[ { "id": "authors:yjvcz-nty79", "collection": "authors", "collection_id": "yjvcz-nty79", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160510-141139929", "type": "article", "title": "Recognition of all four base pairs of double-helical DNA by triple-helix formation: design of nonnatural deoxyribonucleosides for pyrimidine\u2022purine base pair binding", "author": [ { "family_name": "Griffin", "given_name": "Linda C.", "clpid": "Griffin-L-C" }, { "family_name": "Kiessling", "given_name": "Laura L.", "clpid": "Kiessling-L-L" }, { "family_name": "Beal", "given_name": "Peter A.", "clpid": "Beal-P-A" }, { "family_name": "Gillespie", "given_name": "Paul", "clpid": "Gillespie-P" }, { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" } ], "abstract": "The sequence-specific recognition of double-helical DNA by oligonucleotide-directed triple-helix formation is limited mostly to purine tracts. Design leads that could expand the recognition code to all four Watson-Crick base pairs would provide one step toward a general solution targeting single sites in megabase size DNA. The nonnatural deoxyribonucleoside 1-(2-deoxy-beta-D-ribofuranosyl)-4-(3-benzamidophenyl)imidazole (D3) was synthesized in four steps and incorporated by automated methods into pyrimidine oligodeoxyribonucleotides. Within a pyrimidine oligonucleotide, D3 binds pyrimidine.purine base pairs with higher affinity than it binds purine.pyrimidine base pairs. From affinity-cleaving analysis, the stabilities of base triplets decrease in the order D3.TA is similar to D3.CG > D3.AT > D3.GC. Such specificity allows binding by triple-helix formation at an 18 base pair site in SV40 DNA containing all four base pairs at physiologically relevant pH and temperature. The stabilities of these novel triplets may be an example of shape-selective recognition of CG and TA Watson-Crick base pairs in the major groove.", "doi": "10.1021/ja00047a003", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "1992-10-07", "series_number": "21", "volume": "114", "issue": "21", "pages": "7976-7982" }, { "id": "authors:gxqf3-61209", "collection": "authors", "collection_id": "gxqf3-61209", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160510-141948690", "type": "article", "title": "Recognition of double helical DNA by alternate strand triple helix formation", "author": [ { "family_name": "Beal", "given_name": "Peter A.", "clpid": "Beal-P-A" }, { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" } ], "abstract": "The triplet specificities and required strand orientations of two classes of DNA triple helices can be combined to\ntarget double helical sequences containing all four base pairs by alternate strand triple helix formation. This allows for the\nuse of oligonucleotides containing only natural 3'-5' phosphodiester linkages to simultaneously bind both strands of double\nhelical DNA in the major groove. The stabilities and structures of these alternate strand triple helices depend on whether\nthe binding site sequence is 5'-(purine)_m(pyrimidine)_n-3' or 5'-(pyrimidine)_m(purine)_n-3'. The sequence type 5'-(purine)_m-(pyrimidine)_n-3' was targeted with an oligonucleotide consisting of a pyrimidine domain and a purine domain linked by a 3'-5'\nphosphodiester. To bind the duplex sequence type 5'-(pyrimidine)_m(purine)_n-3', the third strand requires at least two nucleotides\nlinking binding domains at the site of crossover in the major groove. A new class of oligonucleotides capable of binding mixed\nduplex sequences by crossovers in the major groove may be possible.", "doi": "10.1021/ja00039a004", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "1992-06-17", "series_number": "13", "volume": "114", "issue": "13", "pages": "4976-4982" }, { "id": "authors:ck73j-64y67", "collection": "authors", "collection_id": "ck73j-64y67", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160510-142116893", "type": "article", "title": "The influence of single base triplet changes on the stability of a Pur\u00b7Pur\u00b7Pyr triple helix determined by affinity cleaving", "author": [ { "family_name": "Beal", "given_name": "Peter A.", "clpid": "Beal-P-A" }, { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" } ], "abstract": "The influence of sixteen base triplet changes at a single position within a pur\u00b7pur\u00b7pyr triple helix was examined by affinity cleaving. For the 15 base pair target site studied here, G\u00b7GC, A\u00b7AT and T\u00b7AT triplets stabilize a triple helix to a greater extent than the other 13 natural triplets (pH = 7.4, 25\u00b0C). Weaker interactions were detected for the C\u00b7AT, A\u00b7GC and T\u00b7CG triplets. The absence of specific, highly stabilizing interactions between third strand bases and the CG or TA base pairs demonstrates a current sequence limitation to formation of this structure. Models for the two dimensional base triplet interactions for all possible 16 natural triplets are presented.", "doi": "10.1093/nar/20.11.2773", "pmcid": "PMC336921", "issn": "0305-1048", "publisher": "Oxford University Press", "publication": "Nucleic Acids Research", "publication_date": "1992-06-11", "series_number": "11", "volume": "20", "issue": "11", "pages": "2773-2776" }, { "id": "authors:614qn-1vk70", "collection": "authors", "collection_id": "614qn-1vk70", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150114-104814879", "type": "article", "title": "Second Structural Motif for Recognition of DNA by Oligonucleotide-Directed Triple-Helix Formation", "author": [ { "family_name": "Beal", "given_name": "Peter A.", "clpid": "Beal-P-A" }, { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" } ], "abstract": "Relative orientations of the DNA strands within a purine.purine.pyrimidine triple helix have been determined by affinity cleaving. A purine-rich oligonucleotide bound in the major groove of double-helical DNA antiparallel to the Watson-Crick purine strand. Binding depended upon the concentration of multivalent cations such as spermine or Mg^(2+), and appeared to be relatively independent of pH. Two models with specific hydrogen-bonding patterns for base triplets (G.GC, A.AT, and T.AT) are proposed to explain the sequence specificity of binding. The two models differ in the conformation about the glycosyl bond (syn or anti) and the location of the phosphate-deoxyribose backbone in the major groove of DNA. This motif broadens the structural frameworks available as a basis for the design of sequence-specific DNA binding molecules.", "doi": "10.1126/science.2003222", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "1991-03-15", "series_number": "4999", "volume": "251", "issue": "4999", "pages": "1360-1363" } ]