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For: Strauss BS. The "A" rule revisited: polymerases as determinants of mutational specificity. DNA Repair (Amst) 2002;1:125-35. [PMID: 12509259 DOI: 10.1016/s1568-7864(01)00014-3] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Number Cited by Other Article(s)
51
Xia S, Vashishtha A, Bulkley D, Eom SH, Wang J, Konigsberg WH. Contribution of partial charge interactions and base stacking to the efficiency of primer extension at and beyond abasic sites in DNA. Biochemistry 2012;51:4922-31. [PMID: 22630605 DOI: 10.1021/bi300296q] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
52
Stathis D, Lischke U, Koch SC, Deiml CA, Carell T. Discovery and mutagenicity of a guanidinoformimine lesion as a new intermediate of the oxidative deoxyguanosine degradation pathway. J Am Chem Soc 2012;134:4925-30. [PMID: 22329783 DOI: 10.1021/ja211435d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
53
Obeid S, Welte W, Diederichs K, Marx A. Amino acid templating mechanisms in selection of nucleotides opposite abasic sites by a family a DNA polymerase. J Biol Chem 2012;287:14099-108. [PMID: 22318723 DOI: 10.1074/jbc.m111.334904] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]  Open
54
Motea EA, Lee I, Berdis AJ. Development of a 'clickable' non-natural nucleotide to visualize the replication of non-instructional DNA lesions. Nucleic Acids Res 2011;40:2357-67. [PMID: 22086959 PMCID: PMC3300027 DOI: 10.1093/nar/gkr980] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]  Open
55
Zahn KE, Averill A, Wallace SS, Doublié S. The miscoding potential of 5-hydroxycytosine arises due to template instability in the replicative polymerase active site. Biochemistry 2011;50:10350-8. [PMID: 22026756 DOI: 10.1021/bi201219s] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
56
Obeid S, Schnur A, Gloeckner C, Blatter N, Welte W, Diederichs K, Marx A. Learning from Directed Evolution: Thermus aquaticus DNA Polymerase Mutants with Translesion Synthesis Activity. Chembiochem 2011;12:1574-80. [DOI: 10.1002/cbic.201000783] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Indexed: 12/20/2022]
57
Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK. DNA synthesis across an abasic lesion by yeast REV1 DNA polymerase. J Mol Biol 2010;406:18-28. [PMID: 21167175 DOI: 10.1016/j.jmb.2010.12.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 12/03/2010] [Accepted: 12/07/2010] [Indexed: 10/18/2022]
58
Gieseking S, Bergen K, Di Pasquale F, Diederichs K, Welte W, Marx A. Human DNA polymerase beta mutations allowing efficient abasic site bypass. J Biol Chem 2010;286:4011-20. [PMID: 21107011 DOI: 10.1074/jbc.m110.176826] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
59
Motea EA, Lee I, Berdis AJ. Quantifying the energetic contributions of desolvation and π-electron density during translesion DNA synthesis. Nucleic Acids Res 2010;39:1623-37. [PMID: 20952399 PMCID: PMC3045600 DOI: 10.1093/nar/gkq925] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]  Open
60
Settles S, Wang RW, Fronza G, Gold B. Effect of n3-methyladenine and an isosteric stable analogue on DNA polymerization. J Nucleic Acids 2010;2010. [PMID: 20936169 PMCID: PMC2945674 DOI: 10.4061/2010/426505] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 06/25/2010] [Indexed: 01/21/2023]  Open
61
Chandani S, Jacobs C, Loechler EL. Architecture of y-family DNA polymerases relevant to translesion DNA synthesis as revealed in structural and molecular modeling studies. J Nucleic Acids 2010;2010. [PMID: 20936174 PMCID: PMC2945684 DOI: 10.4061/2010/784081] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Accepted: 07/26/2010] [Indexed: 12/22/2022]  Open
62
Heyn P, Stenzel U, Briggs AW, Kircher M, Hofreiter M, Meyer M. Road blocks on paleogenomes--polymerase extension profiling reveals the frequency of blocking lesions in ancient DNA. Nucleic Acids Res 2010;38:e161. [PMID: 20587499 PMCID: PMC2938203 DOI: 10.1093/nar/gkq572] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
63
Obeid S, Blatter N, Kranaster R, Schnur A, Diederichs K, Welte W, Marx A. Replication through an abasic DNA lesion: structural basis for adenine selectivity. EMBO J 2010;29:1738-47. [PMID: 20400942 DOI: 10.1038/emboj.2010.64] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Accepted: 03/17/2010] [Indexed: 01/15/2023]  Open
64
Abasic sites and strand breaks in DNA cause transcriptional mutagenesis in Escherichia coli. Proc Natl Acad Sci U S A 2010;107:3657-62. [PMID: 20142484 DOI: 10.1073/pnas.0913191107] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
65
Dahlmann HA, Vaidyanathan VG, Sturla SJ. Investigating the biochemical impact of DNA damage with structure-based probes: abasic sites, photodimers, alkylation adducts, and oxidative lesions. Biochemistry 2009;48:9347-59. [PMID: 19757831 PMCID: PMC2789562 DOI: 10.1021/bi901059k] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
66
Beard WA, Shock DD, Batra VK, Pedersen LC, Wilson SH. DNA polymerase beta substrate specificity: side chain modulation of the "A-rule". J Biol Chem 2009;284:31680-9. [PMID: 19759017 DOI: 10.1074/jbc.m109.029843] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
67
Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK. DNA synthesis across an abasic lesion by human DNA polymerase iota. Structure 2009;17:530-7. [PMID: 19368886 DOI: 10.1016/j.str.2009.02.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2008] [Revised: 02/17/2009] [Accepted: 02/18/2009] [Indexed: 11/26/2022]
68
Jia L, Geacintov NE, Broyde S. The N-clasp of human DNA polymerase kappa promotes blockage or error-free bypass of adenine- or guanine-benzo[a]pyrenyl lesions. Nucleic Acids Res 2008;36:6571-84. [PMID: 18931375 PMCID: PMC2582633 DOI: 10.1093/nar/gkn719] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2008] [Revised: 09/29/2008] [Accepted: 09/30/2008] [Indexed: 01/10/2023]  Open
69
Berdis AJ. DNA polymerases as therapeutic targets. Biochemistry 2008;47:8253-60. [PMID: 18642851 DOI: 10.1021/bi801179f] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
70
Batra VK, Beard WA, Shock DD, Pedersen LC, Wilson SH. Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation. Mol Cell 2008;30:315-24. [PMID: 18471977 DOI: 10.1016/j.molcel.2008.02.025] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Revised: 01/31/2008] [Accepted: 02/28/2008] [Indexed: 10/22/2022]
71
McCulloch SD, Kunkel TA. The fidelity of DNA synthesis by eukaryotic replicative and translesion synthesis polymerases. Cell Res 2008;18:148-61. [PMID: 18166979 PMCID: PMC3639319 DOI: 10.1038/cr.2008.4] [Citation(s) in RCA: 373] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]  Open
72
Bauer J, Xing G, Yagi H, Sayer JM, Jerina DM, Ling H. A structural gap in Dpo4 supports mutagenic bypass of a major benzo[a]pyrene dG adduct in DNA through template misalignment. Proc Natl Acad Sci U S A 2007;104:14905-10. [PMID: 17848527 PMCID: PMC1986586 DOI: 10.1073/pnas.0700717104] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]  Open
73
Chandani S, Loechler EL. Molecular modeling benzo[a]pyrene N2-dG adducts in the two overlapping active sites of the Y-family DNA polymerase Dpo4. J Mol Graph Model 2007;25:658-70. [PMID: 16782374 DOI: 10.1016/j.jmgm.2006.05.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2006] [Revised: 05/03/2006] [Accepted: 05/03/2006] [Indexed: 11/18/2022]
74
McCulloch SD, Kunkel TA. Multiple solutions to inefficient lesion bypass by T7 DNA polymerase. DNA Repair (Amst) 2006;5:1373-83. [PMID: 16876489 PMCID: PMC1892196 DOI: 10.1016/j.dnarep.2006.06.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2006] [Revised: 06/08/2006] [Accepted: 06/13/2006] [Indexed: 10/24/2022]
75
Phadnis N, Mehta R, Meednu N, Sia EA. Ntg1p, the base excision repair protein, generates mutagenic intermediates in yeast mitochondrial DNA. DNA Repair (Amst) 2006;5:829-39. [PMID: 16730479 DOI: 10.1016/j.dnarep.2006.04.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2006] [Revised: 04/12/2006] [Accepted: 04/13/2006] [Indexed: 11/25/2022]
76
Lee CH, Chandani S, Loechler EL. Homology modeling of four Y-family, lesion-bypass DNA polymerases: the case that E. coli Pol IV and human Pol kappa are orthologs, and E. coli Pol V and human Pol eta are orthologs. J Mol Graph Model 2006;25:87-102. [PMID: 16386932 DOI: 10.1016/j.jmgm.2005.10.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2005] [Revised: 10/21/2005] [Accepted: 10/21/2005] [Indexed: 01/25/2023]
77
Spencer J, Dunn-Walters DK. Hypermutation at A-T base pairs: the A nucleotide replacement spectrum is affected by adjacent nucleotides and there is no reverse complementarity of sequences flanking mutated A and T nucleotides. THE JOURNAL OF IMMUNOLOGY 2005;175:5170-7. [PMID: 16210621 DOI: 10.4049/jimmunol.175.8.5170] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
78
Chiapperino D, Cai M, Sayer JM, Yagi H, Kroth H, Masutani C, Hanaoka F, Jerina DM, Cheh AM. Error-prone translesion synthesis by human DNA polymerase eta on DNA-containing deoxyadenosine adducts of 7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene. J Biol Chem 2005;280:39684-92. [PMID: 16188888 DOI: 10.1074/jbc.m508008200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]  Open
79
Franklin A, Blanden RV. Hypothesis: biological role for J-C intronic matrix attachment regions in the molecular mechanism of antigen-driven somatic hypermutation. Immunol Cell Biol 2005;83:383-91. [PMID: 16033533 DOI: 10.1111/j.1440-1711.2005.01327.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
80
Holmberg RC, Henry AA, Romesberg FE. Directed evolution of novel polymerases. ACTA ACUST UNITED AC 2005;22:39-49. [PMID: 15857782 DOI: 10.1016/j.bioeng.2004.12.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2004] [Revised: 12/09/2004] [Accepted: 12/09/2004] [Indexed: 10/25/2022]
81
Wilson DM. Ape1 abasic endonuclease activity is regulated by magnesium and potassium concentrations and is robust on alternative DNA structures. J Mol Biol 2004;345:1003-14. [PMID: 15644200 DOI: 10.1016/j.jmb.2004.11.028] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2004] [Revised: 11/11/2004] [Accepted: 11/12/2004] [Indexed: 11/18/2022]
82
Franklin A, Blanden RV. On the molecular mechanism of somatic hypermutation of rearranged immunoglobulin genes. Immunol Cell Biol 2004;82:557-67. [PMID: 15550113 DOI: 10.1111/j.1440-1711.2004.01289.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
83
Seki M, Masutani C, Yang LW, Schuffert A, Iwai S, Bahar I, Wood RD. High-efficiency bypass of DNA damage by human DNA polymerase Q. EMBO J 2004;23:4484-94. [PMID: 15496986 PMCID: PMC526458 DOI: 10.1038/sj.emboj.7600424] [Citation(s) in RCA: 160] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2004] [Accepted: 08/27/2004] [Indexed: 01/03/2023]  Open
84
Gaskell M, McLuckie KIE, Farmer PB. Comparison of the mutagenic activity of the benzene metabolites, hydroquinone and para-benzoquinone in the supF forward mutation assay: a role for minor DNA adducts formed from hydroquinone in benzene mutagenicity. Mutat Res 2004;554:387-98. [PMID: 15450434 DOI: 10.1016/j.mrfmmm.2004.06.032] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2004] [Revised: 05/28/2004] [Accepted: 06/09/2004] [Indexed: 11/16/2022]
85
Taylor JS. New structural and mechanistic insight into the A-rule and the instructional and non-instructional behavior of DNA photoproducts and other lesions. Mutat Res 2002;510:55-70. [PMID: 12459443 DOI: 10.1016/s0027-5107(02)00252-x] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
86
Villani G, Tanguy Le Gac N, Wasungu L, Burnouf D, Fuchs RP, Boehmer PE. Effect of manganese on in vitro replication of damaged DNA catalyzed by the herpes simplex virus type-1 DNA polymerase. Nucleic Acids Res 2002;30:3323-32. [PMID: 12140316 PMCID: PMC137087 DOI: 10.1093/nar/gkf463] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
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