[ { "id": "https://authors.library.caltech.edu/records/xjq9y-zn524", "eprint_id": 85215, "eprint_status": "archive", "datestamp": "2023-08-19 08:19:04", "lastmod": "2024-01-14 19:31:32", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Barton-J-K", "name": { "family": "Barton", "given": "Jacqueline K." }, "orcid": "0000-0001-9883-1600" }, { "id": "Boynton-Adam-Nathaniel", "name": { "family": "Boynton", "given": "Adam N." }, "orcid": "0000-0003-4427-513X" }, { "id": "Boyle-Kelsey-M", "name": { "family": "Boyle", "given": "Kelsey M." }, "orcid": "0000-0002-6728-8403" } ] }, "title": "Targeting DNA Mismatches with Coordination Complexes", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 2018 The Royal Society of Chemistry. \n\nPrint publication date: 12 Mar 2018. \n\nWe are grateful to our many coworkers and collaborators for their efforts in carrying out the research described. We thank also the NIH, Moore Foundation, and Amgen for their financial support of this research.", "abstract": "DNA base pair mismatches occur naturally in cells as a result of incorporation errors and damage. Most cells are able to identify and correct these mistakes before replication, allowing for high genome fidelity between cellular generations. In some forms of cancer, however, proteins involved in the machinery of mismatch repair (MMR) undergo mutation, making those cells unable to correct mismatches and leading to an increase in mutations. Since higher mismatch frequency serves as an early indicator of cancer progression, for many researchers mismatches have provided a novel target for the design of organic and inorganic small-molecule therapeutics. In particular, transition metal complexes have shown great promise in this context owing to their valuable spectroscopic and photophysical properties and flexibility with respect to modification of their coordination spheres. Thus far, experimental designs have ranged from targeting the thermodynamic destabilization of mismatched sites to the hydrogen-bonding pattern of specific mismatched base pairs. Here, we review the diversity, practical application, and evolution of mismatch-targeting small molecules, with an emphasis on rhodium metalloinsertors and luminescent ruthenium compounds. Importantly, we highlight the discovery of metalloinsertion, a noncovalent DNA binding mode that is specific towards destabilized sites, such as mismatches, within the DNA duplex.", "date": "2018-03-12", "date_type": "published", "publisher": "Royal Society of Chemistry", "place_of_pub": "Cambridge", "pagerange": "367-390", "id_number": "CaltechAUTHORS:20180309-071202119", "isbn": "978-1-78262-992-4", "book_title": "DNA-targeting Molecules as Therapeutic Agents", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180309-071202119", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Amgen" } ] }, "contributors": { "items": [ { "id": "Waring-M-J", "name": { "family": "Waring", "given": "Michael J." } } ] }, "doi": "10.1039/9781788012928-00367", "resource_type": "book_section", "pub_year": "2018", "author_list": "Barton, Jacqueline K.; Boynton, Adam N.; et el." }, { "id": "https://authors.library.caltech.edu/records/9adpm-m2130", "eprint_id": 78756, "eprint_status": "archive", "datestamp": "2023-08-21 21:02:34", "lastmod": "2024-01-13 20:29:28", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Barton-J-K", "name": { "family": "Barton", "given": "Jacqueline K." }, "orcid": "0000-0001-9883-1600" }, { "id": "Bartels-P-L", "name": { "family": "Bartels", "given": "Phillip L." } }, { "id": "Deng-Yingxin", "name": { "family": "Deng", "given": "Yingxin" } }, { "id": "O'Brien-Elizabeth", "name": { "family": "O'Brien", "given": "Elizabeth" } } ] }, "title": "Electrical Probes of DNA-Binding Proteins", "ispublished": "unpub", "full_text_status": "public", "keywords": "DNA glycosylase; Nucleotide flipping; Base flipping; Transient kinetics; DNA binding; DNA modification; Kinetic simulation; Stopped flow; DNA alkylation repair; Base excision repair", "note": "\u00a9 Academic Press 2017. \n\nAvailable online 10 May 2017. Published: 20th June 2017. \n\nWe are grateful to the NIH for their support of this research and to our coworkers and collaborators for their insights, efforts, and hard work.\n\n
Accepted Version - nihms-999521.pdf
", "abstract": "A DNA electrochemistry platform has been developed to probe proteins bound to DNA electrically. Here gold electrodes are modified with thiol-modified DNA, and DNA charge transport chemistry is used to probe DNA binding and enzymatic reaction both with redox-silent and redox-active proteins. For redox-active proteins, the electrochemistry permits the determination of redox potentials in the DNA-bound form, where comparisons to DNA-free potentials can be made using graphite electrodes without DNA modification. Importantly, electrochemistry on the DNA-modified electrodes facilitates reaction under aqueous, physiological conditions with a sensitive electrical measurement of binding and activity.", "date": "2017-05-10", "date_type": "published", "publisher": "Academic Press", "place_of_pub": "San Diego, CA", "pagerange": "355-414", "id_number": "CaltechAUTHORS:20170705-093949953", "isbn": "9780128118467", "book_title": "DNA Repair Enzymes: Cell, Molecular, and Chemical Biology", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170705-093949953", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" } ] }, "contributors": { "items": [ { "id": "Eichman-B-F", "name": { "family": "Eichman", "given": "Brandt F." } } ] }, "doi": "10.1016/bs.mie.2017.03.024", "pmcid": "PMC6314295", "primary_object": { "basename": "nihms-999521.pdf", "url": "https://authors.library.caltech.edu/records/9adpm-m2130/files/nihms-999521.pdf" }, "resource_type": "book_section", "pub_year": "2017", "author_list": "Barton, Jacqueline K.; Bartels, Phillip L.; et el." }, { "id": "https://authors.library.caltech.edu/records/xjd2g-d8v37", "eprint_id": 107878, "eprint_status": "archive", "datestamp": "2023-08-22 14:32:37", "lastmod": "2023-10-23 16:18:23", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Barton-J-K", "name": { "family": "Barton", "given": "Jacqueline K." }, "orcid": "0000-0001-9883-1600" }, { "id": "Furst-Ariel-L", "name": { "family": "Furst", "given": "Ariel L." } }, { "id": "Grodick-Michael-A", "name": { "family": "Grodick", "given": "Michael A." }, "orcid": "0000-0001-6618-6731" } ] }, "title": "DNA Sensors Using DNA Charge Transport Chemistry", "ispublished": "unpub", "full_text_status": "public", "keywords": "biochemical applications; DNA charge transport chemistry; DNA sensors; DNA\u2010binding proteins; DNA\u2010functionalized electrochemical sensors", "note": "\u00a9 2015 John Wiley & Sons, Ltd. \n\nPublished Online: 21 June 2017; Published Print: 23 December 2014.", "abstract": "This chapter describes applications of DNA charge transport (DNA CT) in sensing, illustrating how this chemistry is used for the construction of sensitive devices for biochemical applications. It talks about the models for how this sensing technology might also be applied within the cell, how Nature may take advantage of DNA CT chemistry. Electrochemical devices utilizing DNA CT have evolved over time. The first DNA CT\u2010based detection platforms contained only a single electrode. DNA CT platforms are advantageous for the detection of proteins that interact with DNA. The chapter focuses on a variety of proteins that bind to DNA in different ways but which can all be detected sensitively using DNA electrochemistry. DNA CT can occur over long molecular distances, is sensitive to and can be modulated by DNA\u2010binding proteins, and reports electrically on the integrity of DNA. This chemistry can therefore be powerfully applied in sensing.", "date": "2014-12-23", "date_type": "published", "publisher": "Wiley", "place_of_pub": "Chichester", "pagerange": "105-120", "id_number": "CaltechAUTHORS:20210202-134852557", "isbn": "9781118696880", "book_title": "DNA in Supramolecular Chemistry and Nanotechnology", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210202-134852557", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "Stulz-Eugen", "name": { "family": "Stulz", "given": "Eugen" } }, { "id": "Clever-Guido-H", "name": { "family": "Clever", "given": "Guido H." } } ] }, "doi": "10.1002/9781118696880.ch2.3", "resource_type": "book_section", "pub_year": "2014", "author_list": "Barton, Jacqueline K.; Furst, Ariel L.; et el." }, { "id": "https://authors.library.caltech.edu/records/ph5p2-nms82", "eprint_id": 64350, "eprint_status": "archive", "datestamp": "2023-08-19 07:42:29", "lastmod": "2023-10-17 20:52:11", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Jackson-B-A", "name": { "family": "Jackson", "given": "Brian A." } }, { "id": "Barton-J-K", "name": { "family": "Barton", "given": "Jacqueline K." }, "orcid": "0000-0001-9883-1600" } ] }, "title": "Probing Nucleic Acid Structure with Shape-Selective Rhodium and Ruthenium Complexes", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 2003 by John Wiley and Sons. \n\nThe work described here was supported by the NIH (GM33309) and performed by many able graduate students who are referenced as indicated. B.A.J. would also like to acknowledge the NSF for a predoctoral fellowship.", "abstract": "In this unit, transition metal complexes are used as photochemical probes for the structure of RNA and DNA. The transition metal ion provides a rigid substitutionally inert framework and an octahedral geometry for ligand coordination. The complexes can be constructed to define shapes, symmetries, and functionalities that complement those of the nucleic acid target. Complex formation is easily detected by light-induced nucleic acid cleavage. The modular construction of the complexes makes it possible to generate probes to examine a wide variety of structural characteristics of nucleic acids.", "date": "2001-05-01", "date_type": "published", "id_number": "CaltechAUTHORS:20160209-153402366", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160209-153402366", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM33309" }, { "agency": "NSF Predoctoral Fellowship" } ] }, "doi": "10.1002/0471142700.nc0602s00", "resource_type": "book_section", "pub_year": "2001", "author_list": "Jackson, Brian A. and Barton, Jacqueline K." }, { "id": "https://authors.library.caltech.edu/records/jcm4d-ct567", "eprint_id": 63955, "eprint_status": "archive", "datestamp": "2023-08-19 04:08:32", "lastmod": "2024-01-13 16:32:15", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kelley-S-O", "name": { "family": "Kelley", "given": "Shana O." }, "orcid": "0000-0003-3360-5359" }, { "id": "Barton-J-K", "name": { "family": "Barton", "given": "Jacqueline K." }, "orcid": "0000-0001-9883-1600" } ] }, "title": "Radical migration through the DNA helix: chemistry at a distance", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 1999 Marcel Dekker. \n\nWe are grateful to the National Institutes of Health and the National Foundation for Cancer Research for their financial support of this work. In addition, we thank our colleagues and collaborators, as referenced throughout the chapter, for their efforts and their ideas.", "abstract": "The reaction of the DNA bases with radical species generated by radiation, carcinogens, or oxidative stress can lead to mutagenic damage [1]. The efficiency and dynamics of radical transport through the DNA helix therefore hold profound biological implications. Intriguing questions concerning charge migration through DNA arise that can now begin to be addressed through well-defined chemical experiments. Does radical migration through DNA occur over long molecular distances? How is it modulated by DNA sequence and the structural variations in DNA? Is it physiologically important? How general is this phenomenon? These are issues that need to be addressed in the context of delineating mechanisms of DNA damage and repair.", "date": "1999-03-10", "date_type": "published", "publisher": "Marcel Dekker", "place_of_pub": "New York, NY", "pagerange": "211-249", "id_number": "CaltechAUTHORS:20160125-201652834", "isbn": "9780824719562", "book_title": "Interrelations Between Free Radicals and Metal Ions in Life Processes", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160125-201652834", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" }, { "agency": "National Foundation for Cancer Research" } ] }, "contributors": { "items": [ { "id": "Sigel-A", "name": { "family": "Sigel", "given": "Astrid" } }, { "id": "Sigel-H", "name": { "family": "Sigel", "given": "Helmut" } } ] }, "resource_type": "book_section", "pub_year": "1999", "author_list": "Kelley, Shana O. and Barton, Jacqueline K." }, { "id": "https://authors.library.caltech.edu/records/qf7yk-rzg69", "eprint_id": 85674, "eprint_status": "archive", "datestamp": "2023-08-20 07:35:38", "lastmod": "2024-01-14 19:35:35", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Arkin-M-R", "name": { "family": "Arkin", "given": "Michelle R." } }, { "id": "Jenkins-Y", "name": { "family": "Jenkins", "given": "Yonchu" } }, { "id": "Murphy-C-J", "name": { "family": "Murphy", "given": "Catherine J." } }, { "id": "Turro-N-J", "name": { "family": "Turro", "given": "Nicholas J." } }, { "id": "Barton-J-K", "name": { "family": "Barton", "given": "Jacqueline K." }, "orcid": "0000-0001-9883-1600" } ] }, "title": "Metallointercalators as Probes of the DNA \u03c0-way", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 1995 American Chemical Society. \n\nReceived for review August 23, 1993. Accepted revised manuscript December 21, 1993. Published in print 5 May 1996. \n\nWe are grateful to the efforts of our collaborators and co-workers, as noted in the individual references. We acknowledge in particular the contributions of C. V. Kumar, who first discovered the remarkable efficiency of DNA in promoting reactions between transition metal complexes. We thank also Jay Winkler, who has provided expert technical assistance in the Beckman Institute laser laboratory. In addition we thank the National Institutes of Health, the National Science Foundation, the Air Force Office of Scientific Research, the Ralph M. Parsons Foundation, and the National Foundation for Cancer Research for financial support.", "abstract": "This chapter describes efforts in our laboratory to characterize the role of double helical DNA in catalyzing electron-transfer reactions. Using intercalating metal complexes as donor and acceptor, we have shown that the luminescence of [Ru(phen)_2(dppz)]^(2+*) is efficiently quenched by [Rh(phi)_2(phen)]^(3+) in the presence of B-form DNA. Covalent attachment of these metal complexes to either ends of a short duplex leads to complete quenching of luminescence over a separation distance between intercalated donor and acceptor of >40\u00c5. These results with metallointercalators point to the \u03c0-stacked array of heterocyclic DNA base pairs as an effective intervening medium for long-range electron transfer and provides a new approach in applying the DNA helical polymer as a \"molecular wire.\"", "date": "1996-05-05", "date_type": "published", "publisher": "American Chemical Society", "place_of_pub": "Washington, DC", "pagerange": "449-469", "id_number": "CaltechAUTHORS:20180406-080327207", "isbn": "9780841230620", "book_title": "Mechanistic Bioinorganic Chemistry", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180406-080327207", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" }, { "agency": "NSF" }, { "agency": "Air Force Office of Scientific Research (AFOSR)" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "National Foundation for Cancer Research" } ] }, "doi": "10.1021/ba-1995-0246.ch017", "resource_type": "book_section", "pub_year": "1996", "author_list": "Arkin, Michelle R.; Jenkins, Yonchu; et el." }, { "id": "https://authors.library.caltech.edu/records/ps8q0-3hg85", "eprint_id": 106765, "eprint_status": "archive", "datestamp": "2023-08-20 07:03:08", "lastmod": "2024-01-15 18:15:07", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "H\u00f6rmann-A", "name": { "family": "H\u00f6rmann", "given": "A." } }, { "id": "Olson-E-J-C", "name": { "family": "Olson", "given": "E. J. C." } }, { "id": "Barbara-P-F", "name": { "family": "Barbara", "given": "P. F." } }, { "id": "Arkin-M-R", "name": { "family": "Arkin", "given": "M. R." } }, { "id": "Stemp-E-D-A", "name": { "family": "Stemp", "given": "E. D. A." }, "orcid": "0000-0003-2098-4214" }, { "id": "Holmlin-R-E", "name": { "family": "Holmlin", "given": "R. E." } }, { "id": "Barton-J-K", "name": { "family": "Barton", "given": "J. K." }, "orcid": "0000-0001-9883-1600" } ] }, "title": "Time resolved electron transfer studies between metallointercalators in DNA", "ispublished": "unpub", "full_text_status": "restricted", "keywords": "Electron Transfer, Kinetic Reverse, Electron Transfer, Back Electron, Transfer Solvent, Isotope Effect, Ultrafast Phenomenon", "note": "\u00a9 Springer-Verlag Berlin Heidelberg 1996. \n\nThis work supported by the NSF and the NIH.", "abstract": "Ultrafast studies on the rates of DNA-mediated forward and reverse electron transfer between photoexcited [Ru(phen)\u2082dppz]\u00b2\u207a and various acceptors are reported. We also present the first results that resolve the ultrafast emission decay of the so-called \"light-switch\" molecule [Ru(phen)\u2082dppz]\u00b2\u207a in aqueous solution, distinguishing the diverse photophysical mechanisms of [Ru(phen)\u2082dppz]\u00b2\u207a.", "date": "1996", "date_type": "published", "publisher": "Springer Berlin Heidelberg", "place_of_pub": "Berlin, Heidelberg", "pagerange": "359-360", "id_number": "CaltechAUTHORS:20201120-120817888", "isbn": "9783642803161", "book_title": "Ultrafast Phenomena X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201120-120817888", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF" }, { "agency": "NIH" } ] }, "contributors": { "items": [ { "id": "Barbara-P-F", "name": { "family": "Barbara", "given": "Paul F." } }, { "id": "Fujimoto-James-G", "name": { "family": "Fujimoto", "given": "James G." } }, { "id": "Knox-W-H", "name": { "family": "Knox", "given": "Wayne H." } }, { "id": "Zinth-W", "name": { "family": "Zinth", "given": "Wolfgang" } } ] }, "doi": "10.1007/978-3-642-80314-7_157", "resource_type": "book_section", "pub_year": "1996", "author_list": "H\u00f6rmann, A.; Olson, E. J. C.; et el." }, { "id": "https://authors.library.caltech.edu/records/v4dfz-x9q33", "eprint_id": 63973, "eprint_status": "archive", "datestamp": "2023-08-20 03:36:49", "lastmod": "2024-01-13 16:32:19", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Klakamp-S-L", "name": { "family": "Klakamp", "given": "Scott L." } }, { "id": "Barton-J-K", "name": { "family": "Barton", "given": "Jacqueline K." }, "orcid": "0000-0001-9883-1600" } ] }, "title": "DNA photofootprinting with Rh(phi)_2bpy^(3+)", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 1994 Humana Press. \n\nWe are grateful to the National Institutes of Health (GM33309 to J. K. Barton; NRSA CA08891 to S. L. Klakamp) for their financial support of this research.", "abstract": "This chapter describes one method for high resolution photofootprinting of proteins or small drugs bound to DNA (1). DNA footprinting is an electrophoretic method that permits the visualization (footprint) of the binding site of a molecule site-specifically bound to DNA. The method entails the nonspecific cleavage of a radioactively end-labeled DNA containing the site-specifically bound molecule. Protection from this sequence neutral cleavage at the binding site reveals the footprint. Photofootprinting differs from other conventional footprinting techniques in that DNA cleavage occurs directly on irradiation of a photocleaving reagent, which binds to the target DNA sequence. Alternative photofootprinting methods produce DNA cleavage indirectly by creating photo-damaged DNA adducts that are labile to base treatment after irradiation of the DNA (2,3). Traditional footprinting procedures utilize either a protein like DNase I for cleavage or small molecule reagents that cleave DNA under specific chemical conditions (4\u20138).", "date": "1994", "date_type": "published", "publisher": "Humana Press", "place_of_pub": "Totowa, NJ", "pagerange": "331-338", "id_number": "CaltechAUTHORS:20160126-112520082", "isbn": "978-0-89603-258-3", "book_title": "Protocols for Gene Analysis", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160126-112520082", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM33309" }, { "agency": "NIH", "grant_number": "CA08891" } ] }, "contributors": { "items": [ { "id": "Harwood-A-J", "name": { "family": "Harwood", "given": "A. J." } } ] }, "doi": "10.1385/0-89603-258-2:331", "resource_type": "book_section", "pub_year": "1994", "author_list": "Klakamp, Scott L. and Barton, Jacqueline K." }, { "id": "https://authors.library.caltech.edu/records/zhqr2-7n273", "eprint_id": 71232, "eprint_status": "archive", "datestamp": "2023-08-20 02:44:15", "lastmod": "2024-01-13 16:54:43", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Jenkins-Y", "name": { "family": "Jenkins", "given": "Yonchu" } }, { "id": "Barton-J-K", "name": { "family": "Barton", "given": "Jacqueline" }, "orcid": "0000-0001-9883-1600" } ] }, "title": "How to make a molecular light switch sequence-specific: tethering of an oligonucleotide to a dipyridophenazine complex of ruthenium (II)", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 1993 SPIE. \n\nWe are grateful to the NIH (GM33309 and an NRSA for Y.J.) and the Ralph M. Parsons Foundation for their financial support.\n\nPublished - 129_1.pdf
", "abstract": "Considerable attention has been given recently to the design and development of nonradiative methods of recognizing DNA in a sequence-specific manner. Earlier, we reported that Ru(bpy)_2dppz^(2+)(bpy equals 2,2'-bipyridine, dppz equals dipyrido[3,2:a-2',3':c]phenazine) shows no luminescence in aqueous solution, but upon intercalation into double-helical DNA, bright photoluminescence is observed (A. E. Friedman, et al., J. Am. Chem. Soc., 1990, 112, 4960). Based upon this observation, a sequence-specific molecular light switch has been designed in which a dppz complex of ruthenium(II) is tethered onto an oligonucleotide. An oligonucleotide modified at its 5 foot end has been constructed by coupling the sequence 5'-H_2N(CH_2)_6AGTGCCAAGCTTGCA-3' to Ru(phen')_2dppz^(2+) (phen' equals 5-amido-glutaric acid-1,10-phenanthroline). Like the parent complex Ru(bpy)_2dppz^(2+), the single-stranded metal-oligonucleotide conjugate shows little detectable luminescence in aqueous solution. Addition of the complementary strand results in intense photoluminescence; time-resolved studies show that the emission is biphasic with excited state lifetimes of 500 (60%) and 110 (40%) ns. As expected, addition of a non- complementary strand produces no luminescence enhancement over that of the single-stranded metal-oligonucleotide. These results demonstrate that this oligonucleotide derivatized metal complex can be used to recognize and target specific sequences on DNA, a valuable feature which may lead to interesting and novel applications in hybridization technology.", "date": "1993-05-18", "date_type": "published", "publisher": "Society of Photo-Optical Instrumentation Engineers", "place_of_pub": "Bellingham, WA", "pagerange": "129-137", "id_number": "CaltechAUTHORS:20161018-141749842", "isbn": "9780819411129", "book_title": "Advances in Fluorescence Sensing Technology", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161018-141749842", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM33309" }, { "agency": "NIH Predoctoral Fellowship" }, { "agency": "Ralph M. Parsons Foundation" } ] }, "contributors": { "items": [ { "id": "Lakowicz-J-R", "name": { "family": "Lakowicz", "given": "Joseph R." } }, { "id": "Thompson-R-B", "name": { "family": "Thompson", "given": "Richard B." } } ] }, "doi": "10.1117/12.144704", "primary_object": { "basename": "129_1.pdf", "url": "https://authors.library.caltech.edu/records/zhqr2-7n273/files/129_1.pdf" }, "resource_type": "book_section", "pub_year": "1993", "author_list": "Jenkins, Yonchu and Barton, Jacqueline" }, { "id": "https://authors.library.caltech.edu/records/kc34b-fx877", "eprint_id": 65185, "eprint_status": "archive", "datestamp": "2023-08-20 02:09:46", "lastmod": "2024-01-13 16:43:28", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Murphy-C-J", "name": { "family": "Murphy", "given": "Catherine J." } }, { "id": "Barton-J-K", "name": { "family": "Barton", "given": "Jacqueline K." }, "orcid": "0000-0001-9883-1600" } ] }, "title": "Ruthenium complexes as luminescent reporters of DNA", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 1993 Academic Press, Inc. \n\nWe are grateful to the National Institute of General Medical Science (GM33309) and to the National Science Foundation (postdoctoral fellowship to C.J.M.) for financial support. We are also grateful to our co-workers and collaborators, as described in the individual references, for scientific contributions in developing the methodology described here. Essential to the development of this research has also been the insights of our long-time collaborator, Nicholas J. Turro.", "abstract": "Coordination chemistry provides a wealth of characteristics that may be exploited in probing nucleic acids. Structurally and stereochemically well-defined transition metal complexes have been designed to probe nucleic acid structure and the recognition process. Reactive transition metal complexes have been tethered onto DNA-binding moieties to report sensitively on their recognition characteristics. This chapter discusses coordination complexes that have been remarkably useful as spectroscopic tags. In particular, it describes the application of ruthenium complexes to probe nucleic acid structure and recognition. Polypyridyl complexes of ruthenium(II) and their derivatives possess several features that may be exploited in developing spectroscopic probes for nucleic acids. The complexes possess an intense metal-toligand charge transfer (MLCT) transition in the visible region which yields a luminscent excited state; the excited state characteristics of these complexes have been amply characterized. Most importantly, this transition is perturbed on binding to DNA. The complexes are coordinatively saturated. They are inert to substitution and are stable in aqueous solution. Because the complexes are octahedral and possess three bidentate ligands, the complexes are chiral.", "date": "1993", "date_type": "published", "publisher": "Academic Press", "place_of_pub": "San Diego, CA", "pagerange": "576-594", "id_number": "CaltechAUTHORS:20160308-093657057", "isbn": "9780121821272", "book_title": "Metallobiochemistry Part C: Spectroscopic and Physical Methods for Probing Metal Ion Environments in Metalloenzymes and Metalloproteins", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160308-093657057", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM33309" }, { "agency": "NSF Postdoctoral Fellowship" } ] }, "contributors": { "items": [ { "id": "Riordan-J-F", "name": { "family": "Riordan", "given": "James F." } }, { "id": "Vallee-B-L", "name": { "family": "Vallee", "given": "Bert L." } } ] }, "doi": "10.1016/0076-6879(93)26027-7", "resource_type": "book_section", "pub_year": "1993", "author_list": "Murphy, Catherine J. and Barton, Jacqueline K." }, { "id": "https://authors.library.caltech.edu/records/at4ef-y2x87", "eprint_id": 65152, "eprint_status": "archive", "datestamp": "2023-08-20 00:51:08", "lastmod": "2024-01-13 16:43:17", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chow-Christine-S", "name": { "family": "Chow", "given": "Christine S." } }, { "id": "Barton-J-K", "name": { "family": "Barton", "given": "Jacqueline K." }, "orcid": "0000-0001-9883-1600" } ] }, "title": "Transition metal complexes as probes of nucleic acids", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 1992 by Academic Press, Inc. \n\nWe are grateful to the National Institute of General Medical Science (GM33309 and GM08346) and to the Ralph M. Parsons Foundation for financial support of research.", "abstract": "This chapter discusses a series of transition metal complexes that recognize the nucleic acid binding sites based on shape selection. By matching the shapes and symmetries of the metal complexes to particular variations in local nucleic acid conformation, a family of molecules that target different DNA sites have been developed. The recognition of a site depends on the local conformation, or shape, rather than on the sequence directly. Indeed, based purely on such considerations of shape and symmetry, a high level of specificity may be achieved. The molecules prepared serve as a novel series of conformation-selective probes, and these may be utilized to map the topological variations in structure along the nucleic acid polymer. The chapter also discusses the sequence-neutral cleavage complex, Rh(phi)^2bpy^(3+) (where bpy is bipyridine), a useful reagent for high-resolution photofootprinting, as well as several conformation specific tools to examine nucleic acid structure. These various ruthenium and rhodium complexes may be applied to detect subtle variations in B-DNA conformations or to investigate global secondary structures of a polynucleotide such as DNA cruciforms, left-handed Z-DNA, and A-form DNA. The chapter describes the way the secondary and tertiary structure of RNA may be examined using this methodology. The different information that may be gained from these methods is also discussed. In general, studies with these complexes provide a unique and sensitive handle to probe elements of nucleic acid polymorphism in solution.", "date": "1992", "date_type": "published", "publisher": "Academic Press", "place_of_pub": "San Diego, CA", "pagerange": "219-242", "id_number": "CaltechAUTHORS:20160307-150932721", "isbn": "9780121821135", "book_title": "DNA Structures Part B: Chemical and Electrophoretic Analysis of DNA", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160307-150932721", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM33309" }, { "agency": "NIH", "grant_number": "GM08346" }, { "agency": "Ralph M. Parsons Foundation" } ] }, "contributors": { "items": [ { "id": "Lilley-D-M-J", "name": { "family": "Lilley", "given": "David M. J." } }, { "id": "Dahlberg-J-E", "name": { "family": "Dahlberg", "given": "James E." } } ] }, "doi": "10.1016/0076-6879(92)12014-H", "resource_type": "book_section", "pub_year": "1992", "author_list": "Chow, Christine S. and Barton, Jacqueline K." }, { "id": "https://authors.library.caltech.edu/records/eczrc-fjj24", "eprint_id": 106638, "eprint_status": "archive", "datestamp": "2023-08-22 07:55:57", "lastmod": "2023-10-20 23:39:39", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Turro-N-J", "name": { "family": "Turro", "given": "Nicholas J." } }, { "id": "Barton-J-K", "name": { "family": "Barton", "given": "Jacqueline K." }, "orcid": "0000-0001-9883-1600" }, { "id": "Tomalia-D-A", "name": { "family": "Tomalia", "given": "Donald" } } ] }, "title": "Photoelectron transfer between molecules adsorbed in restricted spaces", "ispublished": "unpub", "full_text_status": "restricted", "keywords": "Photoinduced Electron Transfer; PAMAM Dendrimers; Anionic Surface; Restricted Space; Electron Transfer Step", "note": "\u00a9 Springer Science+Business Media Dordrecht 1991. \n\nThe authors thank the NSF, the NIH and the AFOSR for their generous support of this research. The intellectual contributions and scientific skills of the following students and postdoctorals were responsible for the realization of the research reported here: V. J. Kumar, M. D. Purugganan, G. Jaycox, M. C. Moreno-Bondi, G. Orellana, G. Caminati, A. Kirsch-DeMesmaeker and A. Friedman.", "abstract": "The photophysics and photoelectron transfer reactions of metal complexes bound to anionic surfaces which provide restricted spaces in aqueous solutions have been investigated by steady state and time resolved luminescence spectroscopy. The electron transfer systems were generated by systematically variation of structures derived from the Ru (II) tris-bipyridyl family as electron donors and methyl viologens and other metal tris-bipyridyl complexes as electron acceptors. The structure of the bipyridyl ligand in the complex was varied with respect to its functionality, size and shape in order to provide electron donors of similar driving force for electron transfer, but of differing binding selectivity and dynamics. In the same vein, metal substitution, e.g., Co (III) for Ru (II), provides a family of acceptors whose structures may be readily varied systematically. In addition, the inherent chirality of the tris-bipyridyl complexes allows opportunities for investigation of enantiomeric selection in binding and in the electron transfer step. The anionic surfaces selected for these investigations include those provided by micelles polyelectrolyte polymers, DNA double helix and starburst dendrimers. However, only the latter two surfaces are considered in detail in this report.", "date": "1991", "date_type": "published", "publisher": "Springer Netherlands", "place_of_pub": "Dordrecht", "pagerange": "121-139", "id_number": "CaltechAUTHORS:20201111-190742675", "isbn": "9789401055024", "book_title": "Photochemical Conversion and Storage of Solar Energy", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201111-190742675", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF" }, { "agency": "NIH" }, { "agency": "Air Force Office of Scientific Research (AFOSR)" } ] }, "contributors": { "items": [ { "id": "Pelizzetti-E", "name": { "family": "Pelizzetti", "given": "E." } }, { "id": "Schiavello-M", "name": { "family": "Schiavello", "given": "M." } } ] }, "doi": "10.1007/978-94-011-3396-8_8", "resource_type": "book_section", "pub_year": "1991", "author_list": "Turro, Nicholas J.; Barton, Jacqueline K.; et el." }, { "id": "https://authors.library.caltech.edu/records/2xaw2-n7643", "eprint_id": 67213, "eprint_status": "archive", "datestamp": "2023-08-19 20:08:39", "lastmod": "2023-10-18 20:57:46", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Barton-J-K", "name": { "family": "Barton", "given": "Jacqueline K." }, "orcid": "0000-0001-9883-1600" } ] }, "title": "What is biotechnology?", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 1988 American Chemical Society.", "abstract": "I have been given the task and opportunity of introducing chapters that describe some of the exciting new chemical advances in the field we call \"biotechnology\". You may notice that neither the words \"chemical\" nor \"molecular\" is incorporated into \"biotechnology\", but really the heart of what I think is exciting about this are is indeed chemical.", "date": "1988", "date_type": "published", "publisher": "American Chemical Society", "place_of_pub": "Washington, DC", "pagerange": "3-6", "id_number": "CaltechAUTHORS:20160520-131936011", "isbn": "9780841214736", "book_title": "Biotechnology and Materials Science: Chemistry for the Future", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160520-131936011", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "Good-M-L", "name": { "family": "Good", "given": "Mary L." } } ] }, "resource_type": "book_section", "pub_year": "1988", "author_list": "Barton, Jacqueline K." } ]