linking and yielded information on MutY side chains that interact with this base. On the basis of photooxidative cross-linking of the wild type but not K142A mutant, it is evident that, within the protein complex, lysine 142 makes important contacts with 8-oxo-G.", "doi": "10.1021/bi012068c", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "2002-07-01", "series_number": "26", "volume": "41", "issue": "26", "pages": "8464-8470" }, { "id": "authors:cjbw9-89z96", "collection": "authors", "collection_id": "cjbw9-89z96", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160127-111126226", "type": "article", "title": "Charge transport in DNA", "author": [ { "family_name": "Boon", "given_name": "Elizabeth M.", "orcid": "0000-0003-1891-839X", "clpid": "Boon-E-M" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The base pair stack within double helical DNA provides an effective medium for charge transport. The DNA \u03c0-stack mediates oxidative DNA damage over long molecular distances in a reaction that is exquisitely sensitive to the sequence-dependent conformation and dynamics of DNA. A mixture of tunneling and hopping mechanisms have been proposed to account for this long-range chemistry, which is gated by dynamical variations within the stack. Electrochemical sensors have also been developed, based upon the sensitivity of DNA charge transport to base pair stacking, and these sensors provide a completely new approach to diagnosing single base mismatches in DNA and monitoring protein\u2013DNA interactions electrically. DNA charge transport, furthermore, may play a role within the cell and, indeed, oxidative damage to DNA from a distance has been demonstrated in the cell nucleus. As a result, the biological consequences of and opportunities for DNA-mediated charge transport now require consideration.", "doi": "10.1016/S0959-440X(02)00327-5", "issn": "0959-440X", "publisher": "Elsevier", "publication": "Current Opinion in Structural Biology", "publication_date": "2002-06-01", "series_number": "3", "volume": "12", "issue": "3", "pages": "320-329" }, { "id": "authors:xh0av-xsb18", "collection": "authors", "collection_id": "xh0av-xsb18", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160209-164250806", "type": "article", "title": "Oxidative Damage by Ruthenium Complexes Containing the Dipyridophenazine Ligand or Its Derivatives: A Focus on Intercalation", "author": [ { "family_name": "Delaney", "given_name": "Sarah", "clpid": "Delaney-S" }, { "family_name": "Pascaly", "given_name": "Matthias", "clpid": "Pascaly-M" }, { "family_name": "Bhattacharya", "given_name": "Pratip K.", "clpid": "Bhattacharya-P-K" }, { "family_name": "Han", "given_name": "Koun", "clpid": "Han-Koun" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Interactions with DNA by a family of ruthenium(II) complexes bearing the dppz (dppz = dipyridophenazine) ligand or its derivatives have been examined. The complexes include Ru(bpy)_2(dppx)^(2+) (dppx = 7,8-dimethyldipyridophenazine), Ru(bpy)_2(dpq)^(2+) (dpq = dipyridoquinoxaline), and Ru(bpy)_2(dpqC)^(2+) (dpqC = dipyrido-6,7,8,9-tetrahydrophenazine). Their ground and excited state oxidation/reduction potentials have been determined using cyclic voltammetry and fluorescence spectroscopy. An intercalative binding mode has been established on the basis of luminescence enhancements in the presence of DNA, excited state quenching, fluorescence polarization values, and enantioselectivity. Oxidative damage to DNA by these complexes using the flash/quench method has been examined. A direct correlation between the amount of guanine oxidation obtained via DNA charge transport and the strength of intercalative binding was observed. Oxidative damage to DNA through DNA-mediated charge transport was also compared directly for two DNA-tethered ruthenium complexes. One contains the dppz ligand that binds avidly by intercalation, and the other contains only bpy ligands, that, while bound covalently, can only associate with the base pairs through groove binding. Long range oxidative damage was observed only with the tethered, intercalating complex. These results, taken together, all support the importance of close association and intercalation for DNA-mediated charge transport. Electronic access to the DNA base pairs, provided by intercalation of the oxidant, is a prerequisite for efficient charge transport through the DNA \u03c0-stack.", "doi": "10.1021/ic0111738", "issn": "0020-1669", "publisher": "American Chemical Society", "publication": "Inorganic Chemistry", "publication_date": "2002-04-01", "series_number": "7", "volume": "41", "issue": "7", "pages": "1966-1974" }, { "id": "authors:q72hr-6dh59", "collection": "authors", "collection_id": "q72hr-6dh59", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160129-080804224", "type": "article", "title": "Oxidative Charge Transport through DNA in Nucleosome Core Particles", "author": [ { "family_name": "N\u00fa\u00f1ez", "given_name": "Megan E.", "clpid": "N\u00fa\u00f1ez-M-E" }, { "family_name": "Noyes", "given_name": "Katherine T.", "clpid": "Noyes-K-T" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Eukaryotic DNA is packaged into nucleosomes, made up of 146 bp of DNA wrapped around a core of histone proteins. We used photoexcited rhodium intercalators to explore DNA charge transport within these assemblies. Although histone proteins inhibit intercalation of the rhodium complex within the core particle, they do not prevent 5\u2032-GG-3\u2032 oxidation, the signature of oxidative charge transport through DNA. Moreover, using rhodium intercalators tethered to the 5\u2032 terminus of the DNA, we found that guanine bases within the nucleosome can be oxidized from a distance of 24 bp. Histone binding did not affect the pattern and extent of this oxidation. Therefore, although the structure of the nucleosome core particle generally protects DNA from damage by solution-borne molecules, packaging within the nucleosome does not protect DNA from charge transfer damage through the base pair stack.", "doi": "10.1016/S1074-5521(02)00121-7", "issn": "1074-5521", "publisher": "Elsevier", "publication": "Chemistry and Biology", "publication_date": "2002-04", "series_number": "4", "volume": "9", "issue": "4", "pages": "403-415" }, { "id": "authors:1znd9-kgz08", "collection": "authors", "collection_id": "1znd9-kgz08", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160208-152444728", "type": "article", "title": "The Effect of Varied Ion Distributions on Long-Range DNA Charge Transport", "author": [ { "family_name": "Williams", "given_name": "Tashica T.", "clpid": "Williams-T-T" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Long-range oxidative damage to DNA was utilized as a probe to delineate the effects of different ion distributions on DNA charge transport. DNA assemblies were constructed, containing a tethered rhodium intercalating photooxidant, spatially separated from two 5'-GG-3' sites of oxidative damage, with either an A_6-tract or a mixed DNA sequence intervening between the guanine doublets; the extent of charge transport was assessed through measurements of the ratio of yields of damage at the guanine doublet distal versus that proximal to the metal binding site. The distal/proximal damage ratios were compared after photooxidation of otherwise identical Rh-tethered assemblies, except for ^(32)P-labeling either at the 5'- or 3'-end; this labeling difference corresponds, in the absence of charge neutralization by condensed counterions, to a shift in negative charge from one end of the duplex to the other. Both with assemblies containing the mixed sequence and the A_6-tract, we observed that moving the negative charges to the proximal end of the duplex significantly decreased hole transport to the distal end. We propose that these results reflect variations in the thermodynamic potential at the proximal and distal guanine sites because of the change in charges at the termini of the oligomer. High values for the internal dielectric constant of the stacked base pairs are suggested by these data. Hence, the longitudinal polarizability of DNA may be important to consider in mechanisms for long-range DNA charge transport.", "doi": "10.1021/ja012217e", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2002-03-01", "series_number": "9", "volume": "124", "issue": "9", "pages": "1840-1841" }, { "id": "authors:znbj3-ay266", "collection": "authors", "collection_id": "znbj3-ay266", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150401-111610690", "type": "article", "title": "An electrical probe of protein-DNA interactions on DNA-modified surfaces", "author": [ { "family_name": "Boon", "given_name": "Elizabeth M.", "orcid": "0000-0003-1891-839X", "clpid": "Boon-E-M" }, { "family_name": "Salas", "given_name": "Julia E.", "clpid": "Salas-J-E" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "DNA charge transport chemistry is found to provide a sensitive method for probing protein-dependent changes in DNA structure and enzymatic reactions. Here we describe the development of an electrochemical assay of protein binding to DNA-modified electrodes based upon the detection of associated perturbations in DNA base stacking. Gold electrode surfaces that were modified with loosely packed DNA duplexes, covalently crosslinked to a redox-active intercalator and containing the binding site of the test protein, were constructed. Charge transport through DNA as a function of protein binding was then assayed. Substantial attenuation in current is seen in the presence of the base-flipping enzymes HhaI methylase and uracil DNA glycosylase, as well as with TATA-binding protein. When restriction endonuclease PvuII (R.PvuII) binds to its methylated target, little base-stacking perturbation occurs and little diminution in current flow is observed. Importantly, the kinetics of restriction by R.PvuII of its nonmethylated target is also easily monitored electrochemically. This approach should be generally applicable to assaying protein\u2013DNA interactions and reactions on surfaces.", "doi": "10.1038/nbt0302-282", "issn": "1087-0156", "publisher": "Nature Publishing Group", "publication": "Nature Biotechnology", "publication_date": "2002-03", "series_number": "3", "volume": "20", "issue": "3", "pages": "282-286" }, { "id": "authors:xp5p8-s7526", "collection": "authors", "collection_id": "xp5p8-s7526", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160209-161227098", "type": "article", "title": "DNA Hydrolysis and Oxidative Cleavage by Metal-Binding Peptides Tethered to Rhodium Intercalators", "author": [ { "family_name": "Copeland", "given_name": "Kimberly D.", "clpid": "Copeland-K-D" }, { "family_name": "Fitzsimons", "given_name": "Marilena P.", "clpid": "Fitzsimons-M-P" }, { "family_name": "Houser", "given_name": "Robert P.", "clpid": "Houser-R-P" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "With the goal of developing artificial nucleases for DNA hydrolysis, metal-coordinating peptides have been tethered to a DNA-intercalating rhodium complex to deliver metal ions to the sugar\u2212phosphate backbone. The intercalator, [Rh(phi)_2bpy']Cl_3 [phi = 9,10-phenanthrenequinone diimine; bpy' = 4-(butyric acid)-4'-methyl-2,2'-bipyridine], provides DNA binding affinity, and a metal-binding peptide contributes reactivity. This strategy for DNA hydrolysis is a general one, and zinc(II)-promoted cleavage has been demonstrated for two widely different tethered metallopeptides. An intercalator coupled with a de novo-designed \u03b1 helix containing two histidine residues has been demonstrated to cleave both supercoiled plasmid and linear DNA substrates. Mutation of this peptide confirms that the two histidine residues are essential for Zn^(2+) binding and cleavage. Zinc(II)-promoted cleavage of supercoiled plasmid has also been demonstrated with an intercalator\u2212peptide conjugate containing acidic residues and modeled after the active site of the BamHI endonuclease. Other redox-active metals, such as copper, have been delivered to DNA with our intercalator\u2212peptide conjugates to effect oxidative chemistry. Copper cleavage experiments and photocleavage experiments with [Rh(phi)_2bpy']^(3+) complement the hydrolysis studies and provide structural information about the interactions between the tethered metallopeptides and DNA. Variation of the rhodium intercalator was also explored, but with a mismatch-specific intercalator, no site-specific hydrolysis was found. These experiments, in which the peptide, the metal cation, and the intercalator components of the conjugate are each varied, illustrate some of the issues involved in creating an artificial nuclease with DNA intercalators and metallopeptides.", "doi": "10.1021/bi011793k", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "2002-01-01", "series_number": "1", "volume": "41", "issue": "1", "pages": "343-356" }, { "id": "authors:yh943-g2n97", "collection": "authors", "collection_id": "yh943-g2n97", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160127-120857206", "type": "article", "title": "Detection of DNA Base Mismatches Using DNA Intercalators", "author": [ { "family_name": "Boon", "given_name": "Elizabeth M.", "orcid": "0000-0003-1891-839X", "clpid": "Boon-E-M" }, { "family_name": "Kisko", "given_name": "Jennifer L.", "clpid": "Kisko-J-L" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The most prevalent mechanisms leading to mutations in DNA are direct mis-incorporation of bases during replication and sustained chemical damage. Under normal circumstances, the cell corrects these problems using DNA polymerase proofreading mechanisms as well as the complex repair machinery of the cell. In certain tissues that contain mismatch repair deficiencies, DNA mispairs may accumulate.1, 2, 3, 4 and 5 Even in healthy cells, however, mismatches and lesions can sometimes go unchecked, resulting in permanent alterations in the gene sequence for subsequent generations. Identification of genetic variations (single-nucleotide polymorphisms, SNPs) among individuals and populations has implications in understanding human disease and treatment, as well as the interaction of the environment and multiple genes during evolution.6 Once these SNPs are identified and understood, rapid and reliable detection of them will be critical for the study, diagnosis, and treatment of genetically linked disease.", "doi": "10.1016/S0076-6879(02)53073-1", "issn": "0076-6879", "publisher": "Academic Press", "publication": "Methods in Enzymology", "publication_date": "2002", "volume": "353", "pages": "506-522" }, { "id": "authors:zv9pj-39z60", "collection": "authors", "collection_id": "zv9pj-39z60", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160209-160226905", "type": "article", "title": "Evidence for DNA Charge Transport in the Nucleus", "author": [ { "family_name": "N\u00fa\u00f1ez", "given_name": "Megan E.", "clpid": "N\u00fa\u00f1ez-M-E" }, { "family_name": "Holmquist", "given_name": "Gerald P.", "clpid": "Holmquist-G-P" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Oxidative damage to DNA bases in isolated HeLa nuclei occurs upon treatment with rhodium intercalators and photoactivation. Oxidation occurs preferentially at the 5'-guanine of 5'-GG-3' sites, indicative of base damage by DNA-mediated charge transfer chemistry. Moreover, oxidative damage occurs at protein-bound sites which are inaccessible to rhodium. Thus, on transcriptionally active DNA within the cell nucleus, DNA-mediated charge transport leads to base damage from a distance, and direct interaction of an oxidant is not necessary to generate a base lesion at a specific site. These observations require consideration in designing new chemotherapeutics and in understanding cellular mechanisms for DNA damage and repair.", "doi": "10.1021/bi011560t", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "2001-10-01", "series_number": "42", "volume": "40", "issue": "42", "pages": "12465-12471" }, { "id": "authors:h21s9-twr30", "collection": "authors", "collection_id": "h21s9-twr30", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160129-155405893", "type": "article", "title": "Synthesis and Spectroelectrochemistry of Ir(bpy)(phen)(phi)^(3+), a Tris(heteroleptic) Metallointercalator", "author": [ { "family_name": "Stinner", "given_name": "Christine", "clpid": "Stinner-C" }, { "family_name": "Wightman", "given_name": "Matthew D.", "clpid": "Wightman-M-D" }, { "family_name": "Kelley", "given_name": "Shana O.", "orcid": "0000-0003-3360-5359", "clpid": "Kelley-S-O" }, { "family_name": "Hill", "given_name": "Michael G.", "clpid": "Hill-M-G" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "A tris(heteroleptic) phenanthrenequinone diimine (phi) complex of Ir(III), Ir(bpy)(phen)(phi)^(3+), was synthesized through the stepwise introduction of three different bidentate ligands, and the \u039b- and \u0394-enantiomers were resolved and characterized by CD spectroscopy. Like other phi complexes, this tris(heteroleptic) iridium complex binds avidly to DNA by intercalation. Electrochemical studies show that Ir(bpy)(phen)(phi)^(3+) undergoes a reversible one-electron reduction at E_0 = -0.025 V in 0.1 M TBAH/DMF (versus Ag/AgCl), and spectroelectrochemical studies indicate that this reduction is centered on the phi ligand. The EPR spectrum of electrochemically generated Ir(bpy)(phen)(phi)^(2+) is consistent with a phi-based radical. The electrochemistry of Ir(bpy)(phen)(phi)^(3+) was also probed at a DNA-modified electrode, where a DNA binding affinity of K = 1.1 x 10^6 M^(-1) was measured. In contrast to Ir(bpy)(phen)(phi)^(3+) free in solution, the complex bound to DNA undergoes a concerted two-electron reduction, to form a diradical species. On the basis of UV-visible and EPR spectroscopies, it is found that disproportionation of electrochemically generated Ir(bpy)(phen) (phi)^(2+) occurs upon DNA binding. These results underscore the rich redox chemistry associated with metallointercalators bound to DNA.", "doi": "10.1021/ic010376t", "issn": "0020-1669", "publisher": "American Chemical Society", "publication": "Inorganic Chemistry", "publication_date": "2001-09-24", "series_number": "20", "volume": "40", "issue": "20", "pages": "5245-5250" }, { "id": "authors:phn0q-kb934", "collection": "authors", "collection_id": "phn0q-kb934", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170427-102105912", "type": "article", "title": "Morphology of 15-mer Duplexes Tethered to Au(111) Probed Using Scanning Probe Microscopy", "author": [ { "family_name": "Sam", "given_name": "Mui", "clpid": "Sam-Mui" }, { "family_name": "Boon", "given_name": "Elizabeth M.", "orcid": "0000-0003-1891-839X", "clpid": "Boon-E-M" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Hill", "given_name": "Michael G.", "clpid": "Hill-M-G" }, { "family_name": "Spain", "given_name": "Eileen M.", "clpid": "SpainE-M" } ], "abstract": "The long-range film structure of 15 base pair, thiol-derivatized duplexes tethered through single 3' and 5' linkages to a Au(111) surface is measured via scanning probe microscopy. Film morphology of the 3' linked duplexes differs from that of its 5' counterpart as observed by scanning probe microscopy in contact mode under buffer solution. No structural features are distinguished in a film formed with the 5' linked duplexes as measured with either a bare silicon nitride or chemically modified probe. However, a distinct pattern in the film structure of the 3' linked duplexes is measured with a chemically modified, hydrophobic tip. Small changes in linker orientation can greatly affect DNA film structure, and a hypothesis for the self-assembly mechanism of the 3' linked duplexes is presented. Factors such as linker placement and composition must be considered in comparing DNA microarrays formed with different tethering methods.", "doi": "10.1021/la010496d", "issn": "0743-7463", "publisher": "American Chemical Society", "publication": "Langmuir", "publication_date": "2001-09-18", "series_number": "19", "volume": "17", "issue": "19", "pages": "5727-5730" }, { "id": "authors:g71hq-6jg67", "collection": "authors", "collection_id": "g71hq-6jg67", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160208-152036536", "type": "article", "title": "Influence of Intervening Mismatches on Long-Range Guanine Oxidation in DNA Duplexes", "author": [ { "family_name": "Bhattacharya", "given_name": "Pratip K.", "clpid": "Bhattacharya-P-K" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "A systematic investigation of the efficiency of oxidative damage at guanine residues through long-range charge transport was carried out as a function of intervening base mismatches. A series of DNA oligonucleotides were synthesized that incorporate a ruthenium intercalator linked covalently to the 5' terminus of one strand and containing two 5'-GG-3' sites in the complementary strand. Single base mismatches were introduced between the two guanine doublet steps, and the efficiency of transport through the mismatches was determined through measurements of the ratio of oxidative damage at the guanine doublets distal versus proximal to the intercalated ruthenium oxidant. Differing relative extents of guanine oxidation were observed for the different mismatches. The damage ratio of oxidation at the distal versus proximal site for the duplexes containing different mismatches varies in the order GC \u223c GG \u223c GT \u223c GA > AA > CC \u223c TT \u223c CA \u223c CT. For all assemblies, damage found with the \u0394-Ru diastereomer was found to be greater than with the \u039b-diastereomer. The extent of distal/proximal guanine oxidation in different mismatch-containing duplexes was compared with the helical stability of the duplexes, electrochemical data for intercalator reduction on different mismatch-containing DNA films, and base-pair lifetimes for oligomers containing the different mismatches derived from ^1H NMR measurements of the imino proton exchange rates. While a clear correlation is evident both with helix stability and electrochemical data monitoring reduction of an intercalator through DNA films, damage ratios correlate most closely with base-pair lifetimes. Competitive hole trapping at the mismatch site does not appear to be a key factor governing the efficiency of transport through the mismatch. These results underscore the importance of base dynamics in modulating long-range charge transport through the DNA base-pair stack.", "doi": "10.1021/ja010996t", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2001-09-01", "series_number": "36", "volume": "123", "issue": "36", "pages": "8649-8656" }, { "id": "authors:23r4j-ftj05", "collection": "authors", "collection_id": "23r4j-ftj05", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160209-160654855", "type": "article", "title": "Long-Range Oxidative Damage in DNA/RNA Duplexes", "author": [ { "family_name": "Odom", "given_name": "Duncan T.", "clpid": "Odom-D-T" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Oxidative damage as a result of DNA-mediated long-range charge transport occurs readily and at high yield in duplex DNA, and it is of interest whether similar damage can occur in duplex oligonucleotides that include both ribo- and deoxyribonucleotides. Assemblies containing RNA and mixed RNA\u00b7DNA strands were constructed containing tethered ethidium as a photooxidant. In photooxidation experiments, long-range oxidative damage to the ribose-containing strand of the oligonucleotide duplexes was examined. Hole injection by photoexcited ethidium followed by radical migration to oxidatively susceptible guanines afforded significant damage on ribose-containing strands at long range (\u223c35 \u00c5). This damage does not differ substantially in yield and location from that found in B-DNA duplexes. No oxidative damage was found upon photooxidation of DNA/RNA duplexes containing tethered metallointercalator, despite the ability of the rhodium complex to promote oxidative damage at a distance in DNA duplexes. This result is attributed to the poor coupling of the rhodium complex into the A-like RNA/DNA duplex. The ability for long-range charge transport to occur in double-stranded nucleic acids of different comformations is considered in light of modeling studies that show interstrand base\u2212base overlap between the opposing, complementary strands that make up RNA/DNA hybrid duplexes. Thus, the possibility of long-range radical migration to effect oxidative damage or signaling may be considered also in the context of transcriptional events.", "doi": "10.1021/bi0102961", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "2001-07-01", "series_number": "30", "volume": "40", "issue": "30", "pages": "8727-8737" }, { "id": "authors:qt6mw-n0337", "collection": "authors", "collection_id": "qt6mw-n0337", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:ODOnar01", "type": "article", "title": "Charge transport through DNA four-way junctions", "author": [ { "family_name": "Odom", "given_name": "Duncan T.", "clpid": "Odom-D-T" }, { "family_name": "Dill", "given_name": "Erik A.", "clpid": "Dill-E-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Long range oxidative damage as a result of charge transport is shown to occur through single crossover junctions assembled from four semi-complementary strands of DNA. When a rhodium complex is tethered to one of the arms of the four-way junction assembly, thereby restricting its intercalation into the {pi}-stack, photo-induced oxidative damage occurs to varying degrees at all guanine doublets in the assembly, though direct strand scission only occurs at the predicted site of intercalation. In studies where the Mg2+ concentration was varied, so as to perturb base stacking at the junction, charge transport was found to be enhanced but not to be strongly localized to the arms that preferentially stack on each other. These data suggest that the conformations of four-way junctions can be relatively mobile. Certainly, in four-way junctions charge transport is less discriminate than in the more rigidly stacked DNA double crossover assemblies.", "pmcid": "PMC55456", "issn": "0305-1048", "publisher": "Oxford University Press", "publication": "Nucleic Acids Research", "publication_date": "2001-05-15", "series_number": "10", "volume": "29", "issue": "10", "pages": "2026-2033" }, { "id": "authors:6mk6k-xhw15", "collection": "authors", "collection_id": "6mk6k-xhw15", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160209-152857175", "type": "article", "title": "How Different DNA-Binding Proteins Affect Long-Range Oxidative Damage to DNA", "author": [ { "family_name": "Rajski", "given_name": "Scott R.", "clpid": "Rajski-S-R" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Here the effect on DNA-mediated charge transport of binding by a variety of proteins is examined. DNA assemblies were constructed that contain a tethered rhodium intercalator, as photooxidant, as well as two 5'-GG-3' sites flanking the DNA-binding site for the different proteins. By monitoring the ratio of oxidative damage promoted at the guanine doublet situated distal to the protein-binding site versus that at the proximal site as a function of protein binding, the effects of binding the proteins on DNA-mediated charge transport were determined. Proteins examined included both the wild-type and mutant methyltransferase, M.HhaI, which are base-flipping enzymes, the restriction endonuclease R.PvuII, a TATA-binding protein, which kinks the DNA, and the transcription factor Antennapedia homeodomain protein, which binds DNA through a helix\u2212turn\u2212helix motif. In general, it was observed that yields of long-range oxidative damage correlate with protein-dependent alterations in DNA base stacking. Interactions that disturb the DNA \u03c0-stack inhibit DNA charge transport. Alternatively, interactions that promote no helix distortion but, as a result of tight packing, may rigidify the \u03c0-stack, serve instead to enhance the ability of the DNA base pairs to serve as a conduit for charge transport. Thus, protein binding to DNA modulates long-range charge transport both negatively and positively, depending upon the specific protein/DNA interactions in play. Long-range DNA charge transport and this modulation by protein binding may be important to consider physiologically.", "doi": "10.1021/bi002684t", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "2001-05-01", "series_number": "18", "volume": "40", "issue": "18", "pages": "5556-5564" }, { "id": "authors:ckfyk-epe05", "collection": "authors", "collection_id": "ckfyk-epe05", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160208-144324209", "type": "article", "title": "Direct Observation of Radical Intermediates in Protein-Dependent DNA Charge Transport", "author": [ { "family_name": "Wagenknecht", "given_name": "Hans-Achim", "clpid": "Wagenknecht-H-A" }, { "family_name": "Rajski", "given_name": "Scott R.", "clpid": "Rajski-S-R" }, { "family_name": "Pascaly", "given_name": "Matthias", "clpid": "Pascaly-M" }, { "family_name": "Stemp", "given_name": "Eric D. A.", "orcid": "0000-0003-2098-4214", "clpid": "Stemp-E-D-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Charge migration through the DNA base stack has been probed both spectroscopically, to observe the formation of radical intermediates, and biochemically, to assess irreversible oxidative DNA damage. Charge transport and radical trapping were examined in DNA assemblies in the presence of a site-specifically bound methyltransferase HhaI mutant and an intercalating ruthenium photooxidant using the flash-quench technique. The methyltransferase mutant, which can flip out a base and insert a tryptophan side chain within the DNA cavity, is found to activate long-range hole transfer through the base pair stack. Protein-dependent DNA charge transport is observed over 50 \u00c5 with guanine radicals formed >10^6 s^(-1); hole transport through DNA over this distance is not rate-limiting. Given the time scale and distance regime, such protein-dependent DNA charge transport chemistry requires consideration physiologically.", "doi": "10.1021/ja003986l", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2001-05-01", "series_number": "19", "volume": "123", "issue": "19", "pages": "4400-4407" }, { "id": "authors:fq0p2-p6e54", "collection": "authors", "collection_id": "fq0p2-p6e54", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:WANpnas00", "type": "article", "title": "Femtosecond direct observation of charge transfer between bases in DNA", "author": [ { "family_name": "Wan", "given_name": "Chaozhi", "clpid": "Wan-Chaozhi" }, { "family_name": "Fiebig", "given_name": "Torsten", "clpid": "Fiebig-T" }, { "family_name": "Schiemann", "given_name": "Olav", "clpid": "Schiemann-O" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Zewail", "given_name": "Ahmed H.", "clpid": "Zewail-A-H" } ], "abstract": "Charge transfer in supramolecular assemblies of DNA is unique because of the notion that the pi-stacked bases within the duplex may mediate the transport, possibly leading to damage and/or repair. The phenomenon of transport through pi-stacked arrays over a long distance has an analogy to conduction in molecular electronics, but the mechanism still needs to be determined. To decipher the elementary steps and the mechanism, one has to directly measure the dynamics in real time and in suitably designed, structurally well characterized DNA assemblies. Here, we report our first observation of the femtosecond dynamics of charge transport processes occurring between bases within duplex DNA. By monitoring the population of an initially excited 2-aminopurine, an isomer of adenine, we can follow the charge transfer process and measure its rate. We then study the effect of different bases next to the donor (acceptor), the base sequence, and the distance dependence between the donor and acceptor. We find that the charge injection to a nearest neighbor base is crucial and the time scale is vastly different: 10 ps for guanine and up to 512 ps for inosine. Depending on the base sequence the transfer can be slowed down or inhibited, and the distance dependence is dramatic over the range of 14 \u00c5. These observations provide the time scale, and the range and efficiency of the transfer. The results suggest the invalidity of an efficient wire-type behavior and indicate that long-range transport is a slow process of a different mechanism.", "doi": "10.1073/pnas.250483297", "pmcid": "PMC18868", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2000-12-19", "series_number": "26", "volume": "97", "issue": "26", "pages": "14052-14055" }, { "id": "authors:drzm3-t9b14", "collection": "authors", "collection_id": "drzm3-t9b14", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160125-195239389", "type": "article", "title": "Luminescence quenching by DNA-bound viologens: effect of reactant identity on efficiency and dynamics of electron transfer in DNA", "author": [ { "family_name": "Kelley", "given_name": "Shana O.", "orcid": "0000-0003-3360-5359", "clpid": "Kelley-S-O" }, { "family_name": "Orellana", "given_name": "Guillermo", "clpid": "Orellana-G" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Photoinduced electron transfer from two intercalating photoactive donors, Ru(phen)_2dppz^(2+) and ethidium, to intercalating viologen acceptors of the N,N\u2032-dialkyl-6-(2\u2032-pyridiniumyl)phenanthridinium family has been investigated through steady-state and time-resolved luminescence quenching measurements. Efficient quenching of the emission from these donors bound to DNA is observed at low concentrations of acceptor (1\u201310 eq.), and in time-resolved emission experiments it is determined that electron transfer occurs on the nanosecond time scale. Furthermore, transient absorption measurements confirm that the quenching is the result of a charge-transfer process; upon photoreaction of intercalated Ru(phen)_2dppz^(2+) with a viologen acceptor, an intermediate with spectral properties resembling the expected charge-separated pair is observed. The quenching yields and kinetics obtained with this quencher are in marked contrast to those observed with these same donors paired with Rh(phi)_2bpy^(3+) as an acceptor. The differing efficiencies of electron transfer for these donor/acceptor pairs bound to DNA as compared to others previously described are discussed qualitatively in terms of the structural and electronic properties of the different reactants.", "doi": "10.1016/S1011-1344(00)00106-8", "issn": "1011-1344", "publisher": "Elsevier", "publication": "Journal of Photochemistry and Photobiology B: Biology", "publication_date": "2000-11", "series_number": "2-3", "volume": "58", "issue": "2-3", "pages": "72-79" }, { "id": "authors:twzhd-jvv64", "collection": "authors", "collection_id": "twzhd-jvv64", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160209-152113459", "type": "article", "title": "Recognition of DNA Base Pair Mismatches by a Cyclometalated Rh(III) Intercalator", "author": [ { "family_name": "Kisko", "given_name": "Jennifer L.", "clpid": "Kisko-J-L" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Two cyclometalated complexes of Rh(III), rac-[Rh(ppy)_2chrysi]^+ and rac-[Rh(ppy)_2phi]^+, have been synthesized and characterized with respect to their binding to DNA. The structure of rac-[Rh(ppy)_2phi]Cl\u00b7H_2O\u00b7CH_2Cl_2 has been determined by X-ray diffraction (monoclinic, P2_1/c, Z = 4, a =18.447(3) \u00c5, b = 9.770(1) \u00c5, c = 17.661(3) \u00c5, \u03b2 = 94.821(11)\u00b0, V = 3172.0(8) \u00c5^3) and reveals that the complex is a distorted octahedron with nearly planar ligands, similar in structure to the DNA mismatch recognition agent [Rh(bpy)_2chrysi]^(3+). The 2-phenylpyridyl nitrogen atoms are shown to be in the axial positions, as a result of trans-directing effects. This tendency simplifies the synthesis and purification of such complexes by limiting the number of possible isomers generated. The abilities of [Rh(ppy)_2chrysi]^+ and [Rh(ppy)_2phi]^+ to bind and, with photoactivation, to cleave DNA have been demonstrated in assays on duplex DNA in the absence and presence of a single CC mismatch. [Rh(ppy)_2chrysi]^+ was shown upon photoactivation to cleave DNA selectively at the base pair mismatch whereas [Rh(ppy)_2phi]^+ cleaves B-DNA nonspecifically. The reactivity of [Rh(ppy)_2chrysi]^+ was also compared to that of the known mismatch recognition agent [Rh(bpy)_2chrysi]^(3+). Competitive photocleavage studies revealed that a 14-fold excess of [Rh(ppy)_2chrysi]^+ was required to achieve the same level of binding as that of [Rh(bpy)_2chrysi]^(3+). However, the ratio of damage induced by [Rh(bpy)_2chrysi]^(3+) to that induced by [Rh(ppy)_2chrysi]^+ is considerably greater than this value, indicating that decreased photoefficiency for the cyclometalated complex must contribute to its significantly attenuated photoreactivity. These cyclometalated intercalators provide the starting points for the design of a new family of metal complexes targeted to DNA.", "doi": "10.1021/ic000549z", "issn": "0020-1669", "publisher": "American Chemical Society", "publication": "Inorganic Chemistry", "publication_date": "2000-10-01", "series_number": "21", "volume": "39", "issue": "21", "pages": "4942-4949" }, { "id": "authors:mddad-ttn90", "collection": "authors", "collection_id": "mddad-ttn90", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150408-152315146", "type": "article", "title": "Mutation detection by electrocatalysis at DNA-modified electrodes", "author": [ { "family_name": "Boon", "given_name": "Elizabeth M.", "orcid": "0000-0003-1891-839X", "clpid": "Boon-E-M" }, { "family_name": "Ceres", "given_name": "Donato M.", "clpid": "Ceres-D-M" }, { "family_name": "Drummond", "given_name": "Thomas G.", "clpid": "Drummond-T-G" }, { "family_name": "Hill", "given_name": "Michael G.", "clpid": "Hill-M-G" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Detection of mutations and damaged DNA bases is important for the early diagnosis of genetic disease. Here we describe an electrocatalytic method for the detection of single-base mismatches as well as DNA base lesions in fully hybridized duplexes, based on charge transport through DNA films. Gold electrodes modified with preassembled DNA duplexes are used to monitor the electrocatalytic signal of methylene blue, a redox-active DNA intercalator, coupled to [Fe(CN)_6]^3-. The presence of mismatched or damaged DNA bases substantially diminishes the electrocatalytic signal. Because this assay is not a measure of differential hybridization, all single-base mismatches, including thermodynamically stable GT and GA mismatches, can be detected without stringent hybridization conditions. Furthermore, many common DNA lesions and \"hot spot\" mutations in the human p53 genome can be distinguished from perfect duplexes. Finally, we have demonstrated the application of this technology in a chip-based format. This system provides a sensitive method for probing the integrity of DNA sequences and a completely new approach to single-base mismatch detection.", "doi": "10.1038/80301", "issn": "1087-0156", "publisher": "Nature Publishing Group", "publication": "Nature Biotechnology", "publication_date": "2000-10", "series_number": "12", "volume": "18", "issue": "12", "pages": "1096-1100" }, { "id": "authors:f1tn6-8fs16", "collection": "authors", "collection_id": "f1tn6-8fs16", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170404-082323148", "type": "article", "title": "Variations in DNA Charge Transport with Nucleotide Composition and Sequence", "author": [ { "family_name": "Williams", "given_name": "Tashica T.", "clpid": "Williams-T-T" }, { "family_name": "Odom", "given_name": "Duncan T.", "clpid": "Odom-D-T" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Long-range oxidative damage to DNA has been demonstrated in experiments using a variety of remotely bound oxidants. However, the mechanism(s) by which charge is transported through the base pair stack needs still to be established. Recent theoretical proposals bring together tunneling and hopping mechanisms to describe charge transport. On the basis of measurements of damage yield, it has been proposed that charge transport occurs by hopping between guanine sites and tunneling through TA steps. In accord with guanine hopping, oxidative damage over long distances was not observed when 5'-TATATA-3' intervened between G sites. Phonon-assisted polaron hopping has been suggested as an alternative mechanism. In this model, the sequence-dependent conformational dynamics of DNA are expected to aid in charge transport.", "doi": "10.1021/ja001552k", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2000-09-20", "series_number": "37", "volume": "122", "issue": "37", "pages": "9048-9049" }, { "id": "authors:130xy-n0440", "collection": "authors", "collection_id": "130xy-n0440", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170404-094144114", "type": "article", "title": "Oxidative Repair of a Thymine Dimer in DNA from a Distance by a Covalently Linked Organic Intercalator", "author": [ { "family_name": "Vicic", "given_name": "David A.", "clpid": "Vicic-D-A" }, { "family_name": "Odom", "given_name": "Duncan T.", "clpid": "Odom-D-T" }, { "family_name": "N\u00fa\u00f1ez", "given_name": "Megan E.", "clpid": "N\u00fa\u00f1ez-M-E" }, { "family_name": "Gianolio", "given_name": "Diego A.", "clpid": "Gianolio-D-A" }, { "family_name": "McLaughlin", "given_name": "Larry W.", "clpid": "McLaughlin-L-W" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "A thymine cyclobutane dimer, site-specifically incorporated in a DNA duplex, is shown to be repaired upon photoexcitation (at 380 nm) of a naphthalene diimide intercalator (NDI), either bound noncovalently to the duplex or covalently appended to the C4 amine of a methylated cytosine base well separated from the thymine dimer. The repair of the thymine dimer is triggered by photooxidation either directly or by DNA-mediated charge transport over a distance of \u223c22 \u00c5, the separation between NDI and the cyclobutane ring. Photooxidative repair with covalently and noncovalently bound NDI is demonstrated using HPLC under denaturing conditions, where the loss of the thymine dimer-containing strand and the formation of the repaired strand are monitored directly, as well as using a novel gel electrophoretic assay. In this assay, two strands of oligonucleotides containing 5'- and 3'-terminal thymidines are first ligated photochemically to yield thymine dimers, and repair is then assayed by monitoring the reversal of the photoligation by intercalators bound either noncovalently or at a distance. Although both NDI and a rhodium intercalator were seen to reverse the photoligation, several anthraquinones and ethidium were unable to promote repair upon irradiation at 350 nm. This photoligation reversal assay provides a rapid screen for thymine dimer repair. The oxidative repair of thymine dimers in a DNA duplex from a distance appears now to be a general phenomenon and requires consideration in developing mechanisms for DNA-mediated charge transport.", "doi": "10.1021/ja000280i", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2000-09-13", "series_number": "36", "volume": "122", "issue": "36", "pages": "8603-8611" }, { "id": "authors:zn9vt-02f68", "collection": "authors", "collection_id": "zn9vt-02f68", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170517-070820804", "type": "article", "title": "EPR Detection of Guanine Radicals in a DNA Duplex under Biological Conditions: Selective Base Oxidation by Ru(phen)_2dppz^(3+)Using the Flash-Quench Technique", "author": [ { "family_name": "Schiemann", "given_name": "Olav", "clpid": "Schiemann-O" }, { "family_name": "Turro", "given_name": "Nicholas J.", "clpid": "Turro-N-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Continuous-wave X-band EPR spectroscopy has been employed in examining the guanine radical within a DNA duplex at ambient temperature using the flash-quench technique. Guanine was selectively oxidized by DNA-bound [Ru(phen)_2dppz]^(3+) (dppz = dipyridophenazine, phen = 1,10-phenanthroline) generated in situ by photolysis in the presence of [Co(NH_3)_5Cl]^(2+) as the oxidative quencher. An EPR signal centered at g_(iso) = 2.0048 is observed in experiments with poly(dG-dC) as substrate. Comparable signals are also detected with a 13-mer oligonucleotide duplex containing only one guanine base and with calf thymus DNA, but no signal is observed with poly(dA-dT) or poly(dI-dC). These observations reflect the base selectivity of the reaction in forming the guanine radical. With ruthenium hexaammine as oxidative quencher, no signal is observed, while, with methyl viologen, a strong signal with hyperfine pattern is seen, characteristic of the reduced viologen radical and indicating that [Ru(phen)_2dppz]^(3+) was generated. The guanine radical signal, once formed upon continuous irradiation in argon-saturated aqueous buffer solution (pH 7), decays with a half-life of 30 s, but vanishes instantaneously in the dark or upon introduction of oxygen. Spin trapping experiments with N-tert-butyl-\u03b1-phenylnitrone substantiate the selectivity in generating the guanine radical; in the presence of poly(dG-dC), calf thymus DNA, the 13-mer oligonucleotide but not with poly(dA-dT) and poly(dI-dC), the detected nitroxide EPR signals are the same with g_(iso) = 2.0059, \u3008a_N\u3009 = 15.05 G, and \u3008a_H\u3009 = 3.11 G. Upon titration of the ruthenium intercalator into poly(dG-dC), the signal intensity increases smoothly as the [base pair]/[intercalator] ratio decreases from 100 to 25, at which point the signal intensity decreases markedly; this result may be an indication of an antiferromagnetic exchange interaction between guanine radicals. Indeed, using the flash-quench technique, EPR spectroscopy of guanine radicals within DNA now will permit the evaluation of how radicals within the DNA base stack may be coupled under biological conditions.", "doi": "10.1021/jp000725p", "issn": "1520-6106", "publisher": "American Chemical Society", "publication": "Journal of Physical Chemistry B", "publication_date": "2000-08-03", "series_number": "30", "volume": "104", "issue": "30", "pages": "7214-7220" }, { "id": "authors:6v6ff-pff37", "collection": "authors", "collection_id": "6v6ff-pff37", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160209-151255707", "type": "article", "title": "The Flash\u2212Quench Technique in Protein\u2212DNA Electron Transfer: Reduction of the Guanine Radical by Ferrocytochrome c", "author": [ { "family_name": "Stemp", "given_name": "Eric D. A.", "orcid": "0000-0003-2098-4214", "clpid": "Stemp-E-D-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Electron transfer from a protein to oxidatively damaged DNA, specifically from ferrocytochrome c to the guanine radical, was examined using the flash\u2212quench technique. Ru(phen)_2dppz^(2+) (dppz = dipyridophenazine) was employed as the photosensitive intercalator, and ferricytochrome c (Fe^(3+) cyt\u2009c), as the oxidative quencher. Using transient absorption and time-resolved luminescence spectroscopies, we examined the electron-transfer reactions following photoexcitation of the ruthenium complex in the presence of poly(dA-dT) or poly(dG-dC). The luminescence-quenching titrations of excited Ru(phen)_2dppz^(2+) by Fe^(3+) cyt\u2009c are nearly identical for the two DNA polymers. However, the spectral characteristics of the long-lived transient produced by the quenching depend strongly upon the DNA. For poly(dA-dT), the transient has a spectrum consistent with formation of a [Ru(phen)_2dppz^(3+), Fe^(2+) cyt\u2009c] intermediate, indicating that the system regenerates itself via electron transfer from the protein to the Ru(III) metallointercalator for this polymer. For poly(dG-dC), however, the transient has the characteristics expected for an intermediate of Fe^(2+) cyt\u2009c and the neutral guanine radical. The characteristics of the transient formed with the GC polymer are consistent with rapid oxidation of guanine by the Ru(III) complex, followed by slow electron transfer from Fe^(2+) cyt\u2009c to the guanine radical. These experiments show that electron holes on DNA can be repaired by protein and demonstrate how the flash\u2212quench technique can be used generally in studying electron transfer from proteins to guanine radicals in duplex DNA.", "doi": "10.1021/ic0000698", "issn": "0020-1669", "publisher": "American Chemical Society", "publication": "Inorganic Chemistry", "publication_date": "2000-08-01", "series_number": "17", "volume": "39", "issue": "17", "pages": "3868-3874" }, { "id": "authors:y11tt-ff583", "collection": "authors", "collection_id": "y11tt-ff583", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160129-080803941", "type": "article", "title": "Robust charge transport in DNA double crossover assemblies", "author": [ { "family_name": "Odom", "given_name": "Duncan T.", "clpid": "Odom-D-T" }, { "family_name": "Dill", "given_name": "Erik A.", "clpid": "Dill-E-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Background: Multiple-stranded DNA assemblies, encoded by sequence, have been constructed in an effort to self-assemble nanodevices of defined molecular architecture. Double-helical DNA has been probed also as a molecular medium for charge transport. Conductivity studies suggest that DNA displays semiconductor properties, whereas biochemical studies have shown that oxidative damage to B-DNA at the 5\u2032-G of a 5\u2032-GG-3\u2032 doublet can occur by charge transport through DNA up to 20 nm from a photo-excited metallointercalator. The possible application of DNA assemblies, in particular double crossover (DX) molecules, in electrical nanodevices prompted the design of a DNA DX assembly with oxidatively sensitive guanine moieties and a tethered rhodium photo-oxidant strategically placed to probe charge transport.\n\nResults: DX assemblies support long-range charge transport selectively down the base stack bearing the intercalated photo-oxidant. Despite tight packing, no electron transfer (ET) crossover to the adjacent base stack is observed. Moreover, the base stack of a DX assembly is well-coupled and less susceptible than duplex DNA to stacking perturbations. Introducing a double mismatch along the path for charge transport entirely disrupts long-range ET in duplex DNA, but only marginally decreases it in the analogous stack within DX molecules.\n\nConclusions: The path for charge transport in a DX DNA assembly is determined directly by base stacking. As a result, the two closely packed stacks within this assembly are electronically insulated from one another. Therefore, DX DNA assemblies may serve as robust, insulated conduits for charge transport in nanoscale devices.", "doi": "10.1016/S1074-5521(00)00133-2", "issn": "1074-5521", "publisher": "Elsevier", "publication": "Chemistry and Biology", "publication_date": "2000-07", "series_number": "7", "volume": "7", "issue": "7", "pages": "475-481" }, { "id": "authors:jk313-ry935", "collection": "authors", "collection_id": "jk313-ry935", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160209-145158250", "type": "article", "title": "DNA-Bound Peptide Radicals Generated through DNA-Mediated Electron Transport", "author": [ { "family_name": "Wagenknecht", "given_name": "Hans-Achim", "clpid": "Wagenknecht-H-A" }, { "family_name": "Stemp", "given_name": "Eric D. A.", "orcid": "0000-0003-2098-4214", "clpid": "Stemp-E-D-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Flash-quench experiments were carried out to explore peptide/DNA electron-transfer reactions. DNA-bound [Ru(phen)_2(dppz)]^(3+) (phen = 1,10-phenanthroline; dppz = dipyridophenazine) and [Ru(phen)(bpy')(dppz)]^(3+) [bpy' = 4-(4'-methyl-2,2'-bipyridyl)valerate], generated in situ by flash-quench methodology, are powerful ground-state oxidants, capable of oxidizing guanine or tyrosine intercalated in DNA. In flash-quench experiments with mixed-sequence oligonucleotides in the presence of Lys-Tyr-Lys, transient absorption spectroscopy yielded a spectrum with a sharp maximum at 405 nm assigned to the tyrosine radical. Experiments with poly(dG\u00b7dC) suggested the intermediacy of the guanine radical, since the rise of the 405 nm signal occurred with the same kinetics as the disappearance of the guanine radical, as monitored at 510 nm. In oligonucleotide duplexes containing [Ru(phen)(bpy')(dppz)]^(2+) tethered at one end, damage to distant guanines was observed by gel electrophoresis, consistent with the mobility of the electron hole through the DNA duplex; the presence of the peptide did not inhibit but instead altered the distribution of guanine damage. Covalent adducts of the DNA and Lys-Tyr-Lys were detected as final irreversible products of this peptide-to-DNA electron-transfer chemistry by mass spectrometric and enzymatic digestive analysis. From these different assays and comparison of reactions of Lys-Trp-Lys and Lys-Tyr-Lys, the reactivity of the DNA-bound tyrosine radical was found to differ considerably from that of the tryptophan radical. These results establish that Lys-Tyr-Lys and Lys-Trp-Lys can participate in long-range electron-transfer reactions through the DNA from a distinct binding site. On that basis, proposals for functional roles for these peptide radicals may be considered.", "doi": "10.1021/bi992897m", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "2000-05-01", "series_number": "18", "volume": "39", "issue": "18", "pages": "5483-5491" }, { "id": "authors:48gzw-jbb72", "collection": "authors", "collection_id": "48gzw-jbb72", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160209-142945831", "type": "article", "title": "Long-Range Guanine Oxidation in DNA Restriction Fragments by a Triplex-Directed Naphthalene Diimide Intercalator", "author": [ { "family_name": "N\u00fa\u00f1ez", "given_name": "Megan E.", "clpid": "N\u00fa\u00f1ez-M-E" }, { "family_name": "Noyes", "given_name": "Katherine T.", "clpid": "Noyes-K-T" }, { "family_name": "Gianolio", "given_name": "Diego A.", "clpid": "Gianolio-D-A" }, { "family_name": "McLaughlin", "given_name": "Larry W.", "clpid": "McLaughlin-L-W" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Naphthalene diimide (NDI), a powerful oxidant that binds avidly to DNA by intercalation, is seen to damage the 5' guanine of 5'-GG-3' sites by photoactivated charge transport through DNA. When covalently tethered to the center of a triplex-forming oligonucleotide and delivered by triplex formation within a pyrimidine\u00b7purine-pyrimidine motif to a specific site on a restriction fragment, NDI can photooxidize guanine over at least 25\u221238 bp in each direction from the site of binding. Charge migration occurs in both directions from the NDI intercalator and on both DNA strands of the target, but the oxidation is significantly more efficient to the 3' side of the triplex. NDI and octahedral rhodium intercalators, when tethered directly to the 5' terminus of the triplex-forming strand as opposed to the center, generate significant amounts of oxidative damage only in the immediate vicinity of the intercalation site. Given that long-range charge transport depends on DNA stacking, these results suggest that the base stack is distorted at the 5' end of the triplex region in the duplex\u2212triplex junction. Targeting of photooxidative damage by triplex formation extends our previous studies of long-range charge transport to significantly longer DNA sequences through a strategy that does not require covalent attachment of the photooxidant to the DNA being probed. Moreover, triplex targeting of oxidative damage provides for the first time a typical distance distribution for genomic charge transport of \u223c200 \u00c5 around the oxidant.", "doi": "10.1021/bi000285s", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "2000-05-01", "series_number": "20", "volume": "39", "issue": "20", "pages": "6190-6199" }, { "id": "authors:r1017-2qr02", "collection": "authors", "collection_id": "r1017-2qr02", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160209-144358626", "type": "article", "title": "Recognition of Base Mismatches in DNA by 5,6-Chrysenequinone Diimine Complexes of Rhodium(III): A Proposed Mechanism for Preferential Binding in Destabilized Regions of the Double Helix", "author": [ { "family_name": "Jackson", "given_name": "Brian A.", "clpid": "Jackson-B-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "5,6-Chrysenequinone diimine (chrysi) complexes of rhodium(III) have been shown to be versatile and specific recognition agents for mismatched base pairs in DNA. The design of these compounds was based on the hypothesis that the sterically expansive chrysi ligand, which should be too wide to readily intercalate into B-DNA, would bind preferentially in the destabilized regions of the DNA helix near base mismatches. In this work, this recognition hypothesis is comprehensively explored. Comparison of the recognition patterns of the complex [Rh(bpy)_2(chrysi)]^(3+) with a nonsterically demanding analogue, [Rh(bpy)_2(phi)]^(3+) (phi = 9,10-phenanthrenequinone diimine), demonstrates that the chrysi ligand does indeed disfavor binding to B-DNA and generate mismatch selectivity. Examination of mismatch recognition by [Rh(bpy)_2(chrysi)]^(3+) in both constant and variable sequence contexts using photocleavage assays indicates that the recognition of base mismatches is influenced by the amount that a mismatch thermodynamically destabilizes the DNA helix. Thermodynamic binding constants for the rhodium complex at a range of mismatch sites have been determined by quantitative photocleavage titration and yield values which vary from 1 \u00d7 10^6 to 20 \u00d7 10^6 M^(-1). These mismatch-specific binding affinities correlate with independent measurements of thermodynamic destabilization, supporting the hypothesis that helix destabilization is a factor determining the binding affinity of the metal complex for the mismatched site. Although not the only factor involved in the binding of [Rh(bpy)_2(chrysi)]^(3+) to mismatch sites, a model is proposed where helix destabilization acts as the \"door\" which permits access of the sterically demanding intercalator to the base stack.", "doi": "10.1021/bi9927033", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "2000-05-01", "series_number": "20", "volume": "39", "issue": "20", "pages": "6176-6182" }, { "id": "authors:hpzrt-6cy44", "collection": "authors", "collection_id": "hpzrt-6cy44", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160129-080803438", "type": "article", "title": "Probing DNA charge transport with metallointercalators", "author": [ { "family_name": "N\u00fa\u00f1ez", "given_name": "Megan E.", "clpid": "N\u00fa\u00f1ez-M-E" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "A wide range of experiments have emerged recently regarding charge transport through DNA, including spectroscopic studies of rates of DNA-mediated electron transfer and biochemical studies of DNA base oxidation over long distances. These experiments have, in turn, led to new proposals about the way in which charge moves through DNA and have prompted the consideration of physiological roles for DNA electron transfer. Importantly, metallointercalators have been key players in many of these experiments. Metallointercalators provide critical probes to examine the migration of charge through the DNA base stack.", "doi": "10.1016/S1367-5931(99)00075-7", "issn": "1367-5931", "publisher": "Elsevier", "publication": "Current Opinion in Chemical Biology", "publication_date": "2000-04", "series_number": "2", "volume": "4", "issue": "2", "pages": "199-206" }, { "id": "authors:nqsd7-pxx36", "collection": "authors", "collection_id": "nqsd7-pxx36", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150108-155222366", "type": "article", "title": "Structure of a photoactive rhodium complex intercalated into DNA", "author": [ { "family_name": "Kielkopf", "given_name": "Clara L.", "clpid": "Kielkopf-C-L" }, { "family_name": "Erkkila", "given_name": "Kathryn E.", "clpid": "Erkkila-K-E" }, { "family_name": "Hudson", "given_name": "Brian P.", "clpid": "Hudson-B-P" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" } ], "abstract": "Intercalating complexes of rhodium(III) are strong photo-oxidants\nthat promote DNA strand cleavage or electron transfer\nthrough the double helix. The 1.2 \u00c5 resolution crystal structure\nof a sequence-specific rhodium intercalator bound to a DNA\nhelix provides a rationale for the sequence specificity of rhodium\nintercalators. It also explains how intercalation in the center\nof an oligonucleotide modifies DNA conformation. The\nrhodium complex intercalates via the major groove where specific\ncontacts are formed with the edges of the bases at the target\nsite. The phi ligand is deeply inserted into the DNA base pair\nstack. The primary conformational change of the DNA is a doubling\nof the rise per residue, with no change in sugar pucker\nfrom B-form DNA. Based upon the five crystallographically\nindependent views of an intercalated DNA helix observed in\nthis structure, the intercalator may be considered as an additional\nbase pair with specific functional groups positioned in\nthe major groove.", "doi": "10.1038/72385", "issn": "1072-8368", "publisher": "Nature Publishing Group", "publication": "Nature Structural Biology", "publication_date": "2000-02", "series_number": "2", "volume": "7", "issue": "2", "pages": "117-121" }, { "id": "authors:5cztd-dqp62", "collection": "authors", "collection_id": "5cztd-dqp62", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160127-111126763", "type": "article", "title": "DNA repair: models for damage and mismatch recognition", "author": [ { "family_name": "Rajski", "given_name": "Scott R.", "clpid": "Rajski-S-R" }, { "family_name": "Jackson", "given_name": "Brian A.", "clpid": "Jackson-B-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Maintaining the integrity of the genome is critical for the survival of any organism. To achieve this, many families of enzymatic repair systems which recognize and repair DNA damage have evolved. Perhaps most intriguing about the workings of these repair systems is the actual damage recognition process. What are the chemical characteristics which are common to sites of nucleic acid damage that DNA repair proteins may exploit in targeting sites? Importantly, thermodynamic and kinetic principles, as much as structural factors, make damage sites distinct from the native DNA bases, and indeed, in many cases, these are the features which are believed to be exploited by repair enzymes. Current proposals for damage recognition may not fulfill all of the demands required of enzymatic repair systems given the sheer size of many genomes, and the efficiency with which the genome is screened for damage. Here we discuss current models for how DNA damage recognition may occur and the chemical characteristics, shared by damaged DNA sites, of which repair proteins may take advantage. These include recognition based upon the thermodynamic and kinetic instabilities associated with aberrant sites. Additionally, we describe how small changes in base pair structure can alter also the unique electronic properties of the DNA base pair \u03c0-stack. Further, we describe photophysical, electrochemical, and biochemical experiments in which mismatches and other local perturbations in structure are detected using DNA-mediated charge transport. Finally, we speculate as to how this DNA electron transfer chemistry might be exploited by repair enzymes in order to scan the genome for sites of damage.", "doi": "10.1016/S0027-5107(99)00195-5", "issn": "0027-5107", "publisher": "Elsevier", "publication": "Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis", "publication_date": "2000-01-17", "series_number": "1", "volume": "447", "issue": "1", "pages": "49-72" }, { "id": "authors:qm78f-2h927", "collection": "authors", "collection_id": "qm78f-2h927", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170425-131010289", "type": "article", "title": "Evidence of Electron Transfer from Peptides to DNA: Oxidation of DNA-Bound Tryptophan Using the Flash-Quench Technique", "author": [ { "family_name": "Wagenknecht", "given_name": "Hans-Achim", "clpid": "Wagenknecht-H-A" }, { "family_name": "Stemp", "given_name": "Eric D. A.", "orcid": "0000-0003-2098-4214", "clpid": "Stemp-E-D-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "A flash-quench method has been employed to probe electron-transfer reactions from peptides to DNA. The photoexcited intercalators [Ru(phen)_2(dppz)]^(2+) (phen = 1,10-phenanthroline; dppz = dipyridophenazine) and [Ru(phen)(bpy')(dppz)]^(2+) (bpy' = 4-(4'-methyl-2,2'-bipyridyl)valerate) are quenched by a nonintercalating and weakly bound electron-transfer quencher to generate the corresponding DNA-bound Ru(III) complexes in situ. Both Ru(III) complexes are powerful ground-state oxidants, capable of oxidizing guanine in DNA or DNA-bound tryptophan of the intercalating peptide, Lys-Trp-Lys. In mixed-sequence oligonucleotide duplexes containing [Ru(phen)(bpy')(dppz)]^(2+) tethered at one end, damage to distant guanines is observed by gel electrophoresis, consistent with the mobility of the electron through the DNA duplex. This damage at guanines is observed in both the presence and absence of Lys-Trp-Lys, but the presence of the peptide affects the distribution. In flash-quench experiments using mixed-sequence oligonucleotides or poly(dG\u00b7dC) in the presence of Lys-Trp-Lys, transient absorption spectroscopy reveals a signal at \u03bb = 510 nm assigned to the tryptophan radical; it decays on the time scale of 60\u2212250 \u03bcs. The final peptide product of this electron-transfer reaction has been described by UV/vis spectroscopy and mass spectrometry. No DNA\u2212peptide adducts were detected. Significantly, the tryptophan radical is not observed in reactions with Ru(III) bound to poly(dA\u00b7dT), an observation that suggests the intermediacy of the guanine radical cation in generating the tryptophan radical. These results indicate that charge migration from tryptophan to [Ru(phen)(bpy')(dppz)]^(3+) occurs to produce the tryptophan radical and that this process is DNA mediated. This work establishes methodology to probe tryptophan intercalation in DNA by protein or peptides. Moreover, this methodology demonstrates an electron-transfer event between peptides and DNA and suggests the consideration of such events within the cell.", "doi": "10.1021/ja991855i", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2000-01-12", "series_number": "1", "volume": "122", "issue": "1", "pages": "1-7" }, { "id": "authors:zkj10-5h671", "collection": "authors", "collection_id": "zkj10-5h671", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160323-092524330", "type": "article", "title": "Electron transfer between metal complexes bound to DNA: variations in sequence, donor, and metal binding mode", "author": [ { "family_name": "Stemp", "given_name": "Eric D. A.", "orcid": "0000-0003-2098-4214", "clpid": "Stemp-E-D-A" }, { "family_name": "Holmlin", "given_name": "R. Erik", "clpid": "Holmlin-R-E" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Using luminescence spectroscopy and single photon counting, photoinduced electron transfer (ET) reactions between photoexcited [M(phen)_2dppz ^(2+) (phen = 1,10-phenanthroline, dppz=dipyridophenazine, M=Ru or Os) and the electron acceptors Rh(phi)_2bpy^(3+) (phi=9,10-phenanthrenequinone diimine, bpy=2,2\u2032-bipyridine) and Ru(NH_3)_6^(3+) were studied as a function of DNA sequence in long DNA polymers. In addition, the thermal back reactions between M(III) and reduced acceptor were also followed by transient absorption spectroscopy. The comparison of ET reactions of the isostructural donors Os and Ru with an intercalated acceptor, Rh(phi)_2bpy^(3+), and an externally bound acceptor, Ru(NH_3)_6^(3+), helps to elucidate which factors are important for electron transfer between DNA-bound intercalators. Ru(phen)_2dppz^(2+) and Os(phen)_2dppz^(2+) show nearly identical quenching by Rh(phi)_2bpy^(3+) for a given DNA polymer, with an efficient quenching process that occurs on a time scale much faster than the excited state lifetime. We find that Rh(phi)_2bpy^(3+) and Ru(NH_3)_6^(3+) show opposite trends for quenching of DNA-bound M(phen)_2dppz^(2+). Quenching by intercalated Rh(phi)_2bpy^(3+) is most efficient in AT-only DNA polymers and less efficient in GC-only polymers, whereas for groove-bound Ru(NH_3)_6^(3+), the reverse is observed. The intrinsic excited state lifetime of Ru(phen)_2dppz^(2+) bound to DNA and the luminescence quenching efficiency by Ru(NH_3)_6^(3+) provide indicators of the solvent accessibility of the DNA-bound dppz donor. On this basis, we attribute the difference in ET reactivity among the various DNA polymers to differences in how well M(phen)_2dppz^(2+) stacks in DNA.", "doi": "10.1016/S0020-1693(99)00289-3", "issn": "0020-1693", "publisher": "Elsevier", "publication": "Inorganica Chimica Acta", "publication_date": "2000-01", "series_number": "1-2", "volume": "297", "issue": "1-2", "pages": "88-97" }, { "id": "authors:4q6tc-7wk13", "collection": "authors", "collection_id": "4q6tc-7wk13", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160127-111127012", "type": "article", "title": "Damage to DNA by long-range charge transport", "author": [ { "family_name": "N\u00fa\u00f1ez", "given_name": "Megan E.", "clpid": "N\u00fa\u00f1ez-M-E" }, { "family_name": "Rajski", "given_name": "Scott R.", "clpid": "Rajski-S-R" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Photochemical reactions on DNA assemblies containing tethered photooxidants, particularly metallointercalating photooxidants, have been critical in establishing that permanent damage to DNA bases can be generated as a result of radical migration from a remote site on the DNA duplex. Induction of a 1-electron deficiency in the oxidant attached covalently to the DNA remote from the oxidizable site leads to this \"chemistry at a distance,\" caused by efficient charge transport through the DNA base pair stack. Double helical DNA may be unique as a polymeric assembly in solution because of this interior core of stacked aromatic heterocyclic base pairs. Similarly stacked solid-state materials tend to be conducting along the stacking direction. This chapter describes the design and construction of DNA assemblies used to probe long-range oxidative damage in DNA. It also includes methodology for the oxidative repair of a thymine dimer lesion in DNA, as this \"chemistry at a distance\" also depends on long-range charge transfer through the DNA base pair stack.", "doi": "10.1016/S0076-6879(00)19018-4", "issn": "0076-6879", "publisher": "Academic Press", "publication": "Methods in Enzymology", "publication_date": "2000", "volume": "319", "pages": "165-188" }, { "id": "authors:0nenw-tas04", "collection": "authors", "collection_id": "0nenw-tas04", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160125-195950967", "type": "article", "title": "DNA-Mediated Electron Transfer: A Sensitive Probe of DNA-Protein Interactions", "author": [ { "family_name": "Rajski", "given_name": "Scott R.", "clpid": "Rajski-S-R" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The ability of the \u03c0-stacked array of heterocyclic DNA bases to behave as an efficient conduit for charge migration has been explored using a wide array of experimental approaches. Spectroscopic studies and biochemical assays show that charge transfer through well-stacked DNA can be extremely facile, although sensitive to structural distortions within the DNA base stack. The efficiency of these long-range reactions depends upon the coupling of the electron donor, acceptor and intervening base pairs within the base stack. As a result, base mismatches and stacking disruptions associated with protein binding to the helix can significantly perturb long range charge transfer. DNA-protein interactions which result in the base flipping of a nucleotide out of the DNA \u03c0-stack, in particular, dramatically inhibit long-range charge transfer through DNA. Whether these reactions that can occur over large molecular distances, be applied in sensing DNA damage, and be modulated by DNA-binding proteins, are exploited within the cell remains to be determined.", "doi": "10.1080/07391102.2000.10506633", "issn": "0739-1102", "publisher": "Adenine Press", "publication": "Journal of Biomolecular Structure and Dynamics", "publication_date": "2000", "series_number": "S1", "volume": "17", "issue": "S1", "pages": "285-291" }, { "id": "authors:s8ncv-nsd23", "collection": "authors", "collection_id": "s8ncv-nsd23", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160412-081002999", "type": "article", "title": "Spectral and Structural Characterization of 5,6-Chrysenequinone Diimine Complexes of Rhodium(III): Evidence for a pH-Dependent Ligand Conformational Switch", "author": [ { "family_name": "Jackson", "given_name": "Brian A.", "clpid": "Jackson-B-A" }, { "family_name": "Henling", "given_name": "Lawrence M.", "clpid": "Henling-L-M" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Rhodium(III) complexes containing 9,10-phenanthrenequinone diimine (phi) ligands have been broadly applied for the construction of DNA binding and recognition molecules, and more recently, derivatives containing the 5,6-chrysenequinone diimine (chrysi) ligand have been shown specifically to recognize base mismatches in DNA. Here the structural properties of [Rh(bpy)_2(chrysi)]Cl_3 and spectroscopic properties of derivatives are examined and compared to those of phi complexes of rhodium. Although similar in many respects, phi and chrysi complexes display distinctly different protonation behavior. The pK_a values of chrysi complexes are as much as 1 unit lower than analogous phi compounds, and visible spectra of the chrysi complexes differ markedly from the phi counterparts in acidic but not basic solution. This protonation behavior is traced to the presence of a steric clash between a proton on the aromatic ring of the chrysi ligand and the acidic immino proton of the metal complex. In avoidance of this steric clash, a significant disruption in the planarity of the chrysi ligand is evident crystallographically in the structure of [Rh(bpy)_2(chrysi)]Cl_3\u00b73CH_3CN\u00b72H_2O (triclinic crystal system, space group P1\u0304 (No. 2), Z = 2, a = 9.079(3) \u00c5, b = 10.970(3) \u00c5, c = 21.192(8) \u00c5, \u03b1 = 86.71(3)\u00b0, \u03b2 = 89.21(3)\u00b0, \u03b3 = 78.58(3)\u00b0, V = 2065.4(12) \u00c5^3). Phi complexes, lacking the additional aromatic ring, require no similar distortion from ligand planarity. NMR spectra support this pH-dependent structural distortion for the chrysi complex. Rhodium complexes of chrysenequinone diimine, therefore, not only represent new DNA binding molecules targeted to mismatches but also provide an illustration of a pH \"gated\" ligand conformational switch.", "doi": "10.1021/ic990824l", "issn": "0020-1669", "publisher": "American Chemical Society", "publication": "Inorganic Chemistry", "publication_date": "1999-12-27", "series_number": "26", "volume": "38", "issue": "26", "pages": "6218-6224" }, { "id": "authors:7bmtn-h1w02", "collection": "authors", "collection_id": "7bmtn-h1w02", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:KELnar99", "type": "article", "title": "Single-base mismatch detection based on charge transduction through DNA", "author": [ { "family_name": "Kelley", "given_name": "Shana O.", "orcid": "0000-0003-3360-5359", "clpid": "Kelley-S-O" }, { "family_name": "Boon", "given_name": "Elizabeth M.", "orcid": "0000-0003-1891-839X", "clpid": "Boon-E-M" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Jackson", "given_name": "Nicole M.", "clpid": "Jackson-N-M" }, { "family_name": "Hill", "given_name": "Michael G.", "clpid": "Hill-M-G" } ], "abstract": "High-throughput DNA sensors capable of detecting single-base mismatches are required for the routine screening of genetic mutations and disease. A new strategy for the electrochemical detection of single-base mismatches in DNA has been developed based upon charge transport through DNA films. Double-helical DNA films on gold surfaces have been prepared and used to detect DNA mismatches electrochemically. The signals obtained from redox-active intercalators bound to DNA-modified gold surfaces display a marked sensitivity to the presence of base mismatches within the immobilized duplexes. Differential mismatch detection was accomplished irrespective of DNA sequence composition and mismatch identity. Single-base changes in sequences hybridized at the electrode surface are also detected accurately. Coupling the redox reactions of intercalated species to electrocatalytic processes in solution considerably increases the sensitivity of this assay. Reporting on the electronic structure of DNA, as opposed to the hybridization energetics of single-stranded oligonucleotides, electrochemical sensors based on charge transport may offer fundamental advantages in both scope and sensitivity.", "doi": "10.1093/nar/27.24.4830", "pmcid": "PMC148785", "issn": "0305-1048", "publisher": "Oxford University Press", "publication": "Nucleic Acids Research", "publication_date": "1999-12-15", "series_number": "24", "volume": "27", "issue": "24", "pages": "4830-4837" }, { "id": "authors:6377y-ngs14", "collection": "authors", "collection_id": "6377y-ngs14", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180202-151812038", "type": "article", "title": "Synthesis of Metallointercalator\u2212DNA Conjugates on a Solid Support", "author": [ { "family_name": "Holmlin", "given_name": "R. Erik", "clpid": "Holmlin-R-E" }, { "family_name": "Dandliker", "given_name": "Peter J.", "clpid": "Dandliker-P-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Metallointercalator\u2212DNA conjugates were prepared by amide bond formation between active esters on the nonintercalating ligands of transition metal complexes and primary amines presented at the 5' or the 3' termini of oligonucleotides attached to solid supports. The conjugates were liberated from the support by aminolysis and purified by HPLC on C18 or C4 stationary phases, which separates the two diastereomeric forms of the conjugates containing either the \u039b or the \u0394 enantiomer of the octahedral metal complex. The coupling reaction proceeds with \u223c75% conversion of the amino-terminated oligonucleotide into the conjugate; the isolated yield is \u223c200 nmol for syntheses initiated on DNA-synthesis columns with a loading of 2 \u03bcmol. The conjugates were characterized by ultraviolet\u2212visible and circular dichorism absorption spectroscopy, electrospray ionization mass spectrometry, enzymatic digestion, and polyacrylamide gel electrophoresis (PAGE). Oligonucleotides bearing [Rh(phi)_2(bpy')]^(3+) (phi = 9,10-phenanthrene quinone diimine; bpy' = 4-butyric acid-4'-methyl bipyridyl) form 1:1 duplexes with the complementary strand, and the electrophoretic mobility under nondenaturating PAGE of duplexes containing \u0394-Rh is notably different from duplexes containing \u039b-Rh. High-resolution PAGE of DNA photocleavage reactions initiated by irradiation of the tethered Rh complexes reveal intercalation of the complex only near the tethered end of the duplex. Analogous DNA-binding properties were observed with [Rh(phi)_2(bpy')]^(3+) tethered to the 3' terminus. By combining the 3' and 5' modification strategies, a mixed-metal DNA conjugate containing both [Os(phen)(bpy')(Me_2-dppz)]^(2+) (Me_2-dppz = 7,8-dimethyldipyridophenazine) on the 3' terminus and [Rh(phi)_2(bpy')]^(3+) on the 5' terminus was prepared and isolated. Taken together, these strategies for preparing metallointercalator\u2212DNA conjugates offer a useful approach to generate chemical assemblies to probe long-range DNA-mediated charge transfer where the redox initiator is confined to and intercalated in a well-defined binding site.", "doi": "10.1021/bc9900791", "issn": "1043-1802", "publisher": "American Chemical Society", "publication": "Bioconjugate Chemistry", "publication_date": "1999-11", "series_number": "6", "volume": "10", "issue": "6", "pages": "1122-1130" }, { "id": "authors:51xr9-nh208", "collection": "authors", "collection_id": "51xr9-nh208", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160405-150256286", "type": "article", "title": "Synthesis of Metallointercalator\u2212DNA Conjugates on a Solid Support", "author": [ { "family_name": "Holmlin", "given_name": "R. Erik", "clpid": "Holmlin-R-E" }, { "family_name": "Dandliker", "given_name": "Peter J.", "clpid": "Dandliker-P-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Metallointercalator\u2212DNA conjugates were prepared by amide bond formation between active esters on the nonintercalating ligands of transition metal complexes and primary amines presented at the 5' or the 3' termini of oligonucleotides attached to solid supports. The conjugates were liberated from the support by aminolysis and purified by HPLC on C18 or C4 stationary phases, which separates the two diastereomeric forms of the conjugates containing either the \u039b or the \u0394 enantiomer of the octahedral metal complex. The coupling reaction proceeds with \u223c75% conversion of the amino-terminated oligonucleotide into the conjugate; the isolated yield is \u223c200 nmol for syntheses initiated on DNA-synthesis columns with a loading of 2 \u03bcmol. The conjugates were characterized by ultraviolet\u2212visible and circular dichorism absorption spectroscopy, electrospray ionization mass spectrometry, enzymatic digestion, and polyacrylamide gel electrophoresis (PAGE). Oligonucleotides bearing [Rh(phi)_2(bpy')]^(3+) (phi = 9,10-phenanthrene quinone diimine; bpy' = 4-butyric acid-4'-methyl bipyridyl) form 1:1 duplexes with the complementary strand, and the electrophoretic mobility under nondenaturating PAGE of duplexes containing \u0394-Rh is notably different from duplexes containing \u039b-Rh. High-resolution PAGE of DNA photocleavage reactions initiated by irradiation of the tethered Rh complexes reveal intercalation of the complex only near the tethered end of the duplex. Analogous DNA-binding properties were observed with [Rh(phi)_2(bpy')]^(3+) tethered to the 3' terminus. By combining the 3' and 5' modification strategies, a mixed-metal DNA conjugate containing both [Os(phen)(bpy')(Me_2-dppz)]^(2+) (Me_2-dppz = 7,8-dimethyldipyridophenazine) on the 3' terminus and [Rh(phi)_2(bpy')]^(3+) on the 5' terminus was prepared and isolated. Taken together, these strategies for preparing metallointercalator\u2212DNA conjugates offer a useful approach to generate chemical assemblies to probe long-range DNA-mediated charge transfer where the redox initiator is confined to and intercalated in a well-defined binding site.", "doi": "10.1021/bc9900791", "issn": "1043-1802", "publisher": "American Chemical Society", "publication": "Bioconjugate Chemistry", "publication_date": "1999-10-21", "series_number": "6", "volume": "10", "issue": "6", "pages": "1122-1130" }, { "id": "authors:np9xs-6g382", "collection": "authors", "collection_id": "np9xs-6g382", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160407-115524676", "type": "article", "title": "Recognition and Reaction of Metallointercalators with DNA", "author": [ { "family_name": "Erkkila", "given_name": "Kathryn E.", "clpid": "Erkkila-K-E" }, { "family_name": "Odom", "given_name": "Duncan T.", "clpid": "Odom-D-T" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The design of small complexes that bind and react at specific sequences of DNA becomes important as we begin to delineate, on a molecular level, how genetic information is expressed. A more complete understanding of how to target DNA sites with specificity will lead not only to novel chemotherapeutics but also to a greatly expanded ability for chemists to probe DNA and to develop highly sensitive diagnostic agents.", "doi": "10.1021/cr9804341", "issn": "0009-2665", "publisher": "American Chemical Society", "publication": "Chemical Reviews", "publication_date": "1999-09", "series_number": "9", "volume": "99", "issue": "9", "pages": "2777-2796" }, { "id": "authors:kw5hp-r8417", "collection": "authors", "collection_id": "kw5hp-r8417", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160407-115523468", "type": "article", "title": "Perturbing the DNA Sequence Selectivity of Metallointercalator\u2212Peptide Conjugates by Single Amino Acid Modification", "author": [ { "family_name": "Hastings", "given_name": "Curtis A.", "clpid": "Hastings-C-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Metallointercalator\u2212peptide conjugates that provide small molecular mimics to explore peptide\u2212nucleic acid recognition have been prepared. Specifically, a family of peptide conjugates of [Rh(phi)_2(phen')]^(3+) [where phi = 9,10-phenanthrenequinone diimine and phen' = 5-(amidoglutaryl)-1,10-phenanthroline] has been synthesized and their DNA-binding characteristics examined. Single amino acid modifications were made from the parent metallointercalator\u2212peptide conjugate [Rh(phi)_2(phen')]^(3+)-AANVAIAAWERAA-CONH_2, which targets 5'-CCA-3' site-specifically. Moving the glutamate at position 10 in the sequence of the appended peptide to position 6 {[Rh(phi)_2(phen')]^(3+)-AANVAEAAWARAA-CONH_2} changed the sequence preference of the metallointercalator\u2212peptide conjugate to 5'-ACA-3'. Subsequent mutation of the glutamate at position 6 to arginine {[Rh(phi)_2(phen')]^(3+)-AANVARAAWARAA-CONH_2} caused more complex changes in DNA recognition. Thermodynamic dissociation constants were determined for these metallointercalator\u2212peptide conjugates by photoactivated DNA cleavage assays with the rhodium intercalators. At 55 \u00b0C in the presence of 5 mM MnCl_2, [Rh(phi)_2(phen')]^(3+)-AANVAIAAWERAA-CONH_2 binds to a 5'-CCA-3' site with K_d = 5.7 \u00d7 10^(-8) M, whereas [Rh(phi)_2(phen')]^(3+)-AANVAEAAWARAA-CONH_2 binds to its target 5'-ACA-3' site with K_d = 9.9 \u00d7 10^(-8) M. The dissociation constant for [Rh(phi)_2(phen')]^(3+) with random-sequence DNA is 7.0 \u00d7 10^(-7) M. Structural models have been developed and refined to account for the observed sequence specificities. As with much larger DNA-binding proteins, with these metal\u2212peptide conjugate mimics, single amino acid changes can lead to single or multiple base changes in the DNA site targeted.", "doi": "10.1021/bi982039a", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "1999-08-03", "series_number": "31", "volume": "38", "issue": "31", "pages": "10042-10051" }, { "id": "authors:j35v6-tp535", "collection": "authors", "collection_id": "j35v6-tp535", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:WANpnas99", "type": "article", "title": "Femtosecond dynamics of DNA-mediated electron transfer", "author": [ { "family_name": "Wan", "given_name": "Chaozhi", "clpid": "Wan-Chaozhi" }, { "family_name": "Fiebig", "given_name": "Torsten", "clpid": "Fiebig-T" }, { "family_name": "Kelley", "given_name": "Shana O.", "orcid": "0000-0003-3360-5359", "clpid": "Kelley-S-O" }, { "family_name": "Treadway", "given_name": "Christopher R.", "clpid": "Treadway-C-R" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Zewail", "given_name": "Ahmed H.", "clpid": "Zewail-A-H" } ], "abstract": "Diverse biophysical and biochemical studies have sought to understand electron transfer (ET) in DNA in part because of its importance to DNA damage and its repair. However, the dynamics and mechanisms of the elementary processes of ET in this medium are not fully understood and have been heavily debated. Two fundamental issues are the distance over which charge is transported and the time-scale on which the transport through the pi-stack of the DNA base pairs may occur. With femtosecond resolution, we report direct observation in DNA of ultrafast ET, initiated by excitation of tethered ethidium (E), the intercalated electron acceptor (A); the electron donor (D) is 7-deazaguanine (Z), a modified base, placed at different, fixed distances from A. The ultrafast ET between these reactants in DNA has been observed with time constants of 5 ps and 75 ps and was found to be essentially independent of the D-A separation (10-17 \u00c5). However, the ET efficiency does depend on the D-A distance. The 5-ps decay corresponds to direct ET observed from 7-deazaguanine but not guanine to E. From measurements of orientation anisotropies, we conclude that the slower 75-ps process requires the reorientation of E before ET, similar to E/nucleotide complexes in water. These results reveal the nature of ultrafast ET and its mechanism: in DNA, ET cannot be described as in proteins simply by a phenomenological parameter, beta. Instead, the involvement of the base pairs controls the time scale and the degree of coherent transport.", "pmcid": "PMC26827", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1999-05-25", "series_number": "11", "volume": "96", "issue": "11", "pages": "6014-6019" }, { "id": "authors:e4v1k-ak897", "collection": "authors", "collection_id": "e4v1k-ak897", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160407-115524241", "type": "article", "title": "Site-Specific Inhibition of Transcription Factor Binding to DNA by a Metallointercalator", "author": [ { "family_name": "Odom", "given_name": "Duncan T.", "clpid": "Odom-D-T" }, { "family_name": "Parker", "given_name": "Carl S.", "orcid": "0000-0001-9795-4211", "clpid": "Parker-C-S" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The metallointercalator \u039b-1-Rh(MGP)_2phi^(5+) binds tightly and specifically to the site 5'-CATATG-3' in the major groove of double helical DNA by a combination of direct readout and shape selection. To examine competitive interactions between this small metal complex and a DNA-binding transcription factor, the preferred binding site for \u039b-1-Rh(MGP)_2phi^(5+) was engineered into the AP-1 recognition element (ARE) of the major-groove binding bZIP transcription factor yAP-1, the yeast analogue of mammalian AP-1. Binding experiments confirmed that the modified ARE retained normal yAP-1 binding affinity. Photocleavage experiments demonstrated that the modified ARE contained a high-affinity binding site for \u039b-1-Rh(MGP)_2phi^(5+), whereas the native ARE showed no interaction. Competition experiments using gel shift mobility assays demonstrated that \u039b-1-Rh(MGP)_2phi^(5+) at 120 nM competes 50% of yAP-1 binding to the 5'-CATATG-3' containing oligonucleotide. In contrast, competitive disruption of protein binding to the native ARE requires 3 \u03bcM \u039b-1-Rh(MGP)_2phi^(5+). Metallointercalator derivatives, including geometric isomers of \u039b-1-Rh(MGP)_2phi^(5+), show no specific binding to the target site and show no inhibition of yAP-1/DNA complexes at concentrations as high as 20 \u03bcM. Thus, metallointercalators can be tuned to show selectivity for major groove sites on DNA comparable to transcription factors and indeed can inhibit transcription factor binding site selectively.", "doi": "10.1021/bi9827969", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "1999-04-20", "series_number": "16", "volume": "38", "issue": "16", "pages": "5155-5163" }, { "id": "authors:dw48p-b7c19", "collection": "authors", "collection_id": "dw48p-b7c19", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160407-115523781", "type": "article", "title": "A Versatile Mismatch Recognition Agent: Specific Cleavage of a Plasmid DNA at a Single Base Mispair", "author": [ { "family_name": "Jackson", "given_name": "Brian A.", "clpid": "Jackson-B-A" }, { "family_name": "Alekseyev", "given_name": "Viktor Y.", "clpid": "Alekseyev-V-Y" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "[Rh(bpy)_2(chrysi)]^(3+) is a novel, sterically bulky DNA intercalator that has been designed to bind specifically in the destabilized regions near DNA base mismatches and, upon photoactivation, to cleave the DNA backbone. Here the molecule is shown to be both a general and remarkably specific mismatch recognition agent. Specific DNA cleavage is observed at over 80% of mismatch sites in all the possible single base pair sequence contexts around the mispaired bases. Moreover, the complex is highly site-specific; it is shown to recognize and photocleave at a single base mismatch in a 2725 base pair linearized plasmid heteroduplex. Sterically demanding intercalators such as [Rh(bpy)_2(chrysi)]^(3+) may have application both in mutation detection systems and as mismatch-specific chemotherapeutic agents.", "doi": "10.1021/bi990255t", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "1999-04-13", "series_number": "15", "volume": "38", "issue": "15", "pages": "4655-4662" }, { "id": "authors:6drxs-2na36", "collection": "authors", "collection_id": "6drxs-2na36", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180507-111150983", "type": "article", "title": "Long-Range Electron Transfer through DNA Films", "author": [ { "family_name": "Kelley", "given_name": "Shana O.", "orcid": "0000-0003-3360-5359", "clpid": "Kelley-S-O" }, { "family_name": "Jackson", "given_name": "Nicole M.", "clpid": "Jackson-N-M" }, { "family_name": "Hill", "given_name": "Michael G.", "clpid": "Hill-M-G" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Regardless of its position within the DNA film, cross\u2010linked daunomycin (DM) is efficiently reduced electrochemically, indicating that the electron transfer exhibits a shallow distance dependence. Upon the introduction of an intervening cytosine\u2013adenine (CA) mismatch, the electrochemical response is dramatically attenuated (shown schematically). Therefore, the DNA double helix can facilitate long\u2010range electron transfer, but only in the presence of a well\u2010stacked pathway.", "doi": "10.1002/(SICI)1521-3773(19990401)38:7<941::AID-ANIE941>3.0.CO;2-7", "issn": "1433-7851", "publisher": "Wiley", "publication": "Angewandte Chemie International Edition", "publication_date": "1999-04-01", "series_number": "7", "volume": "38", "issue": "7", "pages": "941-945" }, { "id": "authors:baba5-vbh63", "collection": "authors", "collection_id": "baba5-vbh63", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160407-115522678", "type": "article", "title": "Metal-Dependent Intramolecular Chiral Induction: The Zn^(2+) Complex of an Ethidium\u2212Peptide Conjugate", "author": [ { "family_name": "Houser", "given_name": "Robert P.", "clpid": "Houser-R-P" }, { "family_name": "Fitzsimons", "given_name": "Marilena P.", "clpid": "Fitzsimons-M-P" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Ethidium bromide is an aromatic organic dye that for many years has been known to bind via intercalation to the minor groove of DNA. When the ethidium cation binds to DNA, the chirality of the right-handed double helix is imposed upon ethidium (Et), producing induced circular dichroism (ICD). Other examples of ICD have been observed in the heme group of hemoglobin and myoglobin as well as synthetic porphyrin assemblies, and in host\u2212guest assemblies. In every case, an ICD spectrum is produced as a result of the close association of an achiral chromophore with a chiral moiety (e.g., a biopolymer). During the course of our ongoing research into artificial hydrolytic nucleases, we prepared an ethidium\u2212peptide conjugate that displays metal-dependent ICD. Here we report the synthesis and spectroscopic characterization of a metal\u2212peptide assembly which may represent a first example of metal-dependent intramolecular chiral induction.", "doi": "10.1021/ic981012c", "issn": "0020-1669", "publisher": "American Chemical Society", "publication": "Inorganic Chemistry", "publication_date": "1999-03-22", "series_number": "6", "volume": "38", "issue": "6", "pages": "1368-1370" }, { "id": "authors:5645k-3d156", "collection": "authors", "collection_id": "5645k-3d156", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:FIEpnas99", "type": "article", "title": "Femtosecond dynamics of the DNA intercalator ethidium and electron transfer with mononucleotides in water", "author": [ { "family_name": "Fiebig", "given_name": "Torsten", "clpid": "Fiebig-T" }, { "family_name": "Wan", "given_name": "Chaozhi", "clpid": "Wan-Chaozhi" }, { "family_name": "Kelley", "given_name": "Shana O.", "orcid": "0000-0003-3360-5359", "clpid": "Kelley-S-O" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Zewail", "given_name": "Ahmed H.", "clpid": "Zewail-A-H" } ], "abstract": "Ethidium (E) is a powerful probe of DNA dynamics and DNA-mediated electron transfer (ET). Molecular dynamical processes, such as solvation and orientation, are important on the time scale of ET. Here, we report studies of the femtosecond and picosecond time-resolved dynamics of E, E with 2'deoxyguanosine triphosphate (GTP) in water, and E with 7-deaza-2'-deoxyguanosine triphosphate (ZTP) in water; E undergoes ET with ZTP but not GTP. These studies elucidate the critical role of relative orientational motions of the donor-acceptor complex on ET processes in solution. For ET from ZTP to E, such motions are in fact the rate-determining step. Our results indicate that these complexes reorient before ET. The time scale for the solvation of E in water is 1 ps, and the orientational relaxation time of E is 70 ps. The impact of orientational and solvation effects on ET between E and mononucleotides must be considered in the application of E as a probe of DNA ET.", "pmcid": "PMC15438", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1999-02-16", "series_number": "4", "volume": "96", "issue": "4", "pages": "1187-1192" }, { "id": "authors:00xdp-93b29", "collection": "authors", "collection_id": "00xdp-93b29", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160330-112528546", "type": "article", "title": "Long-range oxidative damage to DNA: Effects of distance and sequence", "author": [ { "family_name": "N\u00fa\u00f1ez", "given_name": "Megan E.", "clpid": "N\u00fa\u00f1ez-M-E" }, { "family_name": "Hall", "given_name": "Daniel B.", "clpid": "Hall-D-B" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Introduction: Oxidative damage to DNA in vivo can lead to mutations and cancer. DNA damage and repair studies have not yet revealed whether permanent oxidative lesions are generated by charges migrating over long distances. Both photoexcited ^*Rh(III) and ground-state Ru(III) intercalators were previously shown to oxidize guanine bases from a remote site in oligonucleotide duplexes by DNA-mediated electron transfer. Here we examine much longer charge-transport distances and explore the sensitivity of the reaction to intervening sequences.\nResults: Oxidative damage was examined in a series of DNA duplexes containing a pendant intercalating photooxidant. These studies revealed a shallow dependence on distance and no dependence on the phasing orientation of the oxidant relative to the site of damage, 5\u2032-GG-3\u2032. The intervening DNA sequence has a significant effect on the yield of guanine oxidation, however. Oxidation through multiple 5\u2032-TA-3\u2032 steps is substantially diminished compared to through other base steps. We observed intraduplex guanine oxidation by tethered *Rh(III) and Ru(III) over a distance of 200 A. The distribution of oxidized guanine varied as a function of temperature between 5 and 35 \u00b0C, with an increase in the proportion of long-range damage (> 100 A) occurring at higher temperatures.\nConclusions: Guanines are oxidized as a result of DNA-mediated charge transport over significant distances (e.g. 200 A). Although long-range charge transfer is dependent on distance, it appears to be modulated by intervening sequence and sequence-dependent dynamics. These discoveries hold important implications with respect to DNA damage in vivo.", "doi": "10.1016/S1074-5521(99)80005-2", "issn": "1074-5521", "publisher": "Elsevier", "publication": "Chemistry and Biology", "publication_date": "1999-02", "series_number": "2", "volume": "6", "issue": "2", "pages": "85-97" }, { "id": "authors:c4k9z-fkk32", "collection": "authors", "collection_id": "c4k9z-fkk32", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141124-090349421", "type": "article", "title": "Electron Transfer Between Bases in Double Helical DNA", "author": [ { "family_name": "Kelley", "given_name": "Shana O.", "orcid": "0000-0003-3360-5359", "clpid": "Kelley-S-O" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Fluorescent analogs of adenine that selectively oxidize guanine were used to investigate photoinduced electron transfer through the DNA \u03c0-stack as a function of reactant stacking and energetics. Small variations in these factors led to profound changes in the kinetics and distance dependences of DNA-mediated electron-transfer reactions. Values of \u03b2, a parameter reflecting the dependence of electron transfer on distance, ranged from 0.1 to 1.0 per angstrom. Strong stacking interactions result in the fastest electron-transfer kinetics. Electrons are thus transported preferentially through an intrastrand rather than interstrand pathway. Reactant energetics also modulate the distance dependence of DNA-mediated charge transport. These studies may resolve the range of disparate results previously reported, and paradigms must now be developed to describe these properties of the DNA \u03c0-stack, which can range from insulator- to \"wire\"-like.", "doi": "10.1126/science.283.5400.375", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "1999-01-15", "series_number": "5400", "volume": "283", "issue": "5400", "pages": "375-381" }, { "id": "authors:8rfzr-kex28", "collection": "authors", "collection_id": "8rfzr-kex28", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180524-162758977", "type": "article", "title": "Dipyridophenazine Complexes of Os(II) as Red-Emitting DNA Probes:\u2009 Synthesis, Characterization, and Photophysical Properties", "author": [ { "family_name": "Holmlin", "given_name": "R. Erik", "clpid": "Holmlin-R-E" }, { "family_name": "Yao", "given_name": "Johanna A.", "clpid": "Yao-Johanna-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Polypyridyl complexes of Os(II) bearing one dipyridophenazine (dppz) derivative and two ancillary ligands derived from bipyridine (bpy) or phenanthroline (phen) exhibit emission maxima at \u223c740 nm and average excited-state lifetimes in the 10 ns range upon binding to DNA by preferential intercalation of the dppz ligand. A family of [Os(L^1)(L^2)(L^3)]^(2+) and [Os(L^1)_2(L^2)]^(2+) complexes with simple modifications in the ancillary phen or bpy ligands (L^1 and L^3) as well as the intercalating dppz ligand (L^2) was prepared. By cyclic voltammetry, electron-donating substituents on the ancillary ligands lowered the Os(3+/2+) reduction potential but did not affect the reduction potential of the dppz ligand. A methyl substituent at the 7-, 8-, or 6-position of the dppz ligand shifted the phenazine reduction toward the negative but did not affect the Os(3+/2+) potential. Absorption titrations indicated intercalative binding to DNA with high affinity (K_B \u223c10^6 M^(-1)) for the family of complexes, although at high ratios (50:1) of base pairs to metal, complexes with ancillary 4,7-dimethylphenanthroline or 4,4'-dimethylbipyridine ligands exhibit less hypochromism (26\u221227%) in the \u03c0\u2212\u03c0* transition on the dppz ligand compared to complexes with 5,6-dimethylphenanthroline (30\u221237%) or the parent phen (31\u221235%). By steady-state and time-resolved emission spectroscopy, complexes bound to DNA by intercalation with substituents on the 4,7- or 4,4'-positions of the ancillary phen or bpy displayed lower quantum yields for emission (\u03a6_(em)) compared to complexes with the parent phen, while complexes with methyl substituents on the dppz ligand had the greatest \u03a6_(em). Studies with poly d(AT), poly d(GC), and mixed-sequence DNA revealed that the emission yields are also sequence-dependent. Comparative luminescence studies in CH_2Cl_2 demonstrated that these effects arise from a combination of (i) the inherent sensitivity of the excited state to ligand structure and (ii) perturbations in DNA binding geometry introduced by substituents on the ancillary and intercalating ligands. Our results clarify the relationships between ligand architecture and emission yield and lifetime in the presence and absence of DNA and illustrate the utility of dppz complexes of Os(II) as luminescent probes for DNA.", "doi": "10.1021/ic9808955", "issn": "0020-1669", "publisher": "American Chemical Society", "publication": "Inorganic Chemistry", "publication_date": "1999-01-11", "series_number": "1", "volume": "38", "issue": "1", "pages": "174-189" }, { "id": "authors:yyx01-pdd91", "collection": "authors", "collection_id": "yyx01-pdd91", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160407-115522359", "type": "article", "title": "Functionalized Rhodium Intercalators for DNA Recognition", "author": [ { "family_name": "Terbrueggen", "given_name": "Robert H.", "clpid": "Terbrueggen-R-H" }, { "family_name": "Johann", "given_name": "Timothy W.", "clpid": "Johann-T-W" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "A series of rhodium complexes containing the phenanthrenequinone diimine (phi) ligand have been prepared which bind DNA by intercalation and, upon photoactivation, promote DNA strand breaks. In this series, the ancillary, nonintercalating bipyridyl or phenanthroline ligands have been functionalized to yield complexes containing guanidinium, amido, or amino groups arranged with defined stereochemistry for site-specific interaction with the DNA bases. \u039b-1-[Rh(MGP)_2phi]^(5+) (MGP = 4-(guanidylmethyl)-1,10-phenanthroline) site-specifically targets the 6-base pair sequence 5'-CATATG-3' with a binding affinity of 1 (\u00b10.5) \u00d7 10^8 M^(-1) while \u0394-1-[Rh(MGP)_2phi]^(5+) displays an affinity of 5 (\u00b12) \u00d7 10^7 M^(-1) for 5'-CATCTG-3'. Even though these two isomers target sites which differ by only a single base, binding is highly enantioselective. The specificity is derived chiefly from interactions of the pendant guanidinium groups with the DNA bases. For the racemates of 1-[Rh(GEB)_2phi]^(5+) (GEB = (4-(2-guanidylethyl)-4'-methyl-2,2'-bipyridine) and 1-[Rh(GPB)_2phi]^(5+) (GPB = (4-(2-guanidylpropyl)-4'-methyl-2,2'-bipyridine), photocleavage patterns also show the strongest site of photocleavage as 5'-CATCTG-3', the target site for \u0394-1-[Rh(MGP)_2phi]^(5+). Moreover, consistent with the dominance of the guanidinium groups in establishing specificity, significantly enhanced photocleavage is evident for the 1-positional isomer of these complexes, where the guanidinium moieties are directed toward the DNA (above and below the phi ligand) compared to the 2-isomer, in which the guanidinium groups are directed away from the DNA. In contrast to \u039b-1-[Rh(MGP)_2phi]^(5+), \u039b-1-[Rh(GEB)_2phi]^(5+) shows little cleavage at 5'-CATATG-3'; this sensitivity to linker length likely depends on the mode of recognition of 5'-CATATG-3' involving sequence-dependent unwinding of the DNA site. Analogous site-specificity or isomer-specificity is not evident with the complexes which contain pendant amido or amino functionalities. Instead these complexes appear to resemble the parent, unfunctionalized [Rh(phen)_2phi]^(3+) with respect to recognition. Pendant guanidinium functionalities appear to be particularly advantageous in the construction of small molecules which bind DNA with site-specificity.", "doi": "10.1021/ic980837j", "issn": "0020-1669", "publisher": "American Chemical Society", "publication": "Inorganic Chemistry", "publication_date": "1998-12-28", "series_number": "26", "volume": "37", "issue": "26", "pages": "6874-6883" }, { "id": "authors:asa37-wt520", "collection": "authors", "collection_id": "asa37-wt520", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180719-155943234", "type": "article", "title": "Orienting DNA Helices on Gold Using Applied Electric Fields", "author": [ { "family_name": "Kelley", "given_name": "Shana O.", "orcid": "0000-0003-3360-5359", "clpid": "Kelley-S-O" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Jackson", "given_name": "Nicole M.", "clpid": "Jackson-N-M" }, { "family_name": "McPherson", "given_name": "Lee D.", "clpid": "McPherson-L-D" }, { "family_name": "Potter", "given_name": "Aaron B.", "clpid": "Potter-A-B" }, { "family_name": "Spain", "given_name": "Eileen M.", "clpid": "Spain-E-M" }, { "family_name": "Allen", "given_name": "Michael J.", "clpid": "Allen-M-J" }, { "family_name": "Hill", "given_name": "Michael G.", "clpid": "Hill-M-G" } ], "abstract": "Gold surfaces modified with thiol-derivatized DNA duplexes have been investigated as a function of applied electrochemical potential via atomic force microscopy (EC-AFM). At open circuit, monolayers of well-packed DNA helices form with a film depth of 45(3) \u00c5. On the basis of the anisotropic dimensions of these 15 base pair duplexes (20 \u00c5 in diameter versus 50 \u00c5 in length), this corresponds to an average \u223c45\u00b0 orientation of the helical axis with respect to the gold surface. Under potential control, the monolayer thickness (and therefore the orientation of the helices) changes dramatically with applied potential. At potentials negative of \u223c0.45 V (versus a Ag wire quasi-reference electrode) film thicknesses of \u223c55 \u00c5 are observed, whereas at more positive potentials the monolayer thickness drops to a limiting value of \u223c20 \u00c5. These results are consistent with a morphology change in which the helices either stand straight up or lie flat down on the metal surface, depending on the electrode potential relative to the potential of zero charge (pzc). This voltage-induced morphology change is reversible and effectively constitutes a nanoscale mechanical \"switch\".", "doi": "10.1021/la980874n", "issn": "0743-7463", "publisher": "American Chemical Society", "publication": "Langmuir", "publication_date": "1998-11-24", "series_number": "24", "volume": "14", "issue": "24", "pages": "6781-6784" }, { "id": "authors:kb78d-28k57", "collection": "authors", "collection_id": "kb78d-28k57", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160407-115523216", "type": "article", "title": "Differential DNA Recognition by the Enantiomers of 1-Rh(MGP)_2phi: A Combination of Shape Selection and Direct Readout", "author": [ { "family_name": "Franklin", "given_name": "Sonya J.", "clpid": "Franklin-S-F" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The enantiomers of the symmetric metallointercalator complex 1-Rh(MGP)_2phi^(5+) [MGP = 4-(guanidylmethyl)-1,10-phenanthroline; phi = phenanthrenequinone diimine] bound to DNA decamer duplexes containing their respective 6 bp recognition sequences have been investigated using ^1H NMR. Shape selection due to the chirality of the metal center and hydrogen-bonding contacts of ancillary guanidinium groups to 3'-G N7 atoms define the recognition by complexes which bind by intercalation to duplex DNA. The titration of \u039b-Rh into the self-complementary decamer containing the recognition sequence (5'-GACATATGTC-3', L1) resulted in one symmetric bound conformation observed in the ^1H NMR spectrum, indicating that the DNA duplex retains its symmetry in the presence of the metal complex. Upfield chemical shifts of duplex imino protons and the disruption of the NOE base\u2212sugar contacts defined the central T5-A6 intercalation site. The downfield shift of the G8 imino proton supports the conclusion that the pendant guanidinium arms make simultaneous H-bonding contacts to the N7 atoms of 3'-G8 bases on either side of the site. A variable-temperature study of a partially titrated sample (2:3 \u039b-Rh/L1) showed the exchange rate (k_(obs)) at 298 K to be 68 s^(-1) and the activation barrier to exchange (\u0394G^\u29e7 of association) to be 2.7 kcal/mol, a value comparable to the stacking energy of one base step. The results presented coupled with biochemical data are therefore consistent with binding models in which \u039b-1-Rh(MGP)_2phi^(5+) (\u039b-Rh) traps the recognition site 5'-CATATG-3' in an unwound state, permitting intercalation centrally and hydrogen bonding to guanines at the first and sixth base pair positions. The data suggest a different model of binding and recognition by \u0394-Rh. The titration of \u0394-Rh into a DNA decamer containing the 6 bp recognition site (D1, 5'-CGCATCTGAC-3'; D2, 5'-GTCAGATGCG-3') resulted in two, distinct conformers, in slow exchange on the NMR time scale. The rate of exchange between the two conformers (k_(obs)) at 298 K is 37 s^(-1), most likely due to partial dissociation between binding modes. The slower rate relative to \u039b-Rh association reflects the relative rigidity of the D1 and/or D2 sequence in comparison to L1. NOE cross-peaks between the intercalating phi ligand and protons of T5-C6, as well as the upfield shifts observed for imino protons at this step, serve to define the central T5-C6 step as the single site of intercalation. The downfield shift of the 3'-G imino protons indicates the complex makes hydrogen bond contacts with these bases. The complex, which is too small to span a 6 bp B-form DNA sequence, nonetheless makes major groove contacts with 3'-G bases to either side of the site. Notably, both 3'-guanine bases are necessary to impart site specificity and slow dissociation kinetics with the 5'-CATCTG-3' site, as evidenced by the extremely exchange-broadened two-dimensional NOESY spectra of \u0394-Rh bound to modified duplexes containing N7-deazaguanine at either G8 or G18; the loss of one major groove contact completely abolishes specificity for 5'-CATCTG-3'. DNA chemical shifts upon binding and intermolecular NOE contacts therefore support a model in which \u0394-Rh intercalates in one of two canted binding conformations. Within this model, each intercalation mode allows one guanidinium\u2212guanine hydrogen bond at a time, while bringing the other arm close to the phosphate backbone.", "doi": "10.1021/bi981798q", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "1998-11-17", "series_number": "46", "volume": "37", "issue": "46", "pages": "16093-16105" }, { "id": "authors:tv2p1-dj909", "collection": "authors", "collection_id": "tv2p1-dj909", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160407-115522973", "type": "article", "title": "Long-Range and Short-Range Oxidative Damage to DNA: Photoinduced Damage to Guanines in Ethidium\u2212DNA Assemblies", "author": [ { "family_name": "Hall", "given_name": "Daniel B.", "clpid": "Hall-D-B" }, { "family_name": "Kelley", "given_name": "Shana O.", "orcid": "0000-0003-3360-5359", "clpid": "Kelley-S-O" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Short-range and long-range photoreactions between ethidium and DNA have been characterized. While no DNA reaction is observed upon excitation into the visible absorption band of ethidium, higher-energy irradiation (313\u2212340 nm) leads both to direct strand cleavage at the 5'-G of 5'-GG-3' doublets and to piperidine-sensitive lesions at guanine. This reactivity is not consistent with oxidation of guanine by either electron transfer or singlet oxygen as shown by comparison with reactions of a rhodium intercalator and methylene blue, respectively. By covalently tethering ethidium to one end of a DNA duplex, we demonstrate the presence of two distinct reactions, one short-range and the other long-range. The short-range reaction involves a covalent modification of guanine by ethidium, based upon HPLC analysis of the nucleoside products and studies with ethidium derivatives. The long-range reaction is entirely consistent with oxidation of guanine by DNA-mediated electron transfer. The yield of this electron-transfer reaction is not attenuated with distance; equal yields of guanine damage are observed at a proximal (17 \u00c5 Et\u2212GG separation) and distal (44 \u00c5 Et\u2212GG separation) site. These results are quite similar to those previously observed with a covalently tethered rhodium photooxidant and underscore the unique ability of the DNA base stack to facilitate long-range electron transfer so as to effect oxidative damage from a distance.", "doi": "10.1021/bi981750c", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "1998-11-10", "series_number": "45", "volume": "37", "issue": "45", "pages": "15933-15940" }, { "id": "authors:26na4-s1b15", "collection": "authors", "collection_id": "26na4-s1b15", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180524-163555321", "type": "article", "title": "A Reinvestigation by Circular Dichroism and NMR:\u2009 Ruthenium(II) and Rhodium(III) Metallointercalators Do Not Bind Cooperatively to DNA", "author": [ { "family_name": "Franklin", "given_name": "Sonya J.", "clpid": "Franklin-S-F" }, { "family_name": "Treadway", "given_name": "Christopher R.", "clpid": "Treadway-C-R" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Fast, long-range electron transfer mediated by the DNA helix has been questioned by some researchers citing the possible clustering, or cooperative association, of noncovalently bound donors and acceptors on DNA. A systematic investigation of binding to DNA by the metallointercalators \u0394-bis(1,10-phenanthroline)(dipyridophenazine)ruthenium(II) (Ru), \u0394-bis(9,10-phenanthrenequinone diimine)(2,2'-bipyridine)rhodium(III) (Rh), and \u0394-bis(9, 10-phenanthrenequinone diimine)(5-(amidoglutaryl)-1,10-phenanthroline)rhodium(III) (Rh') using circular dichroism and NMR has shown no evidence for their cooperative clustering on a DNA helix. Circular dichroism (CD) studies of Ru and Rh in [poly(dA-dT)]_2, mixed-sequence calf thymus DNA, and [poly(dG-dC)]_2 as a function of loading indicate that the largest perturbations to the CD signal occur upon initial addition of DNA, with no subsequent systematic variation. Difference spectra of the two metallointercalators bound together versus separately are virtually indistinguishable at high and low loadings. Two-dimensional 1H NMR studies of Ru and Rh' binding to a DNA decamer duplex in 90:10 H_2O/D_2O have also been conducted. A more direct structural picture of the site occupancies of these complexes on a DNA helix emerges through examination of the dramatic upfield shifts of the imino protons of the DNA bases that occur upon intercalation. These studies reveal that with both complexes present, each intercalates specifically toward either end of the duplex, with a 4 base pair separation between them. In contrast, the complexes individually bound to the duplex showed low site-selectivity, and preferred more central sites. If anything, these data indicate anti-cooperative binding to the helix, which might be expected based upon electrostatic considerations. Time-resolved measurements of the Ru(II) luminescence reveal substantial subnanosecond quenching (approximately 60%) in the presence of Rh(III). Based upon the NMR results, this quenching must proceed over a distance >14 \u00c5 via electron transfer through the DNA \u03c0-stack. These experiments with noncovalently bound intercalators are fully consistent with earlier studies of electron transfer through DNA utilizing covalently bound donors and acceptors and definitively prove clustering cannot be responsible for the fast photoinduced electron transfer between metallointercalators mediated by the DNA double helix.", "doi": "10.1021/ic9801948", "issn": "0020-1669", "publisher": "American Chemical Society", "publication": "Inorganic Chemistry", "publication_date": "1998-10-05", "series_number": "20", "volume": "37", "issue": "20", "pages": "5198-5210" }, { "id": "authors:vgg58-bq606", "collection": "authors", "collection_id": "vgg58-bq606", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180719-163630672", "type": "article", "title": "Reply to the Comment on \"Resonance Raman Investigation of Ru(phen)_2dppz^(2+) and Related Complexes in Water and in the Presence of DNA\"", "author": [ { "family_name": "Chen", "given_name": "Wei", "clpid": "Chen-Wei" }, { "family_name": "Turro", "given_name": "Claudia", "clpid": "Turro-C" }, { "family_name": "Friedman", "given_name": "Lee A.", "clpid": "Friedman-L-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Turro", "given_name": "Nicholas J.", "clpid": "Turro-N-J" } ], "abstract": "Our recent paper describes the rR spectra of Ru(phen)_2dppz^(2+), Ru(phen)_2(F_2-dppz)^(2+), and Os(phen)_2(dppz)^(2+) (phen = 1,10-phenanthroline, dppz = dipyrido[3,2-a:2',3'-d]phenazine, F_2-dppz = 7,8-difluoro-dppz) obtained utilizing 354.7 nm excitation (fwhm \u223c 10 ns). The spectra collected for Ru(phen)_2(F_2-dppz)^(2+) and Os(phen)_2(dppz)^(2+) were assigned to the ground state of the complexes at both high and low pulse energies. In the case of Ru(phen)_2dppz^(2+), the power dependence of the peaks at 1365 and 1453 cm^(-1) were consistent with an excited state. Our interpretation described below and on the recent paper was not based on the assumption that the ^3\u03c0\u03c0* state of the dppz ligand lies below the MLCT in Ru(phen)_2dppz^(2+), but rather that pumping directly into the dppz ^1\u03c0\u03c0* manifold could lead to trapping of the excitation at short time scales on the lowest LC dppz state (^3\u03c0\u03c0*) if crossing to the MLCT required activation. Lowering of the MLCT relative to the ^3\u03c0\u03c0* in Ru(phen)_2(F_2-dppz)^(2+) and Os(phen)_2(dppz)^(2+) would result in lowering the activation barrier and much faster crossing to the MLCT.", "doi": "10.1021/jp9817123", "issn": "1520-6106", "publisher": "American Chemical Society", "publication": "Journal of Physical Chemistry B", "publication_date": "1998-08-06", "series_number": "32", "volume": "102", "issue": "32", "pages": "6303" }, { "id": "authors:by1vb-rth94", "collection": "authors", "collection_id": "by1vb-rth94", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160330-112529738", "type": "article", "title": "DNA-mediated electron transfer from a modified base to ethidium: \u03c0-stacking as a modulator of reactivity", "author": [ { "family_name": "Kelley", "given_name": "Shana O.", "orcid": "0000-0003-3360-5359", "clpid": "Kelley-S-O" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Background: The DNA double helix is composed of an array of aromatic heterocyclic base pairs and, as a molecular \u03c0-stack, represents a novel system for studying long-range electron transfer. Because many base damage and repair processes result from electron-transfer reactions, the ability of DNA to mediate charge transport holds important biological implications. Seemingly contradictory conclusions have been drawn about electron transfer in DNA from the many different studies that have been carried out. These studies must be reconciled so that this phenomenon can be understood both at a fundamental level and in the context of biological systems.\n\nResults: The photoinduced oxidation of a modified base, 7-deazaguanine, has been examined as a function of distance, sequence, and base stacking in DNA duplexes covalently modified with ethidium. Over ethidium/deazaguanine separations of 6\u201327 \u00c5, the photooxidation reaction proceeded on a subnanosecond time scale, and the quenching yield exhibited a shallow distance dependence. The efficiency of the reaction was highly sensitive to small changes in base composition. Moreover, the overall distance-dependence of the reaction is sensitive to sequence, despite the constancy of photoexcited ethidium as acceptor.\n\nConclusions: The remarkable efficiency of deazaguanine photooxidation by intercalated ethidium over long distances provides new evidence for fast electron-transfer pathways through DNA. By varying sequence as well as reactant separation, this work provides the first experimental demonstration of the importance of reactant stacking in the modulation of long-range DNA-mediated electron transfer.", "doi": "10.1016/S1074-5521(98)90158-2", "issn": "1074-5521", "publisher": "Elsevier", "publication": "Chemistry and Biology", "publication_date": "1998-08", "series_number": "8", "volume": "5", "issue": "8", "pages": "413-425" }, { "id": "authors:nptvb-abb48", "collection": "authors", "collection_id": "nptvb-abb48", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180524-164125514", "type": "article", "title": "A Versatile Synthetic Approach to Rhodium(III) Diimine Metallointercalators:\u2009 Condensation of o-Quinones with Coordinated cis-Ammines", "author": [ { "family_name": "M\u00fcrner", "given_name": "Hansruedi", "clpid": "M\u00fcrner-H" }, { "family_name": "Jackson", "given_name": "Brian A.", "clpid": "Jackson-B-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "A new route to the preparation of rhodium(III) diimine complexes which bind DNA by intercalation was developed by condensation of coordinated ammine ligands with o-quinones. Starting from cis-[Rh(L\u2227L)_2(NH_3)_2]^(3+) (L\u2227L:\u2009 2,2'-bipyridine or 1,10-phenanthroline) and the appropriate quinones the ligands 9,10-phenanthrenequinone diimine (phi) and 5,6-chrysenequinone diimine (chrysi) were introduced in high yields. The reactions are completed within hours at ambient temperature in MeCN/water mixtures, 0.1 M in NaOH. Experiments with enantiomerically pure \u0394-[Rh(phen)_2(NH_3)_2]^(3+) and 9,10-phenanthrenequinone showed that the configuration at the metal center is retained during the course of the reaction. Condensation of rhodium(III) tetraammine starting material with 9,10-phenanthrenequinone allows the selective introduction of one or two phi ligands, depending on the reaction conditions. The ability to incorporate specifically only one phi ligand makes this a promising approach for the synthesis of tris(heteroleptic) coordination compounds, and one example of such a complex, [Rh(phen)(phi)(chrysi)]^(3+), is provided.", "doi": "10.1021/ic9800738", "issn": "0020-1669", "publisher": "American Chemical Society", "publication": "Inorganic Chemistry", "publication_date": "1998-06-15", "series_number": "12", "volume": "37", "issue": "12", "pages": "3007-3012" }, { "id": "authors:ajka8-1wc06", "collection": "authors", "collection_id": "ajka8-1wc06", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160407-101623917", "type": "article", "title": "Rh(Phen)_2Phi^(3+) as a Shape-Selective Probe of Triple Helices", "author": [ { "family_name": "Lim", "given_name": "Ai Ching", "clpid": "Lim-Ai-Ching" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "RNA pur\u2022pur-pyr and pyr\u2022pur-pyr (pur = purine, pyr = pyrimidine) triple helices consisting of a Watson\u2212Crick base-paired 28mer hairpin duplex and a Hoogsteen base-paired purine or pyrimidine 12mer are targeted with photoactivated cleavage by the metal complex Rh(phen)_2phi^(3+) (phen = phenanthroline, phi = 9,10-phenanthrenequinone diimine). The metal complex interacts with these triple helices in a structure-specific manner. Different cleavage patterns are seen with the pyr\u2022pur-pyr and pur\u2022pur-pyr motifs. Cleavage is seen on both of the Watson\u2212Crick strands of the former motif and primarily on the purine Watson\u2212Crick strand of the latter motif. Little cleavage is seen on the Hoogsteen strand for either motif. Importantly, the metal complex shows no detectable cleavage on the A-form RNA duplex in the absence of the third Hoogsteen strand. The cleavage patterns are consistent with an intercalated model for the metal complex in the triple helix. Similar cleavage is seen on DNA triple helices, but over a background of duplex cleavage. Targeting of synthetic RNA triple helices, but not duplex regions, by Rh(phen)_2phi^(3+) provides a basis for the chemical probing of triply bonded sites in folded RNA molecules.", "doi": "10.1021/bi980509v", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "1998-06-05", "series_number": "25", "volume": "37", "issue": "25", "pages": "9138-9146" }, { "id": "authors:98tg8-3vr51", "collection": "authors", "collection_id": "98tg8-3vr51", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160407-101621786", "type": "article", "title": "Oxidative Charge Transfer To Repair Thymine Dimers and Damage Guanine Bases in DNA Assemblies Containing Tethered Metallointercalators", "author": [ { "family_name": "Dandliker", "given_name": "Peter J.", "clpid": "Dandliker-P-J" }, { "family_name": "N\u00fa\u00f1ez", "given_name": "Megan E.", "clpid": "N\u00fa\u00f1ez-M-E" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Potent oxidants which intercalate in DNA serve as tools to probe DNA-mediated electron-transfer reactions. A photoexcited rhodium intercalator, Rh(phi)_2DMB^(3+) (phi = 9,10-phenanthrenequinone diimine and DMB = 4,4'-dimethyl-2,2'-bipyridine), tethered to DNA, promotes both oxidative damage to 5'-GG-3' doublets in DNA and the repair of thymine dimers from a remote site on the DNA duplex. DNA-mediated repair of a thymine dimer lesion by charge transfer from the tethered rhodium intercalator is quantitative, albeit with low photoefficiency, occurs in an intraduplex reaction over long range (36 \u00c5), and requires that the intervening bases be paired. When both oxidative reactions, repair and oxidative damage, are monitored on the same duplex, competition is evident; the presence of both a 5'-GG-3' site and the thymine dimer diminished the dimer repair efficiency by 20\u221240% and decreased damage at the 5'-GG-3' sites 2-fold compared to similar sequences lacking either the guanine doublet or thymine dimer, respectively. In addition to damage at the 5'-G of 5'-GG-3' sites, we also observe oxidation at the 3'-G of the 5'-GT<>TG-3' tetrad only in the presence of thymine dimer. Overall, the yield of repaired thymine strand was at least 10 times higher than the yield of oxidized guanine in the same sequences. While the 5-GG-3' may represent the thermodynamically favored site for oxidative reaction, repair of the thymine dimer appears to be kinetically more favorable. Dipyridophenanzine (dppz) complexes of ruthenium(III), less potent oxidants which intercalate in DNA, oxidize 5'-GG-3' doublets efficiently but cannot trigger the repair of the thymine dimer lesion. Oxidative damage to DNA from a distance, mediated by the DNA base pair stack, can, however, be utilized to probe the disruption in the base stack generated by the thymine dimer. The presence of the dimer does not diminish oxidation by a Ru(III) intercalator at a distal guanine doublet, suggesting that the disruption caused by the dimer does not block charge transfer through the DNA duplex. DNA-mediated electron-transfer reactions of metallointercalators therefore serve to illustrate important aspects of radical migration and its consequence with respect to reactions at a distance through the DNA base pair stack.", "doi": "10.1021/bi980041w", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "1998-05-05", "series_number": "18", "volume": "37", "issue": "18", "pages": "6491-6502" }, { "id": "authors:hjbzs-qv013", "collection": "authors", "collection_id": "hjbzs-qv013", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180808-100416627", "type": "article", "title": "DNA-mediated electron transfer: Chemistry at a distance", "author": [ { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The DNA double helix, containing a \u03c0-stacked array of base pairs in its core, represents a unique and efficient medium for long-range charge transport. DNA assemblies have been constructed containing tethered metallointercalators, and these provide chemically well-defined systems\nthrough which to probe the DNA \u03c0-stack. Using both spectroscopy and chemical assays of reactivity, we find electron transfer reactions mediated by the DNA base pairs to occur over long molecular distances. The structure of DNA facilitates chemistry at a distance. Importantly, these\nlong-range reactions depend sensitively upon base pair stacking, and hence are modulated by and report on the characteristic stacking within the double helix.", "doi": "10.1351/pac199870040873", "issn": "0033-4545", "publisher": "International Union of Pure and Applied Chemistry", "publication": "Pure and Applied Chemistry", "publication_date": "1998-04", "series_number": "4", "volume": "70", "issue": "4", "pages": "873-879" }, { "id": "authors:89qa3-22w58", "collection": "authors", "collection_id": "89qa3-22w58", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160411-102728744", "type": "article", "title": "Ru(phen)_2dppz^(2+) Luminescence: Dependence on DNA Sequences and Groove-Binding Agents", "author": [ { "family_name": "Holmlin", "given_name": "R. Erik", "clpid": "Holmlin-R-E" }, { "family_name": "Stemp", "given_name": "Eric D. A.", "orcid": "0000-0003-2098-4214", "clpid": "Stemp-E-D-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Emission of \u0394-Ru(phen)_2dppz^(2+) bound to nucleic acid polymers of different sequence has been investigated by time-resolved luminescence spectroscopy and the effect of major and minor groove DNA binding agents on the luminescence profile of the complex evaluated. In the presence of a 1:1 mixture of poly d(AT) and poly d(GC), the excited-state decay of \u0394-Ru(phen)_2dppz^(2+) can be described by a linear combination of the decay profiles in the presence of poly d(AT) and poly d(GC) independently. This analysis indicates that \u223c85% of the complexes are bound to poly d(AT) and that the metallointercalator preferentially occupies AT sites in mixed-sequence polymers such as calf thymus or T4 DNA. When rac-Ru(phen)_2dppz^(2+) bound to [d(5'-GAGTGCACTC-3')_2] is titrated with the major groove intercalator \u0394-\u03b1-[Rh[(R,R)-Me_2trien]phi]^(3+), the ruthenium emission yield decreases while the absorbance of the \u03c0\u2212\u03c0^* transition centered on the dppz ligand increases, until saturation behavior is observed at a 1:1 Rh/duplex ratio. These titrations indicate that Ru(phen)_2dppz^(2+) is displaced from the major groove by the rhodium complex. In contrast, for rac-Ru(phen)_2dppz^(2+) bound to poly d(AT), addition of the minor groove binding agent distamycin produces an increase in ruthenium emission which saturates at \u223c1 distamycin/5 bp, consistent with the double helix being able to accommodate major and minor groove binders simultaneously. Distamycin has no effect on the emission of Ru(phen)_2dppz^(2+) emission bound to poly d(GC). These photophysical studies establish a sequence preference in binding to DNA by Ru(phen)_2dppz^(2+) as well as providing support for the original assignment by NMR of ruthenium intercalation from the major groove side of the DNA helix.", "doi": "10.1021/ic970869r", "issn": "0020-1669", "publisher": "American Chemical Society", "publication": "Inorganic Chemistry", "publication_date": "1998-01-12", "series_number": "1", "volume": "37", "issue": "1", "pages": "29-34" }, { "id": "authors:v29m7-zg804", "collection": "authors", "collection_id": "v29m7-zg804", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160324-071825486", "type": "article", "title": "Targeting the Tat-Binding Site of Bovine Immunodeficiency\n Virus TAR RNA with a Shape-Selective Rhodium Complex", "author": [ { "family_name": "Lim", "given_name": "Ai Ching", "clpid": "Lim-Ai-Ching" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The Tat-binding site of the bovine immunodeficiency virus TAR RNA hairpin has been targeted by Rh(phen)_2phi^(3+) (phen = phenanthroline, phi = 9,10-phenanthrenequinone diimine), a photochemical probe of RNA tertiary structure. The primary site cleaved by the rhodium complex, upon photoactivation, is U24, a base which participates in the novel base triple (with bases A13 and U10) characteristic of this folded RNA. \u0394-Rh(phen)_2phi^(3+) binds to this site with an affinity of 2 \u00d7 10^6M^(\u22121). Upon mutation of U24 and A13 to A24 and U13, respectively, so that the RNA oligomer is unable to form the base triple, site-specific cleavage by the rhodium complex is abolished. Moreover, as determined through rhodium photocleavage, at a concentration of 20 \u03bcM, Rh(phen)_2phi^(3+) inhibits specific binding of BIV-Tat peptide (2 \u03bcM) to its target site. Thus the rhodium complex, in matching its shape to the opened major groove of the properly folded RNA, specifically targets its site and is able to compete for its target with the BIV-Tat peptide.", "doi": "10.1016/S0968-0896(97)00049-7", "issn": "0968-0896", "publisher": "Elsevier", "publication": "Bioorganic and Medicinal Chemistry", "publication_date": "1997-06", "series_number": "6", "volume": "5", "issue": "6", "pages": "1131-1136" }, { "id": "authors:81vsv-0sy10", "collection": "authors", "collection_id": "81vsv-0sy10", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160330-112529436", "type": "article", "title": "Long-range oxidation of guanine by Ru(III) in duplex DNA", "author": [ { "family_name": "Arkin", "given_name": "Michelle R.", "clpid": "Arkin-M-R" }, { "family_name": "Stemp", "given_name": "Eric D. A.", "orcid": "0000-0003-2098-4214", "clpid": "Stemp-E-D-A" }, { "family_name": "Pulver", "given_name": "Sabine Coates", "clpid": "Pulver-S-C" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Background: Theoretical and experimental studies have demonstrated that 5\u2032-GG-3\u2032 sequences in DNA are 'hot spots' for oxidative damage, but few studies have definitively addressed whether oxidative damage to DNA may arise from a distance via long-range charge migration. Towards this end, we have prepared tethered ruthenium (Ru)-oligonucleotide duplexes and used a flash\u2014quench strategy to demonstrate long-range charge transport through the DNA double helix.\n\nResults: DNA assemblies containing a tethered Ru(II) intercalator have been synthesized. Ru(III), generated in situ in the presence of externally bound electron-transfer quenchers, promotes base damage selectively at the 5\u2032-G of a 5\u2032-GG-3\u2032 doublet located \u223c 37 \u00c5 from the binding site of the oxidant. In the absence of a guanine doublet, oxidative damage occurs equally at all guanine bases in the strand. Oxidative damage is also observed at long range for guanine in a G\u00b7A mismatch but not in a G\u00b7T mismatch.\n\nConclusions: The present study expands the scope of long-range electron-transfer chemistry in terms of experiments, applications, and possible reactions within the cell. Here we demonstrate oxidative damage to DNA occurring with a high quantum yield over a distance of \u223c37 \u00c5 using a ground-state oxidant. These results point to the equilibration of the radical across the DNA duplex to the sites of lowest energy. In addition, this charge migration is sensitive to the intervening \u03c0-stack formed by DNA base pairs and hence may be useful for the detection of mismatches.", "doi": "10.1016/S1074-5521(97)90129-0", "issn": "1074-5521", "publisher": "Elsevier", "publication": "Chemistry and Biology", "publication_date": "1997-05", "series_number": "5", "volume": "4", "issue": "5", "pages": "389-400" }, { "id": "authors:kr86s-6y249", "collection": "authors", "collection_id": "kr86s-6y249", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141126-103406641", "type": "article", "title": "Oxidative Thymine Dimer Repair in the DNA Helix", "author": [ { "family_name": "Dandliker", "given_name": "Peter J.", "clpid": "Dandliker-P-J" }, { "family_name": "Holmlin", "given_name": "R. Erik", "clpid": "Holmlin-R-E" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The metallointercalator Rh(phi)_2DMB^(3+) (phi, 9,10-phenanthrenequinone diimine; DMB, 4,4\u2032-dimethyl-2,2\u2032-bipyridine) catalyzed the repair of a thymine dimer incorporated site-specifically in a 16-base pair DNA duplex by means of visible light. This repair could be accomplished with rhodium noncovalently bound to the duplex and at long range (16 to 26 angstroms), with the rhodium intercalator tethered to either end of the duplex assembly. This long-range repair was mediated by the DNA helix. Repair efficiency did not decrease with increasing distance between intercalated rhodium and the thymine dimer, but it diminished with disruption of the intervening \u03c0-stack.", "doi": "10.1126/science.275.5305.1465", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "1997-03-07", "series_number": "5305", "volume": "275", "issue": "5305", "pages": "1465-1468" }, { "id": "authors:baeab-9gr07", "collection": "authors", "collection_id": "baeab-9gr07", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160405-110030531", "type": "article", "title": "Electrochemistry of Methylene Blue Bound to a DNA-Modified Electrode", "author": [ { "family_name": "Kelley", "given_name": "Shana O.", "orcid": "0000-0003-3360-5359", "clpid": "Kelley-S-O" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Jackson", "given_name": "Nicole M.", "clpid": "Jackson-N-M" }, { "family_name": "Hill", "given_name": "Michael G.", "clpid": "Hill-M-G" } ], "abstract": "Gold surfaces have been derivatized with 15-base-pair double-stranded DNA oligonucleotides containing a pendant 5' hexanethiol linker. The electrochemistry of intercalated methylene blue has been investigated at these modified electrodes. Chronocoulometry, cyclic voltammetry, ellipsometry, and quantitation via ^(32)P labeling are all consistent with a surface coverage of \u2265 75% with the DNA helices stacked at an angle from the electrode surface. Cyclic voltammetry at low methylene blue/duplex stoichiometries yields well-behaved surface waves with E\u00b0 = \u22120.25 V (vs SCE), a value 0.03 V negative of that in aqueous solution. A binding isotherm for methylene blue at an electrode derivatized with the double-stranded sequence 5' SH-(CH_2)_6-p-AGTACAGTCATCGCG 3' was obtained from coulometric titrations and gave an affinity constant equal to 3.8(5) \u00d7 10^6 M^(-1) with a saturation value of 1.4(2) methylene blue intercalators per DNA duplex. Taken together, these experiments support a model for the surface morphology in which DNA duplexes are densely packed; methylene blue therefore reversibly binds to sites in the DNA that are close to the bulk solution. Electrochemistry at DNA-derivatized electrodes provides a valuable methodology to examine DNA-bound redox reactions and may offer new insight into DNA-mediated electron transfers.", "doi": "10.1021/bc960070o", "issn": "1043-1802", "publisher": "American Chemical Society", "publication": "Bioconjugate Chemistry", "publication_date": "1997-01-29", "series_number": "1", "volume": "8", "issue": "1", "pages": "31-37" }, { "id": "authors:gctfz-fg233", "collection": "authors", "collection_id": "gctfz-fg233", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180515-132544141", "type": "article", "title": "Structural Studies of \u039b- and \u0394-[Ru(phen)_2dppz]^(2+)Bound to d(GTCGAC)_2: Characterization of Enantioselective Intercalation", "author": [ { "family_name": "Dupureur", "given_name": "Cynthia M.", "clpid": "Dupureur-C-M" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "^1H and ^(31)P NMR have been applied in characterizing the enantioselective interactions between \u039b- and \u0394-[Ru(phen)_2dppz]^(2+) and the hexamer oligonucleotide d(GTCGAC)_2. Both isomers intercalate into the helix, and intermolecular NOEs place the \u0394-isomer in the major groove. The NMR results indicate that Ru(phen)_2dppz^(2+) isomers bind to the DNA helix with a population of intercalative geometries and therefore extend earlier structural models based upon luminescence studies.", "doi": "10.1021/ic960738a", "issn": "0020-1669", "publisher": "American Chemical Society", "publication": "Inorganic Chemistry", "publication_date": "1997-01-01", "series_number": "1", "volume": "36", "issue": "1", "pages": "33-43" }, { "id": "authors:h02rq-3xs76", "collection": "authors", "collection_id": "h02rq-3xs76", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150617-092516497", "type": "article", "title": "Oxidative DNA damage through long-range electron transfer", "author": [ { "family_name": "Hall", "given_name": "Daniel B.", "clpid": "Hall-D-B" }, { "family_name": "Holmlin", "given_name": "R. Erik", "clpid": "Holmlin-R-E" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "THE possibility has been considered for almost forty years that the DNA double helix, which contains a \u03c0-stacked array of heterocyclic base pairs, could be a suitable medium for the migration of charge over long molecular distances. This notion of high charge mobility is a critical consideration with respect to DNA damage. We have previously found that the DNA double helix can serve as a molecular bridge for photo-induced electron transfer between metallointercalators, with fast rates (\u226510^(10) S^(\u22121))^(10) and with quenching over a long distance (>40\u00c5)^8. Here we use a metallointercalator to introduce a photoexcited hole into the DNA \u03c0-stack at a specific site in order to evaluate oxidative damage to DNA from a distance. Oligomeric DNA duplexes were prepared with a rhodium inter-calator covalently attached to one end and separated spatially from 5\u2032-GG-3\u2032 doublet sites of oxidation. Rhodium-induced photo-oxidation occurs specifically at the 5\u2032-G in the 5\u2032-GG-3\u2032 doublets and is observed up to 37 \u00c5 away from the site of rhodium intercalation. We find that the yield of oxidative damage depends sensitively upon oxidation potential and \u03c0-stacking, but not on distance. These results demonstrate directly that oxidative damage to DNA may be promoted from a remote site as a result of hole migration through the DNA \u03c0-stack.", "doi": "10.1038/382731a0", "issn": "0028-0836", "publisher": "Nature Publishing Group", "publication": "Nature", "publication_date": "1996-08-22", "series_number": "6593", "volume": "382", "issue": "6593", "pages": "731-735" }, { "id": "authors:sh7ng-gps33", "collection": "authors", "collection_id": "sh7ng-gps33", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141211-093844438", "type": "article", "title": "Rates of DNA-Mediated Electron Transfer Between Metallointercalators", "author": [ { "family_name": "Arkin", "given_name": "M. R.", "clpid": "Arkin-M-R" }, { "family_name": "Stemp", "given_name": "E. D. A.", "orcid": "0000-0003-2098-4214", "clpid": "Stemp-E-D-A" }, { "family_name": "Holmlin", "given_name": "R. E.", "clpid": "Holmlin-R-E" }, { "family_name": "Barton", "given_name": "J. K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "H\u00f6rmann", "given_name": "A.", "clpid": "H\u00f6rmann-A" }, { "family_name": "Olson", "given_name": "E. J. C.", "clpid": "Olson-E-J-C" }, { "family_name": "Barbara", "given_name": "P. F.", "clpid": "Barbara-P-F" } ], "abstract": "Ultrafast emission and absorption spectroscopies were used to measure the kinetics of DNA-mediated electron transfer reactions between metal complexes intercalated into DNA. In the presence of rhodium(III) acceptor, a substantial fraction of photoexcited donor exhibits fast oxidative quenching (>3 \u00d7 10^(10) per second). Transient-absorption experiments indicate that, for a series of donors, the majority of back electron transfer is also very fast (\u223c10^(10) per second). This rate is independent of the loading of acceptors on the helix, but is sensitive to sequence and \u03c0 stacking. The cooperative binding of donor and acceptor is considered unlikely on the basis of structural models and DNA photocleavage studies of binding. These data show that the DNA double helix differs significantly from proteins as a bridge for electron transfer.", "doi": "10.1126/science.273.5274.475", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "1996-07-26", "series_number": "5274", "volume": "273", "issue": "5274", "pages": "475-480" }, { "id": "authors:710eh-3h330", "collection": "authors", "collection_id": "710eh-3h330", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171107-133435500", "type": "article", "title": "Os(phen)_2dppz^(2+) in Photoinduced DNA-Mediated Electron Transfer Reactions", "author": [ { "family_name": "Holmlin", "given_name": "R. Erik", "clpid": "Holmlin-R-E" }, { "family_name": "Stemp", "given_name": "Eric D. A.", "orcid": "0000-0003-2098-4214", "clpid": "Stemp-E-D-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The photoinduced electron transfer chemistry between Os(phen)_2dppz^(2+) and Rh(phi)_2bpy^(3+) bound to DNA has been characterized. Os(phen)_2dppz^(2+) serves as an isostructural analogue for Ru(phen)_2dppz^(2+) with a red-shifted emission spectrum, access to a 3+ oxidation state which is stabilized by \u223c500 mV relative to the ruthenium complex, and excited-state lifetimes below 10 ns in the presence of DNA. Emission from \u0394-Os(phen)_2dppz^(2+) bound to calf thymus DNA is efficiently quenched by \u0394-Rh(phi)_2bpy^(3+), and a lower limit for the quenching constant is set at 7 \u00d7 10^9 s^(-1). The quenching profile over a range of quencher concentrations is found to be remarkably similar to that of the ruthenium analogue, despite an increase of \u223c200 mV in \u0394G for the photoinduced, forward electron transfer reaction. Such an observation may indicate the importance of the HOMO energy in the donor excited state, which is similar for both donors. Owing to the lack of spectral overlap between Os(phen)_2dppz^(2+) emission and Rh(phi)_2bpy^(3+) absorption, energy transfer does not contribute to the observed quenching, and therefore, on the basis of the similarity in quenching profiles for the osmium and ruthenium donors, we can also rule out energy transfer in the photoinduced quenching of intercalated Ru(phen)_2dppz^(2+) by Rh(phi)_2bpy^(3+). Moreover, diffusional processes are found not to contribute to quenching, since the faster intrinsic excited state of the osmium complex compared to ruthenium does not lead to a reduction in quenching efficiency. Transient absorption measurements on the microsecond time scale furthermore reveal a transient signal for this electron transfer process, and this transient intermediate has been assigned to the oxidized donor (Os(III)) on the basis of full spectral characterization and comparison to chemical oxidation of Os(II).", "doi": "10.1021/ja953941y", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "1996-06-05", "series_number": "22", "volume": "118", "issue": "22", "pages": "5236-5244" }, { "id": "authors:j4a06-gzq87", "collection": "authors", "collection_id": "j4a06-gzq87", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170408-162652102", "type": "article", "title": "Excited state properties of Rh(phi)_2(phen)^(3+) and related complexes: a strong photooxidant", "author": [ { "family_name": "Turro", "given_name": "Claudia", "clpid": "Turro-C" }, { "family_name": "Evenzahav", "given_name": "Ariella", "clpid": "Evenzahav-A" }, { "family_name": "Bossmann", "given_name": "Stefan H.", "clpid": "Bossmann-S-H" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Turro", "given_name": "Nicholas J.", "clpid": "Turro-N-J" } ], "abstract": "The excited state properties and reactivity of Rh(phi)_2(phen)^(3+) (phi = 9,10-phenanthrenequinone diimine, phen = 1,10-phenanthroline) were investigated and compared to those of related rhodium(III) and zinc(II) complexes. At 77 K Rh(phi)_2(phen)^(3+) exhibits LC^3\u03c0\u03c0\u2217 dual emission from both phi and phen ligands, whose energies are 2.8 eV and 3.0 eV, respectively, with a biexponential decay that can be fit to 5 ns (98%) and 60 ns (2%) lifetime components. A longer-lived transient is observed by transient absorption both at 77 K and 298 K, which decays monoexponentially with a time constant of 900 ns and 235 ns at each temperature, respectively, in ethanol. The transient can be attained with visible excitation (420 nm to 532 nm) and it is assigned to be intra-ligand charge transfer (ILCT) in nature. It was determined from transient absorption experiments that the ILCT excited state of Rh(phi)_2(phen)^(3+) lies approximately 2.0 eV above the ground state and that it is a powerful oxidizing agent with E_(12)([Rh]^(3+\u2217/2+))\u22482.0V versus NHE. The transient absorption experiments with electron donors reveal that the one-electron reduced Rh(phi)_2(phen)^(2+) absorbs at 540 nm with \u03b5 \u2248 3300 M^(\u22121)cm^(\u22121).", "doi": "10.1016/0020-1693(95)04896-0", "issn": "0020-1693", "publisher": "Elsevier", "publication": "Inorganica Chimica Acta", "publication_date": "1996-02-29", "series_number": "1", "volume": "243", "issue": "1", "pages": "101-108" }, { "id": "authors:22dg4-q3y39", "collection": "authors", "collection_id": "22dg4-q3y39", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150107-105109518", "type": "article", "title": "Recognition of DNA by Octahedral Coordination Complexes", "author": [ { "family_name": "Johann", "given_name": "Timothy W.", "clpid": "Johann-T-W" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Strategies for the site-specific recognition of DNA are described through the design of a family of octahedral metallointercalating complexes. Coordination complexes, which mimic DNA-binding proteins with regard to their affinity and specificity for DNA sites, may be prepared by the specific functionalization of chiral metal complexes so as to achieve the ensemble of non-covalent contacts in the DNA major groove anchored through intercalation.", "issn": "1364-503X", "publisher": "Royal Society of London", "publication": "Philosophical Transactions A: Mathematical, Physical and Engineering Sciences", "publication_date": "1996-02-15", "series_number": "1706", "volume": "354", "issue": "1706", "pages": "299-324" }, { "id": "authors:54071-w2n48", "collection": "authors", "collection_id": "54071-w2n48", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160405-140026070", "type": "article", "title": "Sequence-Selective DNA Recognition and Photocleavage: A Comparison of Enantiomers of Rh(en)_2phi^(3+)", "author": [ { "family_name": "Shields", "given_name": "Thomas P.", "clpid": "Shields-T-P" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The recognition and photoinduced cleavage of DNA by the enantiomers of bis(ethy1enediamine)-(9,10-phenanthrenequinone diimine)Rh(III) [Rh(en)_2phi^(3+)] have been characterized and the basis for\nenantioselective differences delineated. Rh(en)_2phi^(3+) isomers bind strongly to DNA via intercalation\nand, upon photoactivation with near-UV light, produce direct strand cleavage. On the basis of product\nanalysis, the photoinduced DNA cleavage appears to proceed by a mechanism consistent with that observed\nfor the parent Rh(phen)_2phi^(3+), involving direct abstraction of the 3'-hydrogen atom of the deoxyribose by\nthe activated, intercalated phi. Quantitative photocleavage titrations indicate tight binding by both\nenantiomers to the DNA duplex. For A-Rh(en)_2phi^(3+), DNA site affinities range from 0.3 x 10^6 to 8.0 x 10^6 M^(-l), and a distinct preference for GC sites is evident. A-Rh(en)_2phi^(3+) is found to be sequence neutral with an average site affinity of 2 x 10^6 M^(-1). The basis for sequence selectivity of the enantiomers has been examined through comparison of photocleavage patterns to those of several phi complexes of rhodium(III) containing or lacking axial amines; those complexes containing the axial amines are found to target GC sites. DNA photocleavage studies on oligonucleotides containing the modified bases O^6- methylguanine, 7-deazaguanine, and deoxyuracil have been utilized to determine points of interaction on\nthe DNA helix. These results establish binding by both complexes in the major groove of DNA.\nDifferences in site recognition between enantiomers are attributed to the different hydrogen bonding and\nvan der Waals contacts available in the major groove for the ancillary ethylenediamine ligands which\ndiffer in disposition in the two isomers.", "doi": "10.1021/bi00046a009", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "1995-11", "series_number": "46", "volume": "34", "issue": "46", "pages": "15037-15048" }, { "id": "authors:ss5dm-13814", "collection": "authors", "collection_id": "ss5dm-13814", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160405-140025577", "type": "article", "title": "Structural Examination of Enantioselective Intercalation: ^1H NMR of Rh(en)_2phi^(3+) Isomers Bound to d(GTGCAC)_2", "author": [ { "family_name": "Shields", "given_name": "Thomas P.", "clpid": "Shields-T-P" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The enantioselective recognition of d(GTGCAC)_2 by \u0394- and \u039b-Rh(en)_2phi^(3+) (en= ethylenediarnine; phi = 9, 10-phenanthrenequinone diimine) has been examined in a series of one-dimensional (ID) and two-dimensional (2D) 500 MHz ^1H NMR experiments both to extend our understanding of the basis for the enantioselective DNA binding and to gain structural information concerning intercalation by\nthe octahedral metal complexes. \u0394-Rh(en)_2phi^(3+) forms a symmetric 1:1 complex with d(GTGCAC)_2, and the metal complex is in slow exchange with the oligodeoxynucleotide bound form at 295 K. The strong upfield shifts of the phi ligand's aromatic protons (0.6-1.3 ppm) are consistent with full intercalation of the phi ligand into the DNA base stack. 2D-NOESY experiments reveal a loss in internucleotide\nconnectivity between G_3 and C_4 bases, while new NOE cross peaks are observed between the phi ligand and the G_3 deoxyribose sugar. In contrast to binding by \u0394-Rh(en)_2phi^(3+), the 1:1 \u0394-Rh(en)_2phi^(3+)-d(GTGAC)_2 complex shows much broader resonances, and both metal complex and DNA protons appear to be in the intermediate exchange regime. The loss of C_2 symmetry in the 1:1 complex is consistent with binding by \u039b-Rh(en)_2phi^(3+) at the T_2G_3 step. Although the enantiomeric metal complexes display different sequence selectivities and exchange characteristics, \u039b- and \u0394-Rh(en)_2phi^(3+) interact with the\noligonucleotide duplex in a fundamentally similar manner, through the full intercalation of the phi ligand. Upfield movements in chemical shifts of phi protons are nearly identical for the two enantiomers, and both \u039b- and \u0394-Rh(en)_2phi^(3+) stabilize the duplex to melting by 5-10 \u00b0C. Given the common binding mode of the two enantiomers, the differences in their binding characteristics emanate from interactions with the ancillary nonintercalating ligands. Thus, as a general strategy, intercalation may provide an anchor for sequence-selective interactions of octahedral metal complexes in the groove of duplex DNA.", "doi": "10.1021/bi00046a010", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "1995-11", "series_number": "46", "volume": "34", "issue": "46", "pages": "15049-15056" }, { "id": "authors:e6pat-1vf75", "collection": "authors", "collection_id": "e6pat-1vf75", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160405-140026640", "type": "article", "title": "Sequence-Specific DNA Binding by a Rhodium Complex: Recognition Based on Sequence-Dependent Twistability", "author": [ { "family_name": "Terbrueggen", "given_name": "Robert H.", "clpid": "Terbrueggen-R-H" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The chemical construction of small molecules targeted to DNA depends upon the sequence dependent structure of the double helix. Here we describe a new structural element to be considered in the sequence-specific recognition of DNA, sequence-dependent DNA twistability. The importance of\nsequence-dependent DNA twistability is demonstrated in the DNA recognition properties of a novel synthetic rhodium intercalator, A-1-Rh(MGP)_2phi^(5+). This metallointercalator, containing pendant guanidinium groups, binds in the major groove of DNA at subnanomolar concentrations to the 6 base pair sequence 5'-CAT A TG-3' with enantiospecificity. An essential feature of this recognition is the sequence-specific unwinding of the DNA helix, which permits direct contacts between guanidinium\nfunctionalities on the metal complex and guanine residues. Through an assay developed to test for sequence-specific DNA unwinding, a 70 \u00b1 10\u00b0 unwinding of the sequence 5'-CATATG-3' is established with specific binding by the metal complex. This sequence-dependent twistability may be an essential feature of the recognition of sequences by DNA-binding proteins and may be exploited in future design.", "doi": "10.1021/bi00026a003", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "1995-07", "series_number": "26", "volume": "34", "issue": "26", "pages": "8227-8234" }, { "id": "authors:dy12b-w2q17", "collection": "authors", "collection_id": "dy12b-w2q17", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160405-133522969", "type": "article", "title": "Construction of Coordinatively Saturated Rhodium Complexes Containing Appended Peptides", "author": [ { "family_name": "Sardesai", "given_name": "Niranjan Y.", "clpid": "Sardesai-N-Y" }, { "family_name": "Lin", "given_name": "Susanne C.", "clpid": "Lin-Susanne-C" }, { "family_name": "Zimmermann", "given_name": "Kaspar", "clpid": "Zimmermann-K" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Phenanthrenequinone diimine (phi) complexes of rhodium(III) bearing appended peptides have been\nprepared using two complementary solid phase synthetic strategies. The first method involves the\ndirect coupling of the coordinatively saturated rhodium complex containing a pendant carboxylate to\nthe N-terminus of a resin-bound peptide, in a manner analogous to the chain-elongation step in solid\nphase peptide synthesis. The second involves coupling a bidentate chelator containing the pendant\ncarboxylate to the resin-bound peptide, followed by coordination of [Rh(phi_)2]^(3+) to the bidentate chelator\nattached to the peptide. Peptides of length 5-30 residues have been covalently attached to rhodium\ncomplexes in 5-18% yield using both methods. Despite the low overall yields, the regioselective\nmodification of the peptide chain afforded by these strategies is a distinct advantage over solution\nphase methods. With coordination complexes which are stable to peptide deprotection and cleavage\nconditions from the resin, the solid phase synthetic strategies are convenient to apply. Amino acid\nanalysis, electronic spectroscopy, and circular dichroism confirm the presence of the two components\nin the metal-peptide chimeras; the metal-peptide complexes exhibit the combined spectral properties\nof the parent metal complex and the appended peptide. Significantly, plasma desorption mass\nspectrometry reveals a novel pattern of peptide fragmentation for the metal-peptide chimeras that\nis not observed in the absence of the tethered metal complex; this fragmentation facilitates the sequence\nanalysis of the appended peptide. Thus, metal-peptide chimeras may be conveniently prepared using\nsolid phase methodologies, and features of coordination chemistry may be exploited for new peptide\ndesign and analysis.", "doi": "10.1021/bc00033a011", "issn": "1043-1802", "publisher": "American Chemical Society", "publication": "Bioconjugate Chemistry", "publication_date": "1995-05", "series_number": "3", "volume": "6", "issue": "3", "pages": "302-312" }, { "id": "authors:6rr8a-j5b75", "collection": "authors", "collection_id": "6rr8a-j5b75", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160406-085310442", "type": "article", "title": "Sequence-Specific Recognition of DNA by Phenanthrenequinone Diimine Complexes of Rhodium(III): Importance of Steric and van der Waals Interactions", "author": [ { "family_name": "Sitlani", "given_name": "Ayesha", "clpid": "Sitlani-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The importance of steric and van der Waals interactions in the sequence-specific recognition of DNA by [Rh(phi)]^(3+) complexes has been explored through the synthesis and application of a series of Rh(phi)^(3+) (phi: 9,10-phenanthrenequinone diimine) derivatives. [Rh(phi)]^(3+) complexes intercalate in the\nmajor groove of DNA via the phi ligand and promote strand scission in the presence of UV light. The complexes reported here are derivatives of the parent molecules [Rh(phi)_2bpy]^(3+)and [Rh(bpy)_2phi]^(3+)(bpy:2,2'-bipyridyl). The [Rh(phi)]^(3+) complexes have comparable photoefficiencies; therefore, their different photocleavage patterns on ^(32)P-end-labeled DNA fragments reflect their unique sequence-specific recognition\ncharacteristics. The shapes of the [Rh(phi)]^(3+) complexes are found to govern DNA recognition and reaction. Importantly and generally, the more sterically bulky complexes, containing methyl or phenyl groups on the ancillary ligands, cleave DNA at a subset of sequences recognized by their parent molecules. [Rh(diphenylbpy)_2phi]^(3+) specifically targets the site 5'-CTCTAGAG-3'. Furthermore, chiral discrimination in site selectivity is observed; the different isomers target different sites. \u0394- and \u039b-[Rh(5,5'-dimethylbpy)_2phi]^(3+) cleave specifically at sites that are defined by the consensus sequences 5'-C-T-N-G-3' and 5'-A-C/G-T-C/G-3', respectively. The sequence selectivities may be understood on the basis of both negative\nsteric clashes and positive van der Waals interactions between methyl groups on the metal complex and thymine methyl groups in the DNA major groove.", "doi": "10.1021/bi00206a013", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "1994-10", "series_number": "40", "volume": "33", "issue": "40", "pages": "12100-12108" }, { "id": "authors:k9wp5-6d081", "collection": "authors", "collection_id": "k9wp5-6d081", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180601-153001625", "type": "article", "title": "DNA Recognition by Peptide Complexes of Rhodium(III): Example of a Glutamate Switch", "author": [ { "family_name": "Sardesai", "given_name": "Niranjan Y.", "clpid": "Sardesai-N-Y" }, { "family_name": "Zimmermann", "given_name": "Kaspar", "clpid": "Zimmermann-K" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "A family of metal-peptide complexes has been synthesized by coupling short oligopeptides (13 residues) onto the metallointercalating [Rh(phi)_2(phen')]^(3+) (phi = 9,10-phenanthrenequinone diimine; phen' = 5-(amidoglutaryl)-1,10-phenanthroline). These complexes were prepared to explore whether the side-chain functionalities of small peptides may be used to augment metal complex recognition. The metal-peptide complexes bind and, with photoactivation, cleave DNA. The DNA site-specificity is seen to depend on the peptide side-chain functional groups. In particular, a single glutamate at position 10 is found to be essential in directing DNA site-recognition to the sequence 5'-CCA-3'. Methylation of the glutamate side chain or direct substitution of glutamine for glutamate abolishes the 5'-CCA-3' selectivity, while substitutions at other likely DNA-binding residues show no appreciable change in selectivity. Significantly, the 5'-CCA-3' selectivity is even sensitive to a highly conservative E10D substitution. DNA photocleavage of oligonucleotides by the metal-peptide complexes and HPLC analysis of DNA products provide evidence for major groove chemistry. Circular dichroism indicates significant \u03b1-helical content in the peptide, which depends upon the presence of the glutamate. A model for the glutamate-dependent site-selectivity is presented using shape-selective intercalation of the metal complex and base-specific contacts of the ancillary peptide. These monomeric metal-peptide complexes appear to serve as particularly useful mimics for larger site-specific DNA-binding proteins and may provide a basis for the design of an array of small, sequence-specific DNA-binding metal complexes.", "doi": "10.1021/ja00096a005", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "1994-08-24", "series_number": "17", "volume": "116", "issue": "17", "pages": "7502-7508" }, { "id": "authors:r1srx-78076", "collection": "authors", "collection_id": "r1srx-78076", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:MURpnas94", "type": "article", "title": "Fast Photoinduced Electron Transfer through DNA Intercalation", "author": [ { "family_name": "Murphy", "given_name": "Catherine J.", "clpid": "Murphy-C-J" }, { "family_name": "Arkin", "given_name": "Michelle R.", "clpid": "Arkin-M-R" }, { "family_name": "Ghatlia", "given_name": "Naresh D.", "clpid": "Ghatlia-N-D" }, { "family_name": "Bossmann", "given_name": "Stefan", "clpid": "Bossmann-S" }, { "family_name": "Turro", "given_name": "Nicholas J.", "clpid": "Turro-N-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "We report evidence for fast photoinduced electron transfer mediated by the DNA helix that requires metal complexes that are avid intercalators of DNA. Here the donor bis(phenanthroline)(dipyridophenazine)ruthenium(II) [Ru(phen)2dppz2+] and acceptor bis(9,10-phenanthrenequinone diimine)(phenanthroline)rhodium(III) [RH(phi)2phen3+] intercalate into DNA with Kb > 106 M-1. Luminescence quenching experiments in the presence of two different lengths of DNA yield upward-curving Stern-Volmer plots and the loss of luminescence intensity far exceeds the change in emission lifetimes. In the presence of a nonintercalative electron acceptor, Ru(NH3)3+6, Ru(phen)2dppz2+ luminescence is quenched much less efficiently compared to that found for the intercalative Rh(phi)2phen3+ quencher and follows linear Stern-Volmer kinetics; steady-state and time-resolved Stern-Volmer plots are comparable in scale. These experiments are consistent with a model involving fast long-range electron transfer between intercalators through the DNA helix.", "pmcid": "PMC43985", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1994-06-07", "series_number": "12", "volume": "91", "issue": "12", "pages": "5315-5319" }, { "id": "authors:1714j-4te68", "collection": "authors", "collection_id": "1714j-4te68", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160406-075128792", "type": "article", "title": "Correlations of Crystal Structures of DNA Oligonucleotides with Enantioselective Recognition by Rh(phen)_2phi^(3+): Probes of DNA Propeller Twisting in Solution", "author": [ { "family_name": "Campisi", "given_name": "Donna", "clpid": "Campisi-D" }, { "family_name": "Morii", "given_name": "Takashi", "clpid": "Morii-Takashi" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Rh(phen)_2phi^(3+) (phen = 1,10-phenanthroline; phi= 9,10-phenanthrenequinonediimine) avidly binds to DNA via intercalation from the major groove and upon photoactivation produces strand scission with single base 5' asymmetry. Enantiomers of Rh(phen)_2phi^(3+), which lack hydrogen-bonding substituents in ancillary positions, distinguish a DNA site through shape-selection; site recognition depends upon the local variations in structure at a binding site. Here, we examine the application of \u0394-Rh(phen)_2phi^(3+) as a sequence-dependent structural probe and, in particular, as a probe of DNA propeller twisting in solution, by comparing directly cleavage results using \u0394- and \u039b-Rh(phen)_2phi^(3+) on crystallographically characterized oligonucleotides with several sequence-dependent crystallographic parameters. The three oligonucleotides examined in this study are the Dickerson-Drew dodecamer, 5'-CGCGAA TTCGCG-3', the Nar I dodecamer, 5'-ACCGGCGCCACA-3', and the CG decamer, 5'-CCAACGTTGG-3', all of which have been crystallized\nin the B-form. Enantioselective cleavage and reaction favored by the \u0394-isomer is found to be governed\nlocally by the opening of the site in the major groove. A correlation is demonstrated between cleavage by\n\u0394-Rh(phen)_2phi^(3+) and the opening in the major groove that results from the change in propeller twist\n(differential propeller twist) at a base step. When the major groove is closed as a result of a change in\npropeller twist, there is little cleavage evident by either enantiomer; at sites which are indicated crystallographically to be open in the major groove, a direct correlation is observed between enantioselective\ncleavage and the degree of opening. A trend of higher enantioselectivity at sites possessing higher twist\nangles is also observed. The roll angle of a site in isolation, the rise per base step, and the groove width\nshow no correlation with cleavage. The distribution of reaction products at a site, as a result of partitioning\nalong oxygen-dependent or oxygen-independent pathways, also provides a sensitive measure of the shapecomplementarity\nbetween metal complex and binding site. These results provide evidence for site-recognition by the metal complex which correlates directly with DNA propeller twisting in oligonucleotide crystals. Importantly, these results indicate that Rh(phen)_2phi^(3+) may be uniquely applied as a chemical probe for sequence-dependent changes in the propeller twisting of DNA.", "doi": "10.1021/bi00180a005", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "1994-04", "series_number": "14", "volume": "33", "issue": "14", "pages": "4130-4139" }, { "id": "authors:3gewe-rwm73", "collection": "authors", "collection_id": "3gewe-rwm73", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180413-144638081", "type": "article", "title": "Ligand-Specific Charge Localization in the MLCT Excited State of Ru(bpy)_2(dpphen)^(2+) Monitored by Time-Resolved Resonance Raman Spectroscopy", "author": [ { "family_name": "Turro", "given_name": "Claudia", "clpid": "Turro-C" }, { "family_name": "Bossmann", "given_name": "Stefan H.", "clpid": "Bossmann-S-H" }, { "family_name": "Leroi", "given_name": "George E.", "clpid": "Leroi-G-E" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Turro", "given_name": "Nicholas J.", "clpid": "Turro-N-J" } ], "abstract": "Time-resolved resonance Raman spectroscopy has been employed to examine the location of the promoted electron\nin the metal-to-ligand charge-transfer (MLCT) excited state of Ru(bpy)_2(dpphen)^(2+) (bpy) = 2,2'-bipyridine; dpphen = 4,7-diphenyl-1,10-phenanthroline). Variations in the environment about Ru(bpy)_2(dpphen)^(2+) shift the localization\nof charge in the MLCT excited state from bpy in neutral micelles (Brij 35) to dpphen in the presence of DNA and\nanionic surfactants (C_(12)H_(25)OSO_3Na, C_(10)H_(23)OSO_3Na, and C_8H_(21)OSO_3Na), whereas in water the electron is localized on both ligands. The shifts in the electronic absorption spectrum and the dependence of the ground-state resonance\nRaman (rR) signal with excitation wavelengths coincident with the high- and low-energy sides of the MLCT absorption band are consistent with a lowering of the energy of the Ru(II)-dpphen transition with respect to that of bpy in anionic micelles.", "doi": "10.1021/ic00085a022", "issn": "0020-1669", "publisher": "American Chemical Society", "publication": "Inorganic Chemistry", "publication_date": "1994-03-01", "series_number": "7", "volume": "33", "issue": "7", "pages": "1344-1347" }, { "id": "authors:5zp2x-5yq44", "collection": "authors", "collection_id": "5zp2x-5yq44", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180529-143627642", "type": "article", "title": "Assembly of DNA recognition elements on an octahedral rhodium intercalator: predictive recognition of 5'-TGCA-3' by \u0394-[Rh[(R,R)-Me_2trien]phi]^(3+)", "author": [ { "family_name": "Krotz", "given_name": "Achim H.", "clpid": "Krotz-A-H" }, { "family_name": "Hudson", "given_name": "Brian P.", "clpid": "Hudson-B-P" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Here we explore the de novo design of rhodium intercalators for predictive four base pair recognition of duplex DNA. Complexes have been constructed which, like DNA-binding proteins, pose several functionalities for site-specific noncovalent interaction with DNA. Octahedral rhodium intercalators are particularly useful in this design since (i) the octahedral coordination specifies the stereochemistry of ligand functionalities and (ii) the intercalating ligands orients these functionalities with respect to the DNA major groove.", "doi": "10.1021/ja00079a044", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "1993-12-29", "series_number": "26", "volume": "115", "issue": "26", "pages": "12577-12578" }, { "id": "authors:gg4sq-n9n88", "collection": "authors", "collection_id": "gg4sq-n9n88", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180529-144212315", "type": "article", "title": "Enantiospecific palindromic recognition of 5'-d(CTCTAGAG)-3' by a novel rhodium intercalator: analogies to a DNA-binding protein", "author": [ { "family_name": "Sitlani", "given_name": "Ayesha", "clpid": "Sitlani-A" }, { "family_name": "Dupureur", "given_name": "Cynthia M.", "clpid": "Dupureur-C-M" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "We are exploring principles of protein-DNA recognition through the design of model 9,10-phenanthrenequinonediimine (phi) complexes of rhodium(II1) which bind site-selectively to DNA. [Rh(phi)]^(3+) complexes intercalate in the DNA major groove through the phi ligand and upon photoactivation promote strand scission via abstraction of the deoxyribose C3'-H atom. Here we report on the metal complex [Rh(DPB)_2phi]^(3+) (DPB = 4,4'-diphenyl-2,2'-bipyridyl) (Figure 1 ), which mimics DNA-binding proteins in DNA site-specificity and affinity.", "doi": "10.1021/ja00079a050", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "1993-12-29", "series_number": "26", "volume": "115", "issue": "26", "pages": "12589-12590" }, { "id": "authors:k7dtq-2x395", "collection": "authors", "collection_id": "k7dtq-2x395", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180601-135454004", "type": "article", "title": "Metallointercalators: syntheses, structures, and photochemical characterizations of phenanthrenequinone diimine complexes of rhodium(III)", "author": [ { "family_name": "Krotz", "given_name": "Achim H.", "clpid": "Krotz-A-H" }, { "family_name": "Kuo", "given_name": "Louis Y.", "clpid": "Kuo-Louis-Y" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Short and very efficient syntheses of a series of d^6 rhodium(II1) complexes, [Rh(X_4)phi]^(3+) (X_4 = (NH_3)_4, (en)_2, tren, [12]aneN_4, [12]aneS_4), containing the 9,10-phenanthrenequinone diimine (phi) ligand and mono-, bi-, and tetradentate amine- or sulfur-containing ligands have been carried out. The synthetic strategies include two-step reaction sequences, in which the coordinated chlorides of [Rh(X_4)Cl_2]^+ are replaced by 9,10-diaminophenanthrene, and a single-step method, in which RhCl_3 is first reacted with 9,10-diaminophenanthrene and then the ancillary ligands are added, followed by oxidation with dioxygen. The complexes have been investigated with respect to their solid-state structure, spectroscopy, and photochemical reactivity. This detailed characterization provides the basis to explore systematically the contributions of hydrogen bonding and van der Waals interaction to sequence-specific recognition of DNA. Crystal structures of [Rh[(NH_3)_4phi]Cl_3\u20223H_2O (triclinic crystal system, space group P1 (No. 2), Z = 2, a = 7.605(2) \u00c5, b = 9.081(2) \u00c5, c = 16.729(4) \u00c5, \u03b1 = 87.95(2)\u00b0, \u03b2 = 76.92(2)\u00b0, \u03b3 = 84.42(2)\u00b0, V= 1119.9(4) \u00c5^3), and [Rh([12]aneN_4)phi](SCN)_3\u20222H_2O triclinic crystal system, space group P1 (No. 2), Z = 2, a = 15.479(5) \u00c5, b = 12.312(2) \u00c5, c = 8.679(2) \u00c5, \u03b1 = 72.10(2)\u00b0, \u03b2 = 83.98(2)\u00b0, \u03b3 = 71.52(2)\u00b0, V = 1492.7(7) \u00c5^3), and Rh([12]aneS_4)phi]Br_3\u20223H_2O (triclinic crystal system, space group P1 (No. 2), Z = 2, a = 8.921(2) \u00c5, b = 12.846(4) \u00c5, c = 13.325(4) \u00c5, \u03b1 = 70.50(2)\u00b0, \u03b2 = 86.43(2)\u00b0, \u03b3 = 86.68(2)\u00b0, V= 1435.5(7) \u00c5^3) are reported. Two isomers, which are also seen in solution in a ratio of 60:40 (\u0394G = 0.99 kJ/mol), of C_(2\u03bd) (14% population) and C_S (86% population) symmetry have been found in the same crystal of [Rh([12]aneN_4)phi](SCN)_3\u20222H_2O, but only one isomer (point group C_S) has been found for the sulfur analogue [Rh([12]aneS_4)phi]Br_3. The substantial distortion of the octahedral geometry in the complexes [Rh([12]aneN_4)phi]^(3+) and [Rh([12]aneS_4)phi]^(3+) is associated with the small hole size of the coordinating macrocycles. Angles N(4)-Rh-N(6) between axial nitrogen atoms are as small as 160\u00b0 in [Rh([12]aneN_4)phil]_3^+ or 168.5\u00b0 for the angle S(1)-Rh-S(3) between the axial sulfur atoms of [Rh( [12]aneS_4)phi]^(3+). The effect on the overall topology of different conformations of the independently coordinating bidentate ligands in [Rh(en)_2phi]^(3+) is compared to the largely restricted conformations of tetradentate macrocycles in [Rh([12]aneN_4)phi]^(3+) and [Rh([12]aneS_4)phi]^(3+). ^(13)C and ^1H NMR spectroscopic data show that the structures seen in the solid state are also retained in solution. The chemical shift of the C1 or C8 hydrogen atom of the phi ligand is systematically influenced by the relative configuration at the heteroatom which is coordinated to the rhodium in the equatorial position. Electronic absorption spectra of the phi complexes of rhodium are found to be quite similar, dominated by strong bands between 250 and 280 nm and a broad transition between 360 and 410 nm. A reversible blue shift and hypochromicity (13-32%) are observed in the UV spectrum upon changing the pH\nfrom 2 to 10. The optical pK_a values for the phi complexes are correlated with the pK_b values of the ancillary ligands. [Rh(X_4)phi]^(3+) complexes undergo photodecomposition upon irradiation with UV light at 325 nm with the preferential\nloss of the phi ligand. The pH dependence of the quantum yields for photoanation supports a mechanism in which light-induced charge transfer from the aromatic phi ligand to the rhodium(II1) center is involved.", "doi": "10.1021/ic00078a012", "issn": "0020-1669", "publisher": "American Chemical Society", "publication": "Inorganic Chemistry", "publication_date": "1993-12-22", "series_number": "26", "volume": "32", "issue": "26", "pages": "5963-5974" }, { "id": "authors:2v6ky-1z614", "collection": "authors", "collection_id": "2v6ky-1z614", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150121-165643265", "type": "article", "title": "Long-range photoinduced electron transfer through a DNA helix", "author": [ { "family_name": "Murphy", "given_name": "C. J.", "clpid": "Murphy-C-J" }, { "family_name": "Arkin", "given_name": "M. R.", "clpid": "Arkin-M-R" }, { "family_name": "Jenkins", "given_name": "Y.", "clpid": "Jenkins-Y" }, { "family_name": "Ghatlia", "given_name": "N. D.", "clpid": "Ghatlia-N-D" }, { "family_name": "Bossmann", "given_name": "S. H.", "clpid": "Bossmann-S-H" }, { "family_name": "Turro", "given_name": "N. J.", "clpid": "Turro-N-J" }, { "family_name": "Barton", "given_name": "J. K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Rapid photoinduced electron transfer is demonstrated over a distance of greater than 40 angstroms between metallointercalators that are tethered to the 5' termini of a 15-base pair DNA duplex. An oligomeric assembly was synthesized in which the donor is Ru(phen)_2dppz^(2+) (phen, phenanthroline, and dppz, dipyridophenazine) and the acceptor is Rh(phi)_2phen^(3+) (phi, phenanthrenequinone diimine). These metal complexes are intercalated either one or two base steps in from the helix termini. Although the ruthenium-modified oligonucleotide hybridized to an unmodified complement luminesces intensely, the ruthenium-modified oligomer hybridized to the rhodium-modified oligomer shows no detectable luminescence. Time-resolved studies point to a lower limit of 10^9 per second for the quenching rate. No quenching was observed upon metallation of two complementary octamers by Ru(phen)_3^(2+) and Rh(phen)_3^(3+) under conditions where the phen complexes do not intercalate. The stacked aromatic heterocycles of the DNA duplex therefore serve as an efficient medium for coupling electron donors and acceptors over very long distances.", "doi": "10.1126/science.7802858", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "1993-11-12", "series_number": "5136", "volume": "262", "issue": "5136", "pages": "1025-1029" }, { "id": "authors:jfy44-qh866", "collection": "authors", "collection_id": "jfy44-qh866", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160405-153102472", "type": "article", "title": "Chemical Probing of tDNA^(Phe) with Transition Metal Complexes: A Structural Comparison of RNA and DNA", "author": [ { "family_name": "Lim", "given_name": "Ai Ching", "clpid": "Lim-Ai-Ching" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The three-dimensional folding of tDNA^(Phe) has been examined and compared to native tRNA^(Phe) using a series of shape-selective transition metal complexes as chemical probes of nucleic acid structure. Rh(phen)_2phi^(3+) (phen = phenanthroline, phi = 9,10-phenanthrenequinonediimine), which targets sites of tertiary interaction in tRNA^(Phe), cleaves specifically at similar sites on tDNA^(Phe). However, this rhodium complex also targets 5'-pyr-pyr-pur-3' sites within the acceptor and anticodon stems of tDNA; Rh(phen)_2phi^(3+)generally targets 5'-pyr-pyr-pur-3' sites in B-form duplex DNA. On tRNA^(Phe), Rh(DIP)_3^(3+) (DIP = 4,7- diphenyl-1,10-phenanthroline) specifically cleaves C70, which neighbors a GU mismatch, and targets \u03c855\nas well, within the hydrophobic region of tRNA^(Phe). On tDNA^(Phe) no specific cleavage by Rh(DIP)_3^(3+) is\nobserved. The cleavage studies, taken together, indicate that globally the tertiary folding of tDNA^(Phe) resembles that of tRNA^(Phe). However, the double helical regions of the DNA analog differ from tRNA^(Phe), likely in adopting a more B-like conformation. As a consequence, the GT mismatch within the acceptor stem of tDNA does not present the same recognition elements as in tRNA, and the GT mismatch is no\nlonger recognized by the shape-selective rhodium complex. The present work underscores the utility of applying DNA analogs to studies of RNA structure and function, since the general folding characteristics of the two polymers are likely to be similar. However, structural probing with transition metal complexes offers a valuable companion to such experiments, since the shape-selective probes, with sensitivity, may be used to delineate locally on the polymer those regions which may differ in structure.", "doi": "10.1021/bi00092a012", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "1993-10", "series_number": "41", "volume": "32", "issue": "41", "pages": "11029-11034" }, { "id": "authors:qqben-z3y45", "collection": "authors", "collection_id": "qqben-z3y45", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160405-140026351", "type": "article", "title": "A Distinct Intron-DNA Structure in Simian Virus 40 T-Antigen and Adenovirus 2 E1A Genes", "author": [ { "family_name": "Lee", "given_name": "Inho", "clpid": "Lee-Inho" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Distinct structures delineating the introns of simian virus 40 T-antigen and adenovirus 2 E1A genes have been discovered. The structures, which are centered around the branch points of the genes inserted in supercoiled double-stranded plasmids, are specifically targeted through photoactivated strand cleavage by the metal complex tris(4,7-diphenyl-1,10-phenanthroline)rhodium(III). The DNA sites that are recognized lack sequence homology but are similar in demarcating functionally important sites on the\nRNA level. The single-stranded DNA fragment corresponding to the coding strand of the E1A gene was also found to fold into a structure apparently identical to that in the supercoiled E1A gene based on the recognition by the metal complex. Further investigation of different single-stranded DNA fragments showed that the structure requires the sequences at both ends of the intron plus the flanking sequences but not the middle of the intron. These results provide direct evidence that the positions of these introns are structurally encoded on the DNA level.", "doi": "10.1021/bi00075a001", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "1993-06-22", "series_number": "24", "volume": "32", "issue": "24", "pages": "6121-6127" }, { "id": "authors:8hwb1-0v864", "collection": "authors", "collection_id": "8hwb1-0v864", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180501-151531707", "type": "article", "title": "NMR evidence for specific intercalation of \u0394-rh(phen)_2phi^(3+) in [d(GTCGAC)_2]", "author": [ { "family_name": "David", "given_name": "Sheila S.", "orcid": "0000-0001-5873-7935", "clpid": "David-S-S" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The anchoring of metal complexes in the major groove of DNA through intercalation has been increasingly useful in the shape-selective design of novel metal complexes which bind DNA with high sequence-selectivity. Toward that goal, direct structural information regarding this intercalative interaction is essential. Phenanthrenequinone diimine (phi) complexes of Rh(III) bind avidly (K_b 1 \u2265 10^7) to DNA by intercalation in the major groove. Here we report the first ^1H-NMR studies of \u0394-rh(phen)_2phi^(3+) bound to an oligonucleotide. These studies provide direct structural evidence for specific intercalation by this octahedral complex in the major groove of DNA.", "doi": "10.1021/ja00060a060", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "1993-04-07", "series_number": "7", "volume": "115", "issue": "7", "pages": "2984-2985" }, { "id": "authors:ntytm-kpg76", "collection": "authors", "collection_id": "ntytm-kpg76", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160914-152612759", "type": "article", "title": "Metallointercalators: structure of rac-bis(ethylenediamine)(9,10-phenanthrenequinone diimine)rhodium(III) tribromide trihydrate", "author": [ { "family_name": "Schaefer", "given_name": "William P.", "clpid": "Schaefer-W-P" }, { "family_name": "Krotz", "given_name": "Achim H.", "clpid": "Krotz-A-H" }, { "family_name": "Kuo", "given_name": "Louis Y.", "clpid": "Kuo-L-Y" }, { "family_name": "Shields", "given_name": "Thomas P.", "clpid": "Shields-T-P" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Bis(ethylenediamine)(phenanthrenequinone diimine)rhodium(III) tribromide trihydrate has a nearly planar phenanthrenequinone diimine ligand and two ordered ethylenediamine ligands, giving a distorted octahedral coordination to the compound. The N-Rh-N angles range from 77.1 (6) to 96.5\u00b0, with the largest deviations from 90\u00b0 associated with the N atoms of the phenanthrenequinone diimine ligand. The two Rh-N distances involving these N atoms are 0.05 \u00c5 shorter than Rh-N distances to ethylenediamine ligands; other distances and angles are within normal ranges.", "doi": "10.1107/S0108270192006917", "issn": "0108-2701", "publisher": "International Union of Crystallography", "publication": "Acta Crystallographica Section C", "publication_date": "1992-11", "series_number": "11", "volume": "48", "issue": "11", "pages": "2071-2073" }, { "id": "authors:49jhd-qbx18", "collection": "authors", "collection_id": "49jhd-qbx18", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160406-091731528", "type": "article", "title": "Characterization of dipyridophenazine complexes of ruthenium(II): The light switch effect as a function of nucleic acid sequence and conformation", "author": [ { "family_name": "Jenkins", "given_name": "Yonchu", "clpid": "Jenkins-Y" }, { "family_name": "Friedman", "given_name": "Alan E.", "clpid": "Friedman-A-E" }, { "family_name": "Turro", "given_name": "Nicholas J.", "clpid": "Turro-N-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Spectroscopic parameters for two novel ruthenium complexes on binding to nucleic acids of varying sequences and conformations have been determined. These complexes, Ru(bpy)_2dppz^(2+) and Ru(phen)_2dppz^(2+) (bpy = 2,2'-bipyridine; phen = 1,10-phenanthroline; dppz = dipyrido[3,2:\u0251-2',3':c]phenazine) serve as \"molecular light switches\" for DNA, displaying no photoluminescence in aqueous\nsolution but luminescing intensely in the presence of DNA. The luminescent enhancement observed upon binding is attributed to the sensitivity of the excited state to quenching by water; in DNA, the metal complex, upon intercalation into the helix, is protected from the aqueous solvent, thereby preserving the\nluminescence. Correlations between the extent of protection (depending upon the DNA conformation) and the luminescence parameters are observed. Indeed, the strongest luminescent enhancement is observed for intercalation into DNA conformations which afford the greatest amount of overlap with access from the major groove, such as in triple helices. Differences are observed in the luminescent parameters between\nthe two complexes which also correlate with the level of water protection. In the presence of nucleic acids, both complexes exhibit biexponential decays in emission. Quenching studies are consistent with two intercalative binding modes for the dppz ligand from the major groove: one in which the metal-phenazine axis lies along the DNA dyad axis and another where the metal-phenazine axis lies almost perpendicular to the DNA dyad axis. Ru(bpy)_2dppz^(2+) and Ru(phen)_2dppz^(2+) are shown here to be unique reporters of nucleic acid structures and may become valuable in the design of new diagnostics for DNA.", "doi": "10.1021/bi00159a023", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "1992-11", "series_number": "44", "volume": "31", "issue": "44", "pages": "10809-10816" }, { "id": "authors:25bw1-5rt70", "collection": "authors", "collection_id": "25bw1-5rt70", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170905-104309030", "type": "article", "title": "Novel dipyridophenazine complexes of ruthenium(II): exploring luminescent reporters of DNA", "author": [ { "family_name": "Hartshorn", "given_name": "Richard M.", "clpid": "Hartshorn-R-M" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "A series of ruthenium(II) complexes have been prepared which contain two phenanthroline ligands and a third bidentate ligand which is one of a set of derivatives of the parent dipyrido[3,2-a:2',3'c]phenazine (DPPZ) ligand. The spectroscopic properties of these complexes in the presence and absence of DNA have also been characterized. The derivatives have been prepared by condensation of different diaminobenzenes or diaminopyridines with the synthetic intermediate bis(1,10-phenanthroline)(1,10-phenanthroline-5,6-dione)ruthenium(II). [Ru(phen)_2DPPz](2+), like [Ru(bpy)_2DPPz]^(2+), acts as a molecular\n\"light switch\" for the presence of DNA, displaying no detectable photoluminescence in aqueous solution but luminescing brightly on binding to DNA. None of the DPPZ derivatives prepared show comparable \"light switch\" enhancements, since some luminescence may be detected in aqueous solution in the absence of DNA. For some complexes, however, luminescence enhancements of a factor of 20-300 are observed on binding to DNA. For these and the parent DPPZ complexes, the large enhancements observed are attributed to a sensitivity of the ruthenium-DPPZ luminescent charge-transfer excited state to quenching by water; although these complexes show little or no luminescence in water, appreciable luminescence is found in acetonitrile. Other derivatives show little solvent sensitivity in luminescence, and these, like Ru(phen)_3^(2+), display moderate enhancements (20-70%) on binding to DNA. [Ru(phen)_2DPPz]^(2+) and its derivatives all show at least biexponential decays in emission. Two binding modes have been proposed to account for these emission characteristics: a perpendicular mode where the DPPZ ligand intercalates from the major groove such that the metal-phenazine axis lies along the DNA dyad axis, and another, side-on mode where the metal-phenazine axis lies along the long axis of the base pairs.", "doi": "10.1021/ja00041a002", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "1992-07-01", "series_number": "15", "volume": "114", "issue": "15", "pages": "5919-5925" }, { "id": "authors:tbkty-4fp46", "collection": "authors", "collection_id": "tbkty-4fp46", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160406-093104747", "type": "article", "title": "Delineation of Structural Domains in Eukaryotic 5S rRNA with a Rhodium Probe", "author": [ { "family_name": "Chow", "given_name": "Christine S.", "clpid": "Chow-Christine-S" }, { "family_name": "Hartmann", "given_name": "Kevin M.", "clpid": "Hartmann-K-M" }, { "family_name": "Rawlings", "given_name": "Stephen L.", "clpid": "Rawlings-S-L" }, { "family_name": "Huber", "given_name": "Paul W.", "clpid": "Huber-P-W" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The three-dimensional folding of Xenopus oocyte SS rRNA has been examined using the coordination complex Rh(phen)_2phi^(3+) (phen = phenanthroline; phi = phenanthrenequinone diimine) as a structural probe. Rh(phen)_2phi^(3+) binds neither double-helical RNA nor unstructured single-stranded regions of RNA. Instead, the complex targets through photoactivated cleavage sites of tertiary interaction which are open in the major groove and accessible to stacking. The sites targeted by the rhodium complex have been mapped on the wild-type Xenopus oocyte RNA, on a truncated RNA representing the arm of the molecule comprised of helix IV-loop E-helix V, and on several single-nucleotide mutants of the SS rRNA. On the wild-type SS rRNA, strong cleavage is found at residues U73, A74, AIOI, and U102 in the E loop and USO and G81 in helix IV; additional sites are evident at A22 and AS6 in the B loop, C29 and A32 in helix III, and C34, C39, A42, and C44 in the C loop. Given the similarity observed in cleavage between the full SS RNA and the truncated fragment as well as the absence of any long-range effects on cleavage in mutant RNAs, the results do not support models which involve long-range tertiary interactions. Cleavage results with Rh(phen)_2phi^(3+) do, however, indicate that the apposition of several noncanonical bases as well as stem-loop junctions may result in intimately stacked structures with opened major grooves. In particular,\non the basis of cleavage results on mutant RNAs, both loops C and E represent structures where the strands constituting each loop are not independent of one another but are intrinsically structured. Stem-loop junctions, helix bulges containing more than one unmatched nucleotide, and a U-U mismatch also appear to provide open major grooves for targeting by Rh(phen)_2phi^(3+). These distinctive structures may also be utilized for specific recognition by proteins, such as the transcription factor TFIIIA, that bind to 5S rRNA.", "doi": "10.1021/bi00128a030", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "1992-04", "series_number": "13", "volume": "31", "issue": "13", "pages": "3534-3542" }, { "id": "authors:gq67f-4am20", "collection": "authors", "collection_id": "gq67f-4am20", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180724-152025087", "type": "article", "title": "DNA photocleavage by phenanthrenequinone diimine complexes of rhodium(III): shape-selective recognition and reaction", "author": [ { "family_name": "Sitlani", "given_name": "Ayesha", "clpid": "Sitlani-A" }, { "family_name": "Long", "given_name": "Eric C.", "clpid": "Long-E-C" }, { "family_name": "Pyle", "given_name": "Anna M.", "clpid": "Pyle-A-M" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Rh(phen)_2phi^(3+) and Rh(phi)_2bpy^(3+) (phi = 9,10-phenanthrenequinone diimine, phen = 1, 10-phenanthroline, bpy = 2,2'-bipyridyl) bind double helical DNA avidly (K \u2265 10^7 M^(-1)) by intercalation and with photoactivation promote strand cleavage. Rh(phen)_2phi^(3+) and Rh(phi)_2bpy^(3+) unwind double helical DNA by 21\u00b0 and 18\u00b0, respectively, per bound complex. The quantum yields for nucleic acid base release at 313 nm are 0.0012 for Rh(phen)_2phi^(3+) and 0.0003 for Rh(phi)_2bpy^(3+). While both complexes have similar photochemical properties, overall binding modes and affinities, their cleavage patterns, observed on ^(32)P-end-labeled DNA restriction fragments and oligonucleotide substrates, indicate substantially different recognition characteristics. Rh(phen)_2phi^(3+) binds DNA with some sequence selectivity, preferring 5'-pyrimidine-pyrimidine-purine-3' sites and cleaving with 5'-asymmetry, while Rh(phi)_2bpy^(3+) binds in a predominantly sequence-neutral fashion. These differences in recognition characteristics may be understood based upon the different shapes of the complexes. Owing to steric interactions of the ancillary phenanthroline ligands, Rh(phen)_2phi^(3+) appears to bind preferentially to sites which are more open in the major groove; since no similar steric constraints arise with an ancillary phi ligand, Rh(phi)_2bpy^(3+) binds all sites with similar affinities. The shapes of these complexes also govern their chemistry of strand scission. Chemical modification studies and HPLC analyses of the DNA termini and monomeric products formed in the Rh(phi)^(3+) induced DNA cleavage reactions have been conducted to characterize the products formed upon photoreaction of the rhodium complexes with 5'-CTGGCATGCCAG-3'. For Rh(phen)_2phi^(3+), the primary products are oligomers containing 3'- and 5'-phosphate termini and nucleic acid bases (in stoichiometric proportion). For Rh(phi)_2bpy^(3+), these same products account for approximately 70% of the reaction, but in addition base propenoic acids and a terminus assigned as a 3'-phosphoglycaldehyde are obtained in a correlated amount (30% of reaction). The formation of base propenoic acids and 3'-phosphoglycaldehydes are found furthermore to depend upon oxygen concentration, while other products are oxygen-independent. The products obtained are consistent with photoreaction of Rh(phi)^(3+), intercalated in the major groove of DNA, via abstraction of a C3'-H atom of the deoxyribose. Subsequent addition of dioxygen to the C3'-H radical or solvation would lead to the degradation products obtained. The partitioning between the oxygen dependent and independent pathways of DNA strand scission is found to correlate best with how the shape of the complex limits access of dioxygen to the C-3' position. While Rh(phi)_2bpy^(3+) was found to promote the oxygen-dependent pathway to an extent of approximately 30%, Rh(phen)_2phi^(3+), with ancillary phenanthrolines that overhang and shelter the C3'-position, appears to disfavor this pathway of DNA degradation. These studies underscore the importance of shape-selection in governing not only recognition but also reaction of molecules on the helix. Such an intimate relationship between recognition and reaction of molecules bound selectively to DNA requires consideration in understanding the reactions of DNA-binding proteins and small molecules.", "doi": "10.1021/ja00033a003", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "1992-03-25", "series_number": "7", "volume": "114", "issue": "7", "pages": "2303-2312" }, { "id": "authors:1kdfe-bg055", "collection": "authors", "collection_id": "1kdfe-bg055", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160406-071104818", "type": "article", "title": "Recognition of Tertiary Structure in tRNAs by Rh(phen)_2phi^(3+) a New Reagent for RNA Structure-Function Mapping", "author": [ { "family_name": "Chow", "given_name": "Christine S.", "clpid": "Chow-Christine-S" }, { "family_name": "Behlen", "given_name": "Linda S.", "clpid": "Behlen-L-S" }, { "family_name": "Uhlenbeck", "given_name": "Olke C.", "clpid": "Uhlenbeck-O-C" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "With photoactivation Rh(phen)_2phi^(3+) promotes strand cleavage at sites of tertiary interaction in tRNA. The rhodium complex, which binds double-helical DNA by intercalation in the major groove, yields no cleavage in double-helical regions of the RNA or in unstructured single-stranded regions. Instead, Rh(phen)_2phi^(3+) appears to target regions which are structured so that the major groove is open and accessible for stacking with the complex, as occurs where bases are triply bonded. So as to examine the specificity of this novel reagent and to evaluate its use in probing structural changes in RNAs, cleavage studies have been conducted on two structurally characterized tRNAs, tRNA^(Phe) and tRNA^(Asp) from yeast, the unmodified yeast tRNA^(Phe) transcript, and a chemically modified tRNA^(phe), as well as on a series of tRNA^(Phe) mutants. On tRNA^(Phe) strong cleavage is observed at residues G22, G45, U47, \u03c855, and U59; weaker cleavage is observed at A44, m^7G46, and C48. On tRNA^(AsP) cleavage is found at residues A21 through G26, \u03c832, and U48, with minor cleavage apparent at A44, G45, A46, \u03c855, U59, and U60. There is a striking similarity in cleavage observed on these tRNAs, and the sites of cleavage mark regions of tertiary folding. Cleavage on the unmodified tRNA^(Phe) transcript resembles closely that found on native yeast tRNA^(Phe), but additional sites, primarily in the anticodon loop and stem, are evident. The results indicate that globally the structures containing or lacking the modified bases appear to be the same; the differences in cleavage observed may reflect a loosening or alteration in the structure due to the absence of the modified bases. Cleavage results on mutants of tRNA^(Phe) illustrate Rh(phen)_2phi^(3+) as a sensitive probe in characterizing tRNA tertiary structure. Results are consistent with other assays for structural or functional changes. Uniquely, Rh-\n(phen)_2phi^(3+) appears to target directly sites of tertiary interaction. Cleavage results on mutants which involve base changes within the triply bonded region of the molecule indicate that it is the structure of the triply\nbonded array rather than the individual nucleotides which are being targeted. Chemical modification to promote selective depurination of the third base (m^7G46) involved in the triple in the folded, native tRNA leads to the reduction of cleavage by the metal complex; this result shows directly the importance of the stacked triple base structure for recognition by the metal complex. The cleavage results are consistent with the notion that Rh(phen)_2phi^(3+) preferentially targets regions of tertiary structure in the tRNA because these regions are structured so that the major grooves are open and accessible to stacking by the complex. Since sites cleaved by the rhodium complex mark a range of tertiary structures, Rh(phen)_2phi^(3+)appears to be a powerful and unique probe in characterizing the folded structures of RNAs.", "doi": "10.1021/bi00119a005", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "1992-02", "series_number": "4", "volume": "31", "issue": "4", "pages": "972-982" }, { "id": "authors:eje16-mv029", "collection": "authors", "collection_id": "eje16-mv029", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180720-112834170", "type": "article", "title": "Imaging of oligonucleotide-metal complexes by scanning tunneling microscopy", "author": [ { "family_name": "Kim", "given_name": "Yun", "clpid": "Kim-Yun" }, { "family_name": "Long", "given_name": "Eric C.", "clpid": "Long-E-C" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Lieber", "given_name": "Charles M.", "clpid": "Lieber-C-M" } ], "abstract": "Scanning tunneling microscopy (STM) has been used to image synthetic oligonucleotide duplexes alone or with an intercalatively bound metal complex with submolecular resolution. The sizes of 12 and 24 base pair (bp) oligonucleotides determined from STM images are in agreement with expected values, and images of isolated duplexes resolve the two nucleotide strands of these molecules. In addition, images of the 12-bp duplex in the presence of bis(9,10-phenanthrenequinone diimine) (2,2'-bipyridyl)rhodium(III) exhibit a new structural feature at 14 \u00c5 from the 12-bp duplex end. This new feature corresponds well to the metal binding sites determined from DNA cleavage and molecular modeling studies. These results indicate that STM can be used to image directly transition-metal complexes bound to DNA and thus suggest that metal complexes bound specifically to biological and other macromolecules could serve as useful labels in STM structural studies.", "doi": "10.1021/la00038a031", "issn": "0743-7463", "publisher": "American Chemical Society", "publication": "Langmuir", "publication_date": "1992-02", "series_number": "2", "volume": "8", "issue": "2", "pages": "496-500" }, { "id": "authors:7g4qa-mf423", "collection": "authors", "collection_id": "7g4qa-mf423", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:HUBpnas91", "type": "article", "title": "Structural polymorphism in the major groove of a 5S RNA gene complements the zinc finger domains of transcription factor IIIA", "author": [ { "family_name": "Huber", "given_name": "Paul W.", "clpid": "Huber-P-W" }, { "family_name": "Morii", "given_name": "Takashi", "clpid": "Morii-Takashi" }, { "family_name": "Mei", "given_name": "Houng-Yau", "clpid": "Mei-Houng-Yau" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Metal complexes that bind to DNA on the basis of shape-selection have been used to map the conformational features of the DNA binding site for transcription factor IIIA. Conformationally distinct segments are detected on the 5S rRNA gene that correspond closely to the binding sites identified for the individual zinc ringer domains of the protein. The local conformations are characterized by a major groove opened because of a change in base pair inclination and/or displacement at a central 5'-pyrimidine-purine-3' step, flanked by a widened minor groove, as would arise at the junctions between alternating B- and A-like DNA segments. Docking experiments with a consensus structure of a zinc finger reveal that the mixed A-B binding site accommodates the peptide domain better than either canonical B- or A-DNA helices. The close structural matching of the conformational variations in the 5S rDNA both to the proposed sites of zinc finger binding and to the shape of an individual zinc ringer domain points to DNA structural polymorphism as providing an important determinant in recognition. In particular, shape selection in the 5' half of the internal control region may orient the multiple finger domains.", "pmcid": "PMC53019", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1991-12-01", "series_number": "23", "volume": "88", "issue": "23", "pages": "10801-10805" }, { "id": "authors:gtjdz-h9x66", "collection": "authors", "collection_id": "gtjdz-h9x66", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170408-155617082", "type": "article", "title": "Molecular recognition and chemistry in restricted reaction spaces. Photophysics and photoinduced electron transfer on the surfaces of micelles, dendrimers, and DNA", "author": [ { "family_name": "Turro", "given_name": "Nicholas J.", "clpid": "Turro-N-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Tomalia", "given_name": "Donald A.", "clpid": "Tomalia-D-A" } ], "abstract": "This Account is concerned with molecular recognition in bimolecular reactions1 that occur in restricted spaces. Bimolecular reactions of interest are photoinduced electron transfers for which the reactants are positively electronically excited metal complexes (Figure 1) and another positively charged gegenion, either a metal complex or methyl viologen (MV^(2+)) that serves as an electron acceptor. The restricted reaction spaces are the interfacial regions of anionically charged polyions such as micelles, starburst dendrimers, and DNA. \n\nMolecular recognition is concerned with how specific sites on a molecular receptor are recognized by a binding substrate. Knowledge of the underlying principles of molecular recognition is useful in diverse activities such as the design of site- and conformation-specific reagents for biomolecules, the rational design of drugs and probes of polymer structure, the design of efficient catalytic systems, the design of strategies leading to the synthesis of new materials, and the design of novel nanoscopic devices.", "doi": "10.1021/ar00011a003", "issn": "0001-4842", "publisher": "American Chemical Society", "publication": "Accounts of Chemical Research", "publication_date": "1991-11", "series_number": "11", "volume": "24", "issue": "11", "pages": "332-340" }, { "id": "authors:vy45e-ycy76", "collection": "authors", "collection_id": "vy45e-ycy76", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160126-113442705", "type": "article", "title": "Photoinduced electron transfer quenching of excited Ru(II) polypyridyls bound to DNA: the role of the nucleic acid double helix", "author": [ { "family_name": "Orellana", "given_name": "Guillermo", "clpid": "Orellana-G" }, { "family_name": "Kirsch-De Mesmaeker", "given_name": "Andree", "clpid": "Kirsch-De Mesmaeker-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Turro", "given_name": "Nicholas J.", "clpid": "Turro-N-J" } ], "abstract": "In the presence of double helical polynucleotides (sodium poly(dA-dT)-poly(dA-dT) or calf thymus DNA), the efficiency of oxidative or reductive electron transfer between photoexcited ruthenium(II) chelates Ru(tap)2(hat)^(2+) or Ru(phen)^(\u2154+) (where tap =1,4,5,8-tetraazaphenanthrene, hat = 1,4,5,8,9,12-hexaazatriphenylene, and phen = 1,10-phenanthroline) and appropriate cationic quenchers (ethidium, Ru(NH3)3/6^+, methyl viologen, or M(phen)3/3^+, where M = Co, Rh, Cr) increases 1\u20132 orders of magnitude compared to the efficiency of the same quenching in microhomogeneous aqueous medium (k_q= 0.3-1.8 \u00d7 10^9 M's^(\u22121)). The enhancement is more pronounced when the binding constant of the quencher (10^3 < Kh < 10^6 M^(\u22121)) is large. Similar trends are found when the biopolymers are replaced by sodium poly(styrenesulfonate) (PSS). The accelerated electron transfer process is proposed to be due mainly to the effect of accumulation of the reagents in the electrostatic field of the polymer; if corrections for this effect are introduced (e.g. ratioing [quencher]/[polynucleotide]), the reaction rate becomes essentially independent of the polymer concentration. Based upon a model for electron transfer reaction of the complexes within a small cylindrical interface around the DNA helix, calculations of the bimolecular electron transfer rate constants are computed to be 10\u2032 times smaller when the reactants are bound to the double-stranded polynucleotides and decreased mobility of the cationic species is apparent. The effect is less pronounced if a simpler polyelectrolyte (PSS) is employed. Emission lifetimes of the Ru(II) polypyridyls bound to the DNA (0.32\u20132\u03bcs, double exponential decays) are discussed as well.", "doi": "10.1111/j.1751-1097.1991.tb02049.x", "issn": "0031-8655", "publisher": "Pergamon Press", "publication": "Photochemistry and Photobiology", "publication_date": "1991-10", "series_number": "4", "volume": "54", "issue": "4", "pages": "499-509" }, { "id": "authors:ve9tc-1b171", "collection": "authors", "collection_id": "ve9tc-1b171", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160406-134002391", "type": "article", "title": "Luminescence of ruthenium(II) polypyridyls: evidence for intercalative binding to Z-DNA", "author": [ { "family_name": "Friedman", "given_name": "Alan E.", "clpid": "Friedman-Alan-E" }, { "family_name": "Kumar", "given_name": "Challa V.", "orcid": "0000-0002-8399-1334", "clpid": "Kumar-Challa-V" }, { "family_name": "Turro", "given_name": "Nicholas J.", "clpid": "Turro-Nicholas-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Photophysical studies have been undertaken to characterize the binding interactions of enantiomers of Ru(phen)\u2083\u00b2\u207a, Ru(DIP)\u2083\u00b2\u207a, and racemic Ru(bpy)\u2082dppz\u00b2\u207a (where phen = 1,10-phenanthroline, DIP = 4,7-diphenylphenanthroline, and dppz = dipyridophenazine) with Z-form poly d(GC). Parallel enhancements in steady state luminescent intensity and a lengthening of luminescent lifetimes are seen for ruthenium enantiomers with Z-DNA as for B-DNA but with enantioselectivities reversed. Greater enhancements are seen for delta-isomers with the right-handed helix but for lambda-isomers with the left-handed helix. Ru(bpy)\u2082dppz\u00b2\u207a, an avid intercalator in B-DNA, displays no luminescence free in aqueous solution, but luminesces brightly bound to either B- or Z-poly d(GC). Stern-Volmer quenching studies also support the enantioselective preference in binding to B-DNA by \u0394-isomers and a reversal with binding to Z-DNA preferentially by the \u039b-isomers. Steady state polarization studies indicate a rigid association of the complexes with both B- and Z-DNA on the time-scale of their emission and again with symmetrical enantioselectivities for the left and right-handed helices. Given the well characterized intercalative association of the complexes with B-DNA, the parallel results seen here with Z-DNA point strongly to a comparable intercalative association with the Z-form helix. That molecules may interact with Z-DNA through intercalation has not been demonstrated previously and now requires consideration in describing the range of interactions of small molecules and proteins with Z-DNA.", "pmcid": "PMC328175", "issn": "0305-1048", "publisher": "Oxford University Press", "publication": "Nucleic Acids Research", "publication_date": "1991-05-25", "series_number": "10", "volume": "19", "issue": "10", "pages": "2595-2602" }, { "id": "authors:tyk2q-3pz10", "collection": "authors", "collection_id": "tyk2q-3pz10", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171108-084900678", "type": "article", "title": "On demonstrating DNA intercalation", "author": [ { "family_name": "Long", "given_name": "Eric C.", "clpid": "Long-E-C" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Considerable attention has focused on new DNA-binding\nand -modifying agents, from natural products to wholly\nsynthetic designs, as probes of DNA structure and as potential chemotherapeutic agents. The application of\nthese molecules necessitates a precise understanding of the\nstructural details of the agents' mode of interaction with\nthe target molecule, double-helical DNA. DNA binding\nagents tend to interact noncovalently with the host molecule\nthrough two general modes: (i) in a groove-bound fashion stabilized by a mixture of hydrophobic, electrostatic,\nand hydrogen-bonding interactions and (ii) through\nan intercalative association in which a planar, heteroaromatic moiety slides between the DNA base pairs.\nSurprisingly, however, only a fraction of known DNA-interactive agents have been structurally characterized to\natomic detail in noncovalent complexes with DNA.", "doi": "10.1021/ar00177a001", "issn": "0001-4842", "publisher": "American Chemical Society", "publication": "Accounts of Chemical Research", "publication_date": "1990-09-01", "series_number": "9", "volume": "23", "issue": "9", "pages": "271-273" }, { "id": "authors:1c6ps-gkk19", "collection": "authors", "collection_id": "1c6ps-gkk19", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160126-113616996", "type": "article", "title": "Ligand-dependent interaction of ruthenium(II) polypyridyl complexes with DNA probed by emission spectroscopy", "author": [ { "family_name": "Kirsch-De Mesmaeker", "given_name": "Andree", "clpid": "Kirsch-De Mesmaeker-A" }, { "family_name": "Orellana", "given_name": "Guillermo", "clpid": "Orellana-G" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Turro", "given_name": "Nicholas J.", "clpid": "Turro-N-J" } ], "abstract": "The nature of the interaction in buffered aqueous solution of several homo and heteroleptic ruthenium(II) polypyridyl complexes containing 2,2'-bipyridine (bpy), 2,2'-bipyrazine (bpz), 1,10-phenanthroline (phen), 4,7-diphenyl-l,10-phenanthroline (dip), 3,4,7,8-tetramethyl-l,10-phenanthroline (tmp), 1,4,5,8-tetraazaphenanthrene (tap), and 1,4,5,8,9,12-hexaazatriphenylene (hat) with calf thymus DNA and poly(dA-dT)-poly(dA-dT) (pdAT) has been investigated by steady-state spectroscopy and emission lifetime measurements. Those complexes containing two or more tap/hat ligands photo-oxidize the guanine base upon binding to DNA with efficiencies that parallel their excited state redox potentials, but display \"normal\" behavior (increase of both the emission intensity and lifetime) when bound to pdAT. However Ru(tap)(hat)^(2/2+) and Ru(hat)^(2/3+) even photooxidize the adenine base of pdAT, so that their excited states are also quenched in the presence of either polynucleotide. The electron transfer quenching mechanism has been confirmed previously by detection of the monoreduced complex in laser flash photolysis experiments in the presence of mononucleotides. Most of the complexes investigated appear to bind to DNA, at least in part via intercalation, with affinities being dependent on the nature of the largest ligand (hat shows the highest ability in heteroleptic complexes). From lifetime quenching experiments, in the presence of moderate amounts of NaCl, surface binding does not appear to be a general mode for the complexes investigated, and it has been demonstrated unequivocally only for Ru(phen)^(2/3+). In addition, the intercalation of complexes into DNA increases as the ionic strength of the medium decreases, the DNA/Ru ratio increases, or when water is partially replaced by glycerol.", "doi": "10.1111/j.1751-1097.1990.tb01787.x", "issn": "0031-8655", "publisher": "Pergamon Press", "publication": "Photochemistry and Photobiology", "publication_date": "1990-09", "series_number": "3", "volume": "52", "issue": "3", "pages": "461-472" }, { "id": "authors:mwg7b-wgk84", "collection": "authors", "collection_id": "mwg7b-wgk84", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180430-145302174", "type": "article", "title": "A molecular light switch for DNA: Ru(bpy)_2(dppz)^(2+)", "author": [ { "family_name": "Friedman", "given_name": "Alan E.", "clpid": "Friedman-A-E" }, { "family_name": "Chambron", "given_name": "Jean Claude", "clpid": "Chambron-J-C" }, { "family_name": "Sauvage", "given_name": "Jean Pierre", "clpid": "Sauvage-J-P" }, { "family_name": "Turro", "given_name": "Nicholas J.", "clpid": "Turro-N-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "[No abstract]", "doi": "10.1021/ja00168a052", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "1990-06-06", "series_number": "12", "volume": "112", "issue": "12", "pages": "4960-4962" }, { "id": "authors:9jsne-k6g95", "collection": "authors", "collection_id": "9jsne-k6g95", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160516-112833530", "type": "article", "title": "^1H NMR Studies of Tris(phenanthroline) Metal Complexes Bound to Oligonucleotides: Characterization of Binding Modest", "author": [ { "family_name": "Rehmann", "given_name": "Jill P.", "clpid": "Rehmann-J-P" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The binding of Ru(phen)_3^(2+), Rh(phen)_3^(3+), and Co(phen)_3^(3+) to the oligonucleotides d(GTGCAC)_2 and 5'-pd(CGCGCG)_i has been examined by ^1H NMR spectroscopy as a function of temperature, concentration, and chirality of the metal complex. The duplex oligonucleotides act as chiral shift reagents for the metal complexes; phenanthroline protons associated with each enantiomer are resolved upon binding to the oligomer. The spectral titrations, consistent with photophysical studies, indicate that the complexes bind to the oligomer through two modes: one assigned as intercalation favoring the A-isomer, and the other assigned as the surface-bound interaction favoring the \u039b-isomer. The ligand protons are perturbed in a\nmanner that implies sensitivity of particular protons to binding mode; specifically, the H4,7 protons appear\nto be altered most for the \u039b-enantiomer while the H5,6 protons are perturbed more for the \u039b-enantiomer.\nThe NMR chemical shift variations appear particularly sensitive to this surface-bound interaction, which,\non the basis of a comparison of binding and photophysical parameters for Ru(phen)_3^(3+), appears more\nprominant in binding to oligonucleotides than that to polynucleotides. With respect to oligonucleotide proton\nshifts, the adenine H2 proton, positioned in the minor groove of the helix, shows the largest upfield shifts\nwith metal binding, and more dramatically with \u039b-isomers. The major groove thymine methyl protons (TMe) shift downfield to a lesser extent, and more so for \u039b-isomers. The different binding modes also differ with respect to their dynamics of association; the longitudinal relaxation rates of \u0394- and \u039b-4,7 phenanthroline protons of Rh(phen)_3^(3+) are 0.88 and 1.14 s, respectively, in the presence of d(GTGCAC)_2. In contrast to studies with the substitutionally inert metal complexes, addition of racemic Co(phen)_3^(3+) to the oligonucleotide solution yields unequal populations of enantiomers, owing to the rapid racemization of the cobalt complex in the presence of oligomer and reequilibration to that form which favors binding. Duplex melting has also been monitored by ^1H NMR spectroscopy; the complexes increase the duplex melting temperature by ~5 \u00baC. In the case of Co(phen)_3^(3+), with increasing temperature, as the helix melts, a reequlibration of the enantiomers occurs, indicating that the chiral discrimination arises from enantioselective interactions with the helix rather than with the single-stranded oligonucleotides.", "doi": "10.1021/bi00459a006", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "1990-02", "series_number": "7", "volume": "29", "issue": "7", "pages": "1701-1709" }, { "id": "authors:5agfw-fcn70", "collection": "authors", "collection_id": "5agfw-fcn70", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160516-112834153", "type": "article", "title": "^1H NMR Studies of Tris(phenanthroline) Metal Complexes Bound to Oligonucleotides: Structural Characterizations via Selective Paramagnetic Relaxation", "author": [ { "family_name": "Rehmann", "given_name": "Jill P.", "clpid": "Rehmann-J-P" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The selective paramagnetic relaxation of oligonucleotide protons of d(GTGCAC)_2 by \u0394- and \u039b-Ni(phen)_3^(3+) and \u0394- and \u039b-Cr(phen)_3^(3+) has been examined to obtain some structural insight into the noncovalent binding of tris(phenanthroline) metal complexes to DNA. The experiments demonstrate that the relative rate of relaxation of different oligonucleotide protons by the paramagnetic metal complex varies with the chirality of the metal complex and, to a lesser extent, the metal charge. The proton most efficiently relaxed in all cases is the adenosine AH2, which is situated in the minor groove of the oligonucleotide helix. For both \u039b-Ni(phen)_3^(2+) and \u039b-Cr(phen)_3^(3+), the order of relaxation rates varies as AH2 \u00bb AH8 > G3H8 = TMe = C4H5. For \u0394-Ni(phen)_3^(2+) it varies as AH2 > G3H8 > AH8 > TMe = C4H5 and for \u0394-Cr(phen)_3^(3+) as AH2 > TMe = G3H8 = AH8 > C4H5. Distances between the metal center and oligonucleotide\nprotons were calculated on the basis of the relaxation data, and these distances were used to generate a set of models to describe the interactions of the rigid metal complex with the helix. For A-isomers, the data are consistent with a predominant surface-bound association in the minor groove of the DNA helix. The results for A-isomers correlate better with models that incorporate also a major groove intercalative mode. Despite the absence of hydrogen-bonding groups in the metal complex, the surface-bound model of the phenanthroline complex in the minor groove of DNA resembles the noncovalent association seen with other DNA groove binding molecules.", "doi": "10.1021/bi00459a007", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "1990-02", "series_number": "7", "volume": "29", "issue": "7", "pages": "1710-1717" }, { "id": "authors:41n41-s3e30", "collection": "authors", "collection_id": "41n41-s3e30", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160513-121954121", "type": "article", "title": "High resolution footprinting of EcoRI and distamycin with Rh(phi)_2(bpy)^(3+), a new photofootprinting reagent", "author": [ { "family_name": "Uchida", "given_name": "Kiyoshi", "clpid": "Uchida-Kiyoshi" }, { "family_name": "Pyle", "given_name": "Anna Marie", "clpid": "Pyle-A-M" }, { "family_name": "Morii", "given_name": "Takashi", "clpid": "Morii-Takashi" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The complex bis(phenanthrenequinone diimine)(bipyridyl)rhodium(III), Rh(phi)_2(bpy)^(3+), cleaves DNA efficiently in a sequence-neutral fashion upon photoactivation so as to provide a novel, high resolution, chemical photofootprinting reagent. Photofootprinting of two crystallographically characterized DNA-binding agents, distamycin, a small natural product which binds to DNA in the minor groove, and the endonuclease EcoRI, which binds in the major groove, gave respectively a 5\u20137 base pair footprint for the drug at its A_6 binding site and a 10\u201312 base pair footprint for the enzyme centered at its recognition site (5\u2032-GAATTC-3\u2032). Both footprints agree closely with the crystallographic results. The photocleavage reaction can be performed using either a high intensity lamp or, conveniently, a simple transilluminator box, and the photoreaction is not inhibited by moderate concentrations of reagents which are sometimes required for examining interactions of molecules with DNA. When compared with other popular footprinting agents, the rhodium complex shows a number of distinct advantages: sequence-neutrality, high resolution, ability to footprint major as well as minor groove-binding ligands, applicability in the presence of additives such as Mg^(2+) or glycerol, ease of handling, and a sharply footprinted pattern. Light activated footprinting reactions furthermore offer the possibility of examining DNA-binding interactions with time resolution and within the cell.", "doi": "10.1093/nar/17.24.10259", "pmcid": "PMC335299", "issn": "0305-1048", "publisher": "IRL Press", "publication": "Nucleic Acids Research", "publication_date": "1989-12-25", "series_number": "24", "volume": "17", "issue": "24", "pages": "10259-10279" }, { "id": "authors:f6ajk-vwn38", "collection": "authors", "collection_id": "f6ajk-vwn38", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160513-104502311", "type": "article", "title": "Accelerated Electron Transfer Between Metal Complexes Mediated by DNA", "author": [ { "family_name": "Purugganan", "given_name": "Michael D.", "clpid": "Purugganan-M-D" }, { "family_name": "Kumar", "given_name": "Challa V.", "clpid": "Kumar-C-V" }, { "family_name": "Turro", "given_name": "Nicholas J.", "clpid": "Turro-N-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "DNA-mediated long-range electron transfer from photoexcited 1,10-phenanthroline complexes of ruthenium, Ru(phen)^(2+)_3, to isostructural complexes of cobalt(III), rhodium(III), and chromium(III) bound along the helical strand. The efficiency of transfer depended upon binding mode and driving force. For a given donor-acceptor pair, surface-bound complexes showed greater rate enhancements than those that were intercalatively bound. Even in rigid glycerol at 253 K, the rates for donor-acceptor pairs bound to DNA remained enhanced. For the series of acceptors, the greatest enhancement in electron-transfer rate was found with chromium, the acceptor of intermediate driving force. The DNA polymer appears to provide an efficient intervening medium to couple donor and acceptor metal complexes for electron transfer.", "doi": "10.1126/science.3420416", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "1988-09-23", "series_number": "4873", "volume": "241", "issue": "4873", "pages": "1645-1649" }, { "id": "authors:jjc9b-64968", "collection": "authors", "collection_id": "jjc9b-64968", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160513-104524679", "type": "article", "title": "In vivo photoreaction of a chiral cobalt complex: DNA cleavage by Co(DIP)_3^(3+) in mammalian cells", "author": [ { "family_name": "Chapnick", "given_name": "Lowell B.", "clpid": "Chapnick-L-B" }, { "family_name": "Chasin", "given_name": "Lawrence A.", "clpid": "Chasin-L-A" }, { "family_name": "Raphael", "given_name": "Adrienne L.", "clpid": "Raphael-A-L" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The chiral complex tris (diphenylphenanthroline) cobalt (III) (Co(DIP)_3^(3+) provides a photoreactive probe for chromatin structure in mammalian cells. The complex, which upon photoactivation cleaves DNA in a conformation-specific fashion in vitro, is shown also to cleave DNA in vivo upon irradiation with ultraviolet light (>300 nm). \u0394- and \u039b-Co (DIP)_3^(3+) isomers are taken up efficiently into cultured Chinese hamster ovary cells and concentrate within cell nuclei. In the absence of light the complexes are toxic to the cells (10% survival at \u223c 300 nM), but after ultraviolet irradiation, the toxicity is markedly (>10-fold) increased. The synergism between irradiation and Co(DIP)_3^(3+) administration may lie in photoreactions with DNA elicited by the cobalt complex. Alkaline sucrose gradient of DNA from cells exposed to \u039b-Co(DIP)_3^(3+) and irradiation show single-stranded DNA fragmentation under conditions where little cleavage is seen in cells either incubated with \u039b-Co(DIP)_3^(3+) or irradiated with > 300 nm A ultraviolet light. Cellular DNA is cleaved with lower efficiency than naked DNA, likely due to decreased accessibility of sites in vivo. Hybridization of fragments obtained from the alkaline sucrose gradients to a probe specific for the amplified dihydrofolate reductase gene reveals a similar distribution of dhfr sequences and total DNA, indicating that the family of conformations recognized by \u039b-Co(DIP)_3^(3+) are dispersed throughout the genome.", "doi": "10.1016/0027-5107(88)90107-8", "issn": "0027-5107", "publisher": "Elsevier", "publication": "Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis", "publication_date": "1988-09", "series_number": "1", "volume": "201", "issue": "1", "pages": "17-26" }, { "id": "authors:xd00s-s7q13", "collection": "authors", "collection_id": "xd00s-s7q13", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:MEIpnas88", "type": "article", "title": "Tris(tetramethylphenanthroline)ruthenium(II): A chiral probe that cleaves A-DNA conformations", "author": [ { "family_name": "Mei", "given_name": "Houng-Yau", "clpid": "Mei-Houng-Yau" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "A-Tris(3,4,7,8-tetramethyl-1,10-phenanthroline) ruthenium(II) [A-Ru(TMP)2/3+] was found to be a distinctive molecular tool to examine the local variations in conformation along the strand. The metal complex binds cooperatively to A-form helices of various base sequences under conditions where little or no binding was found to analogous B-form DNAs. Photoactivated DNA cleavage may be coupled to this conformation-specific binding by taking advantage of the photophysical properties of ruthenium(II) complexes. A(TMP)2/3+ cleaves preferentially 3H-labeled A-form polynucleotides upon irradiation with visible light. The photoinduced DNA strand scission is likely to be mediated by singlet oxygen, which leads to a preferential cleavage of guanine residues. Comparative mapping of cleavage sites on a linear pBR322 fragment for tris(phenanthroline)ruthenium(II), which binds to B-DNA and cleaves also by sensitization of singlet oxygen, and for Ru(TMP)2/3+ shows the selective binding of ARu(TMP)2/3+ to conformationally distinct sites along the fragment. These sites correspond to 5- to 13-base-pair homopyrimidine stretches.", "pmcid": "PMC279766", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1988-03-01", "series_number": "5", "volume": "85", "issue": "5", "pages": "1339-1343" }, { "id": "authors:tgzcf-n7z59", "collection": "authors", "collection_id": "tgzcf-n7z59", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160513-123130441", "type": "article", "title": "Rh(DIP)_3^(3+): a shape-selective metal complex which targets cruciforms", "author": [ { "family_name": "Kirshenbaum", "given_name": "Mindy R.", "clpid": "Kirshenbaum-M-R" }, { "family_name": "Tribolet", "given_name": "Roger", "clpid": "Tribolet-R" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The coordination complex tris(4,7-diphenylphenanthroline)rhodium(III), Rh(DIP)_3^(3+) binds to and, upon photoactivation, cleaves both DNA strands near the base of a DNA cruciform Sites of photoinduced double-stranded DNA cleavage by the rhodium complex map to regions containing cruciforms on closed circular pBR322, pColE1 and \u03c6X174 (replicative form) DNAs. Neither cleavage nor binding by the metal complex, assayed using S1 nuclease, is found on the linear plasmid which lacks the extruded cruciform. High resolution mapping experiments reveal that h(DIP)_3^(3+) cleaves at a specific AT-rich site neighboring the stem of the minor cruciform on pBR322. The primary site of cleavage is found at position 3238 on the 3'-strand and 3250 on the 5-strand and is remarkably specific. The pattern of cleavage, to one side only of the cruciform stem, indicates an asymmetry in the cruciform structure recognized by the complex. These results suggest that Rh(DIP)_3^(3+) may provide a useful reagent to probe cruciform sites. In addition, the high degree of specificity found in targeting the cruciform structure with this simple metal complex underscores the utility of shape-selection for the recognition of specific sites on a DNA strand.", "doi": "10.1093/nar/16.16.7943", "pmcid": "PMC338502", "issn": "0305-1048", "publisher": "Oxford University Press", "publication": "Nucleic Acids Research", "publication_date": "1988", "series_number": "16", "volume": "16", "issue": "16", "pages": "7943-7960" }, { "id": "authors:zgbzp-33d02", "collection": "authors", "collection_id": "zgbzp-33d02", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:MULpnas87", "type": "article", "title": "Evidence for altered DNA conformations in the simian virus 40 genome: Site-specific DNA cleavage by the chiral complex Lambda-tris(4,7-diphenyl-1,10-phenanthroline)cobalt(III)", "author": [ { "family_name": "M\u00fcller", "given_name": "Barbara C.", "clpid": "M\u00fcller-B-C" }, { "family_name": "Raphael", "given_name": "Adrienne L.", "clpid": "Raphael-A-L" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Lambda-Tris(4,7-diphenyl-1,10-phenanthroline)cobalt(III), a photoactivated DNA-cleaving agent, is a small molecular probe of DNA structure. Because of its chirality, the complex cannot bind to regular right-handed B-form DNA but exhibits site-specific cleavage along the polymer strand at conformationally distinct sites such as those in a left-handed conformation. Both coarse and higher resolution mapping experiments using the chiral cobalt complex indicate intriguing conformational variations along the simian virus 40 genome. Highly specific cleavage is evident in the enhancer and promoter blocks and in the region downstream of 3' termini. A specific cleavage pattern borders an alternating purine/pyrimidine stretch within the enhancer, which was found earlier to bind anti-Z-DNA antibodies. Throughout the simian virus 40 genome, variations in structure delineated with the cobalt complex appear to correlate with regions important for control of gene expression.", "pmcid": "PMC304521", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1987-04-01", "series_number": "7", "volume": "84", "issue": "7", "pages": "1764-1768" }, { "id": "authors:xyrp6-62d58", "collection": "authors", "collection_id": "xyrp6-62d58", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160513-113952809", "type": "article", "title": "Metals and DNA: molecular left-handed complements", "author": [ { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Chiral metal complexes provide unique molecular probes for DNA. Chiral reagents that \"recognize\" different local structures along the DNA strand have been designed by a process in which the asymmetry in shape and size of the complex is matched to that of the DNA helical groove. As a result, the chiral metal complexes provide very sensitive probes for local helical structure, both left- and right-handed. Direct coordination of chiral complexes to the DNA bases adds an element of sequence selectivity to the probe design. With a suitable reactive metal center, reagents that target chemically specific sites along the strand may be developed. One such chiral reagent, which cleaves left-handed DNA sites with photoactivation, has been useful in mapping this distinct conformation and examining its biological role. The conformation-specific molecular cleaver, much like a DNA-binding enzyme, recognizes and reacts at discrete sites along the DNA strand. These site-specific chiral metal complexes provide exciting new tools for probing the local variations in DNA structure and its role in the regulation of gene expression.", "doi": "10.1126/science.3016894", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "1986-08-11", "series_number": "4765", "volume": "233", "issue": "4765", "pages": "727-734" }, { "id": "authors:v72b2-fn428", "collection": "authors", "collection_id": "v72b2-fn428", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160516-132218229", "type": "article", "title": "Restriction Endonuclease EcoRI Alters the Enantiomeric Preference of Chiral Metallointercalators for DNA: An Illustration of a Protein-Induced DNA Conformational Change", "author": [ { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Paranawithana", "given_name": "Shanthi R.", "clpid": "Paranawithana-S-R" } ], "abstract": "A conformational change in the DNA plasmid ColE_1 appears to occur upon specific binding of the restriction endonuclease EcoRI. Enzyme association alters the chiral discrimination found in binding metallointercalators to DNA sites. The complexes tris(l,10-henanthroline)ruthenium(II), Ru(phen)_3^(2+), tris( 4,7-diphenyl-1, 10-phenanthroline) ruthenium(II), Ru(DIP)_3^(2+), and tris( 4,7-diphenyl- l, 10-phenanthroline)cobalt(III), Co(DIP)_3^(3+), in general, bind stereoselectively to DNA helices, with enantiomers\npossessing the \u0394 configuration bound preferentially by right-handed B-DNA. In the presence of EcoRI, however, this enantioselectivity is altered. The chiral intercalators, at micromolar concentrations, inhibit the reaction of EcoRI, but for each enantiomeric pair it is the \u039b enantiomer, which binds only poorly to a B-DNA helix, that inhibits EcoRI preferentially. Kinetic studies in the presence of \u039b-Ru(DIP)_3^(2+) indicate that the enzyme inhibition occurs as a result of the \u039b enantiomer binding to the enzyme-DNA complex as well as to the free enzyme. Furthermore, photolytic strand cleavage experiments using Co(DIP)_3^(3+) indicate that the metal complex interacts directly at the protein-bound DNA site. Increasing concentrations of bound\nEcoRI stimulate photoactivated cleavage of the DNA helix by \u039b-Co(DIP)_3^(3+), until a protein concentration is reached where specific DNA recognition sites are saturated with enzyme. Thus, although \u039b-Co(DIP)_3^(3+) does not bind closely to the DNA in the absence of enzyme, specific binding of EcoRI appears to alter the DNA structure so as to permit the close association of the \u039b isomer to the DNA helix. Mapping experiments demonstrate that this association leads to photocleavage of DNA by the cobalt complex at or very close to the EcoRI recognition site. This study provides evidence that in solution, under enzymatic conditions, a DNA-binding protein may distort the DNA helical structure and furthet illustrates how small molecular probes of DNA conformation might be used in examining the structure of protein-bound DNA sites.", "doi": "10.1021/bi00356a053", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "1986-04-01", "series_number": "8", "volume": "25", "issue": "8", "pages": "2205-2211" }, { "id": "authors:dgb3w-j7y87", "collection": "authors", "collection_id": "dgb3w-j7y87", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:BARpnas85", "type": "article", "title": "Site-Specific Cleavage of Left-Handed DNA in pBR322 by Lambda-tris(diphenylphenanthroline)cobalt(III)", "author": [ { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Raphael", "given_name": "Adrienne L.", "clpid": "Raphael-A-L" } ], "abstract": "The chiral complex tris(4,7-diphenyl-1,10-phenanthroline)cobalt(III), Lambda -Co(DiP)33+, binds to and, with photoactivation, cleaves left-handed DNA helices, thereby providing a unique molecular probe for local DNA conformation. We have mapped the specific left-handed sites where Lambda -Co(DiP)33+ cleaves in the plasmids pBR322 and pLP32, which is the derivative of pBR322 containing a Z-form d(C-G)16 insert. For pLP32, a primary cleavage is at the insert; for native pBR322, cleavage occurs at four discrete sites: 1.45, 2.3, 3.3, and 4.2 kilobase pairs. These sites correspond to segments of alternating purine-pyrimidines. Moreover, these positions map to the ends of the three distinct coding regions in pBR322: the tetracycline-resistance gene, the origin of replication, and either end of the ampicillin-resistance (\u00df -lactamase) gene. The locations of these left-handed segments suggest to us that Z-DNA might serve as a conformational punctuation mark to demarcate the ends of genes.", "pmcid": "PMC390736", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1985-10-01", "series_number": "19", "volume": "82", "issue": "19", "pages": "6460-6464" }, { "id": "authors:ttnkd-0tm95", "collection": "authors", "collection_id": "ttnkd-0tm95", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:BARpnas84", "type": "article", "title": "Chiral probes for the handedness of DNA helices: Enantiomers of tris(4, 7-diphenylphenanthroline)ruthenium(II)", "author": [ { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Basile", "given_name": "Lena A.", "clpid": "Basile-L-A" }, { "family_name": "Danishefsky", "given_name": "Avis", "clpid": "Danishefsky-A" }, { "family_name": "Alexandrescu", "given_name": "Andrei", "clpid": "Alexandrescu-A" } ], "abstract": "The chiral complexes tris(4,7-diphenyl-1,10-\nphenanthroline)ruthenium(II) (RuDIP) are shown to be specific chemical probes with which to distinguish right- and left-handed DNA helices in solution. In spectrophotometric titrations of racemic RuDIP with both B-form calf thymus DNA and Z-form poly[d(G-C)], hypochromicity in the intense metal-to-ligand charge-transfer band is found and enhancement in luminescence is observed. The spectrophotometric assay of DNA binding to the well-resolved enantiomers of RuDIP provides a means to determine the helical conformation. Strong chiral specificity is seen in binding experiments with right-handed B-DNA and, on this basis, the absolute configurations are assigned. Although delta RuDIP can bind by intercalation into the right-handed helix, steric constraints imposed by the helix asymmetry preclude completely binding by the [Lambda] enantiomer. Both isomers, however, are found to bind equally to Z-DNA. Left-handed helices that are more similar structurally to B-DNA would be predicted to display a stereospecific preference for this [Lambda] isomer.", "pmcid": "PMC345416", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1984-04-01", "series_number": "7", "volume": "81", "issue": "7", "pages": "1961-1965" }, { "id": "authors:6az0d-7vh06", "collection": "authors", "collection_id": "6az0d-7vh06", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120629-111938166", "type": "article", "title": "Application of Chiral Lanthanide-induced Shift Reagents to Optically Active Cations: the Use of Tris[3-(trifluoromethylhydroxymethylene)-( + )-camphorato]europium(III) to Determine the Enantiomeric Purity of Tris(phenanthroline)ruthenium(II) Dichloride", "author": [ { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Nowick", "given_name": "James S.", "clpid": "Nowick-J-S" } ], "abstract": "In non-polar solvents, chiral europium complexes provide attractive n. m. r. shift reagents to resolve spectra of optically active cations, and, in particular, for tris(phenanthroline)ruthenium dichloride,^1H n. m. r. shift differences of up to 0.7 p.p.m. between isomers easily permit the determination of absolute enantiomeric purity.", "doi": "10.1039/C39840001650", "issn": "0022-4936", "publisher": "Royal Society of Chemistry", "publication": "Journal of the Chemical Society. Chemical Communications", "publication_date": "1984", "series_number": "24", "volume": "1984", "issue": "24", "pages": "1650-1652" }, { "id": "authors:rxv7g-whk66", "collection": "authors", "collection_id": "rxv7g-whk66", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160126-115600120", "type": "article", "title": "Tris (phenanthroline) Metal Complexes: Probes for DNA Helicity", "author": [ { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "The intercalative binding of chiral tris(phenanthroline) metal complexes to DNA is stereo-selective. The enantiomeric selectivity is based upon the differential steric interactions between the two non-intercalating phenanthroline ligands of each isomer with the DNA phosphate backbone. Gel electrophoretic assays of helical unwinding, optical enrichment studies by equilibrium dialysis and luminescence titrations with separated enantiomers of (phen)_3Ru^(2+) all indicate that the delta isomer binds preferentially to the right-handed duplex. The chiral discrimination is governed by the DNA helical asymmetry. Complete stereospecifity is seen with isomers of the bulkier RuDIP (tris-4,7-diphenylphenanthrolineruthenium(II)). While both isomers bind to Z-DNA, a poor template for discrimination, binding of \u039b-RuDIP to B-DNA is precluded. These chiral complexes therefore serve as a chemical probe to distinguish left and right-handed DNA helices in solution.", "doi": "10.1080/07391102.1983.10507469", "issn": "0739-1102", "publisher": "Adenine Press", "publication": "Journal of Biomolecular Structure and Dynamics", "publication_date": "1983-12", "series_number": "3", "volume": "1", "issue": "3", "pages": "621-632" }, { "id": "authors:319ez-reg77", "collection": "authors", "collection_id": "319ez-reg77", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:TOMpnas83", "type": "article", "title": "Lack of Z-DNA Conformation in Mitomycin-Modified Polynucleotides Having Inverted Circular Dichroism", "author": [ { "family_name": "Tomasz", "given_name": "Maria", "clpid": "Tomasz-M" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Magliozzo", "given_name": "Catherine C.", "clpid": "Magliozzo-C-C" }, { "family_name": "Tucker", "given_name": "David", "clpid": "Tucker-D" }, { "family_name": "Lafer", "given_name": "Eileen M.", "clpid": "Lafer-E-M" }, { "family_name": "Stollar", "given_name": "B. David", "clpid": "Stollar-B-D" } ], "abstract": "Poly(dG-dC)\u00b7 poly(dG-dC) and Micrococcus lysodeikticus DNA were modified by exposure to reductively activated mitomycin C, an antitumor antibiotic. The resulting covalent drug-polynucleotide complexes displayed varying degrees of CD inversions, which are strikingly similar to the inverted spectrum observed with Z-DNA. The following criteria have been used to establish, however, that the inverted CD pattern seen in mitomycin C-polynucleotide complexes does not reflect a Z-DNA conformation. (i) The ethanol-induced transition of poly(dG-dC)\u00b7 poly(dG-dC) from B to Z conformation is not facilitated but rather is inhibited by mitomycin C modification. This may be due to the presence of crosslinks. (ii) Radioimmunoassay indicated no competition for Z-DNA-specific antibody by any of the mitomycin C-modified polynucleotides. (iii) 31P NMR of the complexes yielded a single relatively narrow resonance, which is inconsistent with the dinucleotide repeat characteristic of Z-DNA. Alternative explanations for the inverted CD pattern include a drug-induced left-handed but non-Z conformational change or the superposition of an induced CD onto the CD of B-DNA due to drug-base electronic interactions. These results illustrate the need for caution in interpreting CD changes alone as an indication of Z-DNA conformation.", "pmcid": "PMC393935", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1983-05-15", "series_number": "10", "volume": "80", "issue": "10", "pages": "2874-2878" }, { "id": "authors:knzv4-d0f97", "collection": "authors", "collection_id": "knzv4-d0f97", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160520-112839737", "type": "article", "title": "The presence of zinc in the restriction enzyme Eco RI", "author": [ { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Basile", "given_name": "Lena A.", "clpid": "Basile-L-A" }, { "family_name": "Paranawithana", "given_name": "Shanthi R.", "clpid": "Paranawithana-S-R" } ], "abstract": "We have determined that the restriction endonuclease Eco RI contains 1.0 \u00b1 0.1 eq of zinc/monomeric enzyme. DNA cleavage by Eco RI is inhibited by ortho-phenanthroline after preincubation of the enzyme with the chelating agent. A similar inhibition by the nonchelating meta-phenanthroline is not seen. The sensitivity of the inhibition by the neutral ligand ortho-phenanthroline to preincubation is consistent with the tightly bound and inaccessible nature of the metal site. Extensive dialysis against the ortho-phenanthroline inhibitor leads to the release of the bound metal with the concomitant loss of enzyme activity. The tightly bound Zn^(2+) cation, then, appears to be necessary for enzyme function. The finding of zinc in Eco RI further illustrates the ubiquity of Zn^(2+) to DNA-protein complexes.", "issn": "0021-9258", "publisher": "American Society for Biochemistry and Molecular Biology", "publication": "Journal of Biological Chemistry", "publication_date": "1982-07-25", "series_number": "14", "volume": "257", "issue": "14", "pages": "7911-7914" }, { "id": "authors:3axz2-fme68", "collection": "authors", "collection_id": "3axz2-fme68", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:BARjbact82", "type": "article", "title": "^(13)C nuclear magnetic resonance study of trehalose mobilization in yeast spores", "author": [ { "family_name": "Barton", "given_name": "J. K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "den Hollander", "given_name": "J. A.", "clpid": "den-Hollander-J-A" }, { "family_name": "Hopfield", "given_name": "J. J.", "clpid": "Hopfield-J-J" }, { "family_name": "Shulman", "given_name": "R. G.", "clpid": "Shulman-R-G" } ], "abstract": "Using high-resolution ^(13)C nuclear magnetic resonance, we examined the mobilization of endogenous trehalose in suspensions of yeast asci. Sporulation of yeast cells in [1-^(13)C]acetate resulted in incorporation of label into the C-3 and C-4 positions of trehalose within the asci. During germination of these asci with [1-^(13)C]glucose, the consumption of both endogenous trehalose and exogenous glucose were followed simultaneously by ^(13)C nuclear magnetic resonance, as was the formation of glycerol and ethanol, their glycolytic and products. Time courses for carbohydrate consumption indicated that trehalose, although it decreased to 25% of its initial value upon germination, was not preferentially catabolized and did not provide the primary energy supply for germination with glucose. The ratio of trehalose to glucose catabolized was 0.09. Exogenous glucose levels appeared to regulate trehalose mobilization since trehalose was only consumed when sufficiently high levels (more than 2 mM) of glucose were present. Upon glucose depletion newly synthesized [1-^(13)C]trehalose was observed. Nuclear magnetic resonance spectra of extracts confirmed the trehalose peak assignments and showed products of [1-^(13)C]glucose catabolism. In addition by quantitating trehalose consumption and 2-deoxyglucose incorporation in dormant yeast asci, we found that 3.8 +/- 0.l4 molecules of 2-deoxyglucose were incorporated for each trehalose molecule consumed. Trehalose can therefore function as a carbohydrate source for ATP formation during dormancy.", "pmcid": "PMC220224", "issn": "0021-9193", "publisher": "American Society for Microbiology", "publication": "Journal of Bacteriology", "publication_date": "1982-07", "series_number": "1", "volume": "151", "issue": "1", "pages": "177-185" }, { "id": "authors:yca0k-3nw49", "collection": "authors", "collection_id": "yca0k-3nw49", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:BARpnas80", "type": "article", "title": "Measurement of the Internal pH of Yeast Spores by 31P Nuclear Magnetic Resonance", "author": [ { "family_name": "Barton", "given_name": "J. K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "den Hollander", "given_name": "J. A.", "clpid": "den-Hollander-J-A" }, { "family_name": "Lee", "given_name": "T. M.", "clpid": "Lee-T-M" }, { "family_name": "MacLaughlin", "given_name": "A.", "clpid": "MacLaughlin-A" }, { "family_name": "Shulman", "given_name": "R. G.", "clpid": "Shulman-R-G" } ], "abstract": "The asci and single spores of the yeast Pichia pastoris were examined by using 31P NMR. The pH within the spores was determined from the pH-dependent chemical shifts of the internal orthophosphate (Pi) peaks. In spectra of asci, two internal Pi peaks corresponding to two compartments were observed. Only small variations in the internal pH values were found upon incubation of the asci in buffers ranging in pH from 3 to 10. For this range in external pH, the internal pH values calculated from the Pi chemical shifts were 5.5-6.3 and 5.1-5.9. The two internal Pi peaks, which have line widths of approx 60 Hz, have been assigned to spore and epiplasmic compartments, respectively. Spectra of single spores revealed only one Pi peak, and, upon germination of either the single spores or asci, only this Pi peak disappeared. Peaks corresponding to ATP were not found in the dormant spores and asci but did appear upon germination. These NMR studies show the yeast spore to have a mobile and relatively acidic interior.", "pmcid": "PMC349421", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1980-05", "series_number": "5", "volume": "77", "issue": "5", "pages": "2470-2473" }, { "id": "authors:ky19g-fd411", "collection": "authors", "collection_id": "ky19g-fd411", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171103-154149592", "type": "article", "title": "Chemical and spectroscopic characterization of cis-diammineplatinum \u03b1-pyridone blue in aqueous solution. Comparison with other platinum blues", "author": [ { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Caravana", "given_name": "Carl", "clpid": "Caravana-C" }, { "family_name": "Lippard", "given_name": "Stephen J.", "clpid": "Lippard-S-J" } ], "abstract": "The spectral, redox, and chemical properties of cis-diammineplatinum a-pyridone blue (PPB),\n[Pt2(NH3)4(CsH40N)2]2(N03)5-H20, in aqueous solution have been studied and compared with those of other blue platinum\ncomplexes. The extinction coefficient of the blue chromophore is a sensitive function of the anions present and of the temperature.\nThe approximately axial electron spin resonance spectrum is characterized by g values of 2.38 and 1.976, very similar to\nthose reported from single-crystal ESR studies. Extensive '95Pt hyperfine interactions indicate that PPB maintains its oligomeric\nstructure upon initial dissolution in water. The decomposition of PPB in solution has been monitored by intensity losses\nwith time in both the blue absorption band and the ESR signal. The concomitant decrease observed indicates the correspondence\nof the blue chromophore with the unpaired spin. Oxidative titrations of PPB show a linear decrease in ,4680 and ESR signal\nintensity with the addition of 3 equiv of ceric ion per tetramer. The chemical characteristics of PPB in solution are compared\nto those of platinum acetamide blue (PAB), cis-diammineplatinum uracil blue (PUB), and the newly characterized cisdiammineplatinum\nhypoxanthine green (PHG), the first reported platinum purine \"blue\". The results establish the similarity\nin their chemical composition and electronic structure. The electronic spectra exhibit broad absorption bands in the region\n590-720 nm. These blue chromophores also depend upon the anions present. The ESR spectrum of PUB is strikingly similar\nto that of PPB, although of lower absolute signal intensity. This result may be due to spin-spin coupling since PUB is shown\nto be a longer chain oligomer. Both PHG and PAB exhibit a weak ESR transition. Oxidative titrations using ceric ion of PAB\nand PHG monitored spectrophotometrically show that 1.75 e-/Pt is required for the complete loss of blue color; this result is\nconsistent with oxidation to platinum(lV) from the initial platinum formal oxidation state of 2.25. Classical reductive titrations\nof the cis-diammineplatinum blues to platinum mttal further support the oxidation-state assignment of 2.25. Gel electrophoresis\nof the cis-diammineplatinum blues, assuming the identical charge per monomeric unit, indicates the length of the oligomers\nto increase in the series PPB < PHG < PUB. These studies demonstrate that blue platinum complexes share the properties\nof mixed valency and oligomeric structure.", "doi": "10.1021/ja00518a023", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "1979-11-21", "series_number": "24", "volume": "101", "issue": "24", "pages": "7269-7277" }, { "id": "authors:n9ans-k8n30", "collection": "authors", "collection_id": "n9ans-k8n30", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160126-164902771", "type": "article", "title": "Cooperative binding of a platinum metallointercalation reagent to poly(A)\u2022poly(U)", "author": [ { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Lippard", "given_name": "Stephen J.", "clpid": "Lippard-S-J" } ], "abstract": "The cationic complex (2-hydroxyethanethiolato)(2,2',2\"-terpyridine) platinum(II), [(terpy)Pt( HET)]^+, binds cooperatively to poly(A)\u2022poly(U) by intercalation. The melting temperature of poly(A)\u2022poly(U) in low-salt buffer is increased by 6 \u00b0C in the presence of [(terpy)Pt(HET)]^+, indicating stabilization of the duplex structure by the bound platinum reagent. Viscosity measurements provide evidence for comparable lengthening of the polynucleotide in the presence of [(terpy)Pt(HET)]^+ and the intercalating dye, ethidium bromide. Scatchard plots of the binding of [(terpy)Pt(HET)]^+ to poly(A)\u2022poly(U) and poly(I)\u2022poly(C), determined through ultracentrifugation pelleting methods, show large positive curvature, reflecting the strong cooperativity associated with the platinum complex-RNA interaction. The characteristics of the binding isotherms are interpreted in terms of a model where cooperative pair units of [(terpy)Pt(HET)]^+ intercalate\ninto the double-stranded polymer. At saturation, two platinum molecules are bound for every three base pairs. This stoichiometry may be compared with the nearest-neighbor-exclusion binding observed previously in the interaction of [(terpy)Pt(HET)]^+ and the ethidium cation with DNA, in which one intercalator occupies every other interbase-pair site at saturation. The striking differences observed in the interaction of [(terpy)Pt(HET)]^+ with DNA and RNA suggest that drug recognition is sensitive to the constraints imposed by nucleic acid secondary structure.", "doi": "10.1021/bi00579a036", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "1979-06-12", "series_number": "12", "volume": "18", "issue": "12", "pages": "2661-2668" }, { "id": "authors:retyx-qph35", "collection": "authors", "collection_id": "retyx-qph35", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160126-165802210", "type": "article", "title": "Binding of cis- and trans-dichlorodiammineplatinum(II) to DNA: evidence for unwinding and shortening of the double helix", "author": [ { "family_name": "Cohen", "given_name": "Gary L.", "clpid": "Cohen-G-L" }, { "family_name": "Bauer", "given_name": "William R.", "clpid": "Bauer-W-R" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Lippard", "given_name": "Stephen J.", "clpid": "Lippard-S-J" } ], "abstract": "The antitumor drug cis-dichlorodiammineplatinum(II) (cis-DDP) and the inactive trans isomer bind and produce cooperative changes in closed and nicked circular duplex DNA's. Covalent binding of both platinum complexes to the closed circular DNA alters the degree of supercoiling, presumably by disrupting and unwinding the double helix. Electron micrographs show the platinated DNA's to be shortened by up to 50 percent of their original length. At similar ratios of bound platinum per nucleotide, the electrophoretic mobilities of the DNA's in gels containing the dye ethidium bromide are the same for both isomers. The only detectable difference in the binding of the two platinum isomers is an increase in the electrophoretic mobility in nondye gels of closed circular DNA having small amounts of bound cis-DDP that is not apparent for the trans complex.", "doi": "10.1126/science.370979", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "1979-03-09", "series_number": "4384", "volume": "203", "issue": "4384", "pages": "1014-1016" }, { "id": "authors:h4ktx-zde13", "collection": "authors", "collection_id": "h4ktx-zde13", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160126-164221837", "type": "article", "title": "A crystalline platinum blue: its molecular structure, chemical reactivity, and possible relevance to the mode of action of antitumor platinum drugs", "author": [ { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Lippard", "given_name": "Stephen J.", "clpid": "Lippard-S-J" } ], "abstract": "The simple inorganic complex cis-dichlorodiammineplatinum (II) (DDP) inhibits the division of bacterial cells with little effect on their growth. It was subsequently shown that DDP has substantial antitumor activity on a wide variety of animal malignancies. These findings stimulated numerous investigations of diammineplatinum (II) complexes both to establish their mode of action and to design more effective antitumor platinum drugs.", "doi": "10.1111/j.1749-6632.1978.tb39455.x", "issn": "0077-8923", "publisher": "New York Academy of Sciences", "publication": "Annals of the New York Academy of Sciences", "publication_date": "1978-09", "volume": "313", "pages": "686-700" }, { "id": "authors:mgtz3-aqv69", "collection": "authors", "collection_id": "mgtz3-aqv69", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170707-180501544", "type": "article", "title": "Relationship of cis-diammineplatinum \u03b1-pyridone blue to other platinum blues. An x-ray photoelectron study", "author": [ { "family_name": "Barton", "given_name": "J. K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Best", "given_name": "S. A.", "clpid": "Best-S-A" }, { "family_name": "Lippard", "given_name": "S. J.", "clpid": "Lippard-S-J" }, { "family_name": "Walton", "given_name": "R. A.", "clpid": "Walton-R-A" } ], "abstract": "The x-ray photoelectron spectrum (XPS) of crystalline cis-diammineplatinum a-pyridone blue, [Pt_2(NH_3)_4(C_5H_4ON)_2]_2(NO_3)_5, has been investigated and the Pt 4f binding energies of this complex found to be similar to those exhibited by Pt(II) complexes such as cis-(H_3N)_2PtCl_2. This result is in accord with the previous assignment of a formal platinum oxidation state of 2.25 in the blue a-pyridone complex. The widths of the Pt 4f peaks (fwhm ~ 1.3) indicate that the binding energies associated with the two geometrically different types of Pt environments in the \u03b1-pyridone oligomer are very similar, the implication being that within the Pt4 unit there must be a considerable delocalization of charge. A comparison of the XPS data for the \u03b1-pyridone blue with that found for the platinum uracil and acetamide blues shows that these species have similar electronic structures, there being no evidence that they are pure derivatives of Pt(IV). The XPS of some samples of the acetamide blue (\"Platinblau\") show the presence of small amounts of higher oxidation state contaminants, consistent with the difficulty in preparing this species in a reproducibly pure form. The Pt(III) dimer K_2Pt_2(SO_4)_4\u00b73H_2O possesses Pt 4f binding energies which are much closer to those of coordination complexes of Pt(IV) than Pt(II).", "doi": "10.1021/ja00480a022", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "1978-06-07", "series_number": "12", "volume": "100", "issue": "12", "pages": "3785-3788" }, { "id": "authors:g1j9b-hbf25", "collection": "authors", "collection_id": "g1j9b-hbf25", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170707-172652698", "type": "article", "title": "Study of the binding of cis- and trans-dichlorodiammineplatinum(II) to calf thymus DNA by extended x-ray absorption fine structure spectroscopy", "author": [ { "family_name": "Teo", "given_name": "Boon-Keng", "clpid": "Teo-Boon-Keng" }, { "family_name": "Eisenberger", "given_name": "P.", "clpid": "Eisenberger-P" }, { "family_name": "Reed", "given_name": "J.", "clpid": "Reed-J" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Lippard", "given_name": "Stephen J.", "clpid": "Lippard-S-J" } ], "abstract": "The complex cis-dichlorodiammineplatinum(II) (DDP) is an active antitumor drug while the trans-DDP isomer is ineffective, a result that may reflect differences in their ability to bind DNA.[1-5] While various chemical and physical techniques have been used to explore the interactions of these platinum compounds with DNA, there appears to be no direct structural information about the resulting platinum-DNA complex. Recent crystallographic study[5c] of the blue compound formed between cis-diammineplatinum and a-pyridone (1) suggested[5b] that thymine (2, R = CH3) and guanine (3) bases in DNA might bridge two cis-diammineplatinum units using the deprotonated amide nitrogen and the exocyclic oxygen as donor atoms. The resulting complex would have a short Pt-Pt distance, 2.5-3.2 A, depending upon the platinum oxidation state. To test this possibility and to provide information about the binding sites ofDDP, samples of cis- and trans-[Pt(NH3)iC!i] bound to calf thymus DNA, 4 and 5, respectively, were prepared and studied by extended x-ray absorption fine structure (EXAFS) spectroscopy.", "doi": "10.1021/ja00478a051", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "1978-05-10", "series_number": "10", "volume": "100", "issue": "10", "pages": "3225-3227" }, { "id": "authors:5pqf2-mxj34", "collection": "authors", "collection_id": "5pqf2-mxj34", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170707-154241416", "type": "article", "title": "Synthesis and crystal structure of cis-diammineplatinum \u03b1-pyridone blue", "author": [ { "family_name": "Barton", "given_name": "J. K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Rabinowitz", "given_name": "H. N.", "clpid": "Rabinowitz-H-N" }, { "family_name": "Szalda", "given_name": "D. J.", "clpid": "Szalda-D-J" }, { "family_name": "Lippard", "given_name": "S. J.", "clpid": "Lippard-S-J" } ], "abstract": "The blue compounds formed from aqueous solutions of platinum(II) in the presence of amides have been a subject of study since the original report of \"Platinblau\" in 1908.[1-3] Recent interest in these complexes was sparked by the discovery that aquated products of the antitumor drug cis-dichlorodiammineplatinum(II) undergo a slow reaction with polyuracil, uracil, thymine, and related pyrimidines (1) to form blue complexes. [4] The platinum pyrimidine blues have antitumor activity of their own [4,5] and are useful electron microscopic stains for DNA.[6] Attempts to crystallize these blue complexes have been largely unsuccessful because they are oligomeric mixtures of varying degrees of hydrolytic instability.[7] With synthetic insights provided by the detailed studies of Lerner [7] and the choice of \u03b1-pyridone (2) as the amide ligand [8], we have obtained a crystalline platinum blue and determined its structure by x-ray crystallography.", "doi": "10.1021/ja00450a085", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "1977-04-13", "series_number": "8", "volume": "99", "issue": "8", "pages": "2827-2829" } ]