Structure of DNA Polymerase β with the Mutagenic DNA Lesion 8-Oxodeoxyguanine Reveals Structural Insights into Its Coding Potential
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Oxidative damage to DNA generates 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG). During DNA replication and repair synthesis, 8-oxodG can pair with cytosine or adenine. The ability to accurately replicate through this lesion depends on the DNA polymerase. We report the first structure of a polymerase with a promutagenic DNA lesion, 8-oxodG, in the confines of its active site. The modified guanine residue is in an anti conformation and forms Watson-Crick hydrogen bonds with an incoming dCTP. To accommodate the oxygen at C8, the 5'-phosphate backbone of the templating nucleotide flips 180 degrees. Thus, the flexibility of the template sugar-phosphate backbone near the polymerase active site is one parameter that influences the anti-syn equilibrium of 8-oxodG. Our results provide insights into the mechanisms employed by polymerases to select the complementary dNTP.
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Pol β avoids this inaccurate reaction by flipping the 5'-phosphate backbone of the templating nucleotide 180°, relieving a steric clash with the oxygen at C-8 and allowing non-mutagenic pairing of incoming dCTP with 8-oxy-dG in the Watson-Crick anti conformation.
“However, Pol  avoids this inaccurate reaction by flipping the 5Ј-phosphate backbone of the templating nucleotide 180°, relieving a steric clash with the oxygen at C-8 and allowing non-mutagenic pairing of incoming dCTP with 8-oxy-dG in the Watson-Crick anti conformation ( 46).”
From DNA Replication Fidelity (2004) · cites this paper as [46]
Cites
[20] Processing of X-ray diffraction data collected in oscillation mode
Otwinowski, Z., & Minor, W. (1997) · Methods in Enzymology · doi:10.1016/s0076-6879(97)76066-x · Cited by 33,475 · see citing works
Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination
Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse‐Kunstleve, R. W., Jiang, J., Kuszewski, J. J., Nilges, M., Pannu, N., et al. (1998) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444998003254 · Cited by 15,720 · see citing works
MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures
Kraulis, P. J. (1991) · Journal of Applied Crystallography · doi:10.1107/s0021889891004399 · Cited by 14,011 · see citing works
Jones, T. A., Zou, J.-Y., Cowan, S. W., & Kjeldgaard, M. (1991) · Acta Crystallographica Section A Foundations of Crystallography · doi:10.1107/s0108767390010224 · Cited by 12,650 · see citing works
[26] Raster3D: Photorealistic molecular graphics
Merritt, E. A., & Bacon, D. (1997) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(97)77028-9 · Cited by 3,749 · see citing works
Insertion of specific bases during DNA synthesis past the oxidation-damaged base 8-oxodG
Shibutani, S., Takeshita, M., & Grollman, A. P. (1991) · Nature · doi:10.1038/349431a0 · Cited by 2,224 · see citing works
Self-citationStructure of a B-DNA dodecamer: conformation and dynamics.
Drew, H. R., Wing, R. M., Takano, T., Broka, C. A., Tanaka, S., Itakura, K., & Dickerson, R. E. (1981) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.78.4.2179 · Cited by 1,562 · see citing works
Huang, H., Chopra, R., Verdine, G. L., & Harrison, S. C. (1998) · Science · doi:10.1126/science.282.5394.1669 · Cited by 1,420 · see citing works
Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution
Doublié, S., Tabor, S., Long, A. M., Richardson, C. C., & Ellenberger, T. (1998) · Nature · doi:10.1038/34593 · Cited by 1,177 · see citing works
Structure of a B-DNA dodecamer
Drew, H. R., & Dickerson, R. E. (1981) · Journal of Molecular Biology · doi:10.1016/0022-2836(81)90009-7 · Cited by 921 · see citing works
Structure of a B-DNA dodecamer
Dickerson, R. E., & Drew, H. R. (1981) · Journal of Molecular Biology · doi:10.1016/0022-2836(81)90357-0 · Cited by 893 · see citing works
Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP
Ollis, D. L., Brick, P., Hamlin, R. C., Xuong, N., & Steitz, T. A. (1985) · Nature · doi:10.1038/313762a0 · Cited by 848 · see citing works
Mutagenesis by 8-oxoguanine: an enemy within
Grollman, A. P., & Moriya, M. (1993) · Trends in Genetics · doi:10.1016/0168-9525(93)90089-z · Cited by 807 · see citing works
Self-citationEfficient Bypass of a Thymine-Thymine Dimer by Yeast DNA Polymerase, Polη
Johnson, R. E., Prakash, S., & Prakash, L. (1999) · Science · doi:10.1126/science.283.5404.1001 · Cited by 736 · see citing works
Endogenous mutagens and the causes of aging and cancer
Ames, B. N., & Gold, L. S. (1991) · Mutation research. Fundamental and molecular mechanisms of mutagenesis · doi:10.1016/0027-5107(91)90157-j · Cited by 716 · see citing works
STRUCTURES OF TERNARY COMPLEXES OF RAT DNA POLYMERASE BETA, A DNA TEMPLATE-PRIMER, AND DDCTP
Pelletier, H., Sawaya, M. R., Kumar, A., Wilson, S. H., & Kraut, J. (1994) · Worldwide Protein Data Bank · doi:10.2210/pdb2bpf/pdb · Cited by 694 · see citing works
Self-citationLi, Y., Korolev, S., & Waksman, G. (1998) · The EMBO Journal · doi:10.1093/emboj/17.24.7514 · Cited by 689 · see citing works
Structures of Ternary Complexes of Rat DNA Polymerase β, a DNA Template-Primer, and ddCTP
Pelletier, H., Sawaya, M. R., Kumar, A., Wilson, S. H., & Kraut, J. (1994) · Science · doi:10.1126/science.7516580 · Cited by 598 · see citing works
Self-citationSawaya, M. R., Prasad, R., Wilson, S. H., Kraut, J., & Pelletier, H. (1997) · Biochemistry · doi:10.1021/bi9703812 · Cited by 593 · see citing works
Self-citationStructure of the Replicating Complex of a Pol α Family DNA Polymerase
Franklin, M. C., Wang, J., & Steitz, T. A. (2001) · Cell · doi:10.1016/s0092-8674(01)00367-1 · Cited by 538 · see citing works
Fidelity of Human DNA Polymerase η
Johnson, R. E., Washington, M. T., Prakash, S., & Prakash, L. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.275.11.7447 · Cited by 399 · see citing works
Low fidelity DNA synthesis by human DNA polymerase-η
Matsuda, T., Bebenek, K., Masutani, C., Hanaoka, F., & Kunkel, T. A. (2000) · Nature · doi:10.1038/35010014 · Cited by 372 · see citing works
Efficient and accurate replication in the presence of 7,8-dihydro-8-oxoguanine by DNA polymerase η
Haracska, L., Yu, S.-L., Johnson, R. E., Prakash, L., & Prakash, S. (2000) · Nature Genetics · doi:10.1038/78169 · Cited by 349 · see citing works
Structure of the Catalytic Core of S. cerevisiae DNA Polymerase η
Trincão, J., Johnson, R. E., Escalante, C. R., Prakash, S., Prakash, L., & Aggarwal, A. K. (2001) · Molecular Cell · doi:10.1016/s1097-2765(01)00306-9 · Cited by 344 · see citing works
Kouchakdjian, M., Bodepudi, V., Shibutani, S., Eisenberg, M., Johnson, F., Grollman, A. P., & Patel, D. J. (1991) · Biochemistry · doi:10.1021/bi00219a034 · Cited by 298 · see citing works
Self-citationCrystal Structure of a DNA Duplex Containing 8-Hydroxydeoxyguanine-Adenine Base Pairs
McAuley-Hecht, K. E., Leonard, G. A., Gibson, N. J., Thomson, J. B., Watson, W. P., Hunter, W. N., & Brown, T. P. (1994) · Biochemistry · doi:10.1021/bi00200a006 · Cited by 228 · see citing works
X-ray structure of a DNA decamer containing 7,8-dihydro-8-oxoguanine.
Lipscomb, L. A., Peek, M. E., Morningstar, M., Verghis, S. M., Miller, E. M., Rich, A., Essigmann, J. M., & Williams, L. D. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.3.719 · Cited by 224 · see citing works
NMR studies of a DNA containing 8-hydroxydeoxyguanosine
Oda, Y., Uesugi, S., Ikehara, M., Nishimura, S., Kawase, Y., Ishikawa, H. T., Inoue, H., & Ohtsuka, E. (1991) · Nucleic Acids Research · doi:10.1093/nar/19.7.1407 · Cited by 217 · see citing works
Beard, W. A., Osheroff, W. P., Prasad, R., Sawaya, M. R., Jaju, M., Wood, T. G., Kraut, J., Kunkel, T. A., & Wilson, S. H. (1996) · Journal of Biological Chemistry · doi:10.1074/jbc.271.21.12141 · Cited by 165 · see citing works
Self-citationUesugi, S., & Ikehara, M. (1977) · Journal of the American Chemical Society · doi:10.1021/ja00452a008 · Cited by 159 · see citing works
[11] Purification and domain-mapping of mammalian DNA polymerase β
Beard, W. A., & Wilson, S. H. (1995) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/0076-6879(95)62013-3 · Cited by 157 · see citing works
Self-citationDNA Structure and Aspartate 276 Influence Nucleotide Binding to Human DNA Polymerase β
Berg, B. J. V., Beard, W. A., & Wilson, S. H. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m002884200 · Cited by 154 · see citing works
Self-citationStructural and conformational analyses of 8-hydroxy-2'-deoxyguanosine
Culp, S. J., Cho, B. P., Kadlubar, F. F., & Evans, F. E. (1989) · Chemical Research in Toxicology · doi:10.1021/tx00012a010 · Cited by 153 · see citing works
Structural design of a eukaryotic DNA repair polymerase: DNA polymerase β
Beard, W. A., & Wilson, S. H. (2000) · Mutation Research/DNA Repair · doi:10.1016/s0921-8777(00)00029-x · Cited by 145 · see citing works
Self-citationUnique misinsertion specificity of polι may decrease the mutagenic potential of deaminated cytosines
Vaisman, A., & Woodgate, R. (2001) · The EMBO Journal · doi:10.1093/emboj/20.22.6520 · Cited by 125 · see citing works
Furge, L. L., & Guengerich, F. P. (1997) · Biochemistry · doi:10.1021/bi9627267 · Cited by 105 · see citing works
8-OxodGTP Incorporation by DNA Polymerase β Is Modified by Active-Site Residue Asn279
Miller, H., Prasad, R., Wilson, S. H., Johnson, F., & Grollman, A. P. (2000) · Biochemistry · doi:10.1021/bi991789x · Cited by 104 · see citing works
Self-citationStructural and thermodynamic studies on the adenine.guanine mismatch in B-DNA
Leonard, G. A., Booth, E. D., & Brown, T. (1990) · Nucleic Acids Research · doi:10.1093/nar/18.19.5617 · Cited by 92 · see citing works
Yang, L., Beard, W. A., Wilson, S. H., Broyde, S. B., & Tamar Schlick, A. (2002) · Journal of Molecular Biology · doi:10.1006/jmbi.2002.5450 · Cited by 90 · see citing works
Self-citationTranslesional synthesis on DNA templates containing 8-oxo-7,8-dihydrodeoxyadenosine
Shibutani, S., Bodepudi, V., Johnson, F., & Grollman, A. P. (1993) · Biochemistry · doi:10.1021/bi00068a019 · Cited by 82 · see citing works
Self-citationBeard, W. A., Shock, D. D., Yang, X., DeLauder, S. F., & Wilson, S. H. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m107286200 · Cited by 74 · see citing works
Self-citationMalins, D. C., Polissar, N. L., Ostrander, G. K., & Vinson, M. A. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.230438797 · Cited by 61 · see citing works
Osheroff, W. P., Beard, W. A., Yin, S., Wilson, S. H., & Kunkel, T. A. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m003462200 · Cited by 54 · see citing works
Self-citationBodepudi, V., Iden, C. R., & Johnson, F. (1991) · Nucleosides and Nucleotides · doi:10.1080/07328319108046660 · Cited by 40 · see citing works
DNA Lesion Bypass Polymerases Open Up
Beard, W. A., & Wilson, S. H. (2001) · Structure · doi:10.1016/s0969-2126(01)00646-3 · Cited by 25 · see citing works
Self-citation
Flagged first, then by citations
1 of the 46 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
Base-excision repair of oxidative DNA damage
David, S. S., O'Shea, V. L., & Kundu, S. (2007) · Nature · doi:10.1038/nature05978 · Cited by 1,238 · see citing works
EUKARYOTIC TRANSLESION SYNTHESIS DNA POLYMERASES: Specificity of Structure and Function
Prakash, S., Johnson, R. E., & Prakash, L. (2005) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.74.082803.133250 · Cited by 999 · see citing works
Kunkel, T. A. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.r400006200 · Cited by 754 · see citing works
Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase
Hsu, G. W., Ober, M. S., Carell, T., & Beese, L. S. (2004) · Nature · doi:10.1038/nature02908 · Cited by 316 · see citing works
Structure and Mechanism of DNA Polymerase β
Beard, W. A., & Wilson, S. H. (2006) · Chemical Reviews · doi:10.1021/cr0404904 · Cited by 299 · see citing works
Self-citationBase Excision Repair and Lesion-Dependent Subpathways for Repair of Oxidative DNA Damage
Svilar, D., Goellner, E. M., Almeida, K. H., & Sobol, R. (2011) · Antioxidants and Redox Signaling · doi:10.1089/ars.2010.3466 · Cited by 254 · see citing works
Magnesium-Induced Assembly of a Complete DNA Polymerase Catalytic Complex
Batra, V. K., Beard, W. A., Shock, D. D., Krahn, J. M., Pedersen, L. C., & Wilson, S. H. (2006) · Structure · doi:10.1016/j.str.2006.01.011 · Cited by 255 · see citing works
Self-citationOxidatively induced DNA damage and its repair in cancer
Dizdaroğlu, M. (2014) · Mutation Research/Reviews in Mutation Research · doi:10.1016/j.mrrev.2014.11.002 · Cited by 254 · see citing works
Structure and mechanism of DNA polymerases
Rothwell, P. J., & Waksman, G. (2005) · Advances in protein chemistry · doi:10.1016/s0065-3233(04)71011-6 · Cited by 238 · see citing works
Hitomi, K., Iwai, S., & Tainer, J. A. (2007) · DNA Repair · doi:10.1016/j.dnarep.2006.10.004 · Cited by 220 · see citing works
8-oxo-guanine bypass by human DNA polymerases in the presence of auxiliary proteins
Maga, G., Villani, G., Crespan, E., Wimmer, U., Ferrari, E. S., Bertocci, B., & Hübscher, U. (2007) · Nature · doi:10.1038/nature05843 · Cited by 218 · see citing works
Structural basis for the dual coding potential of 8‐oxoguanosine by a high‐fidelity DNA polymerase
Brieba, L. G., Eichman, B. F., Kokoska, R. J., Doublié, S., Kunkel, T. A., & Ellenberger, T. (2004) · The EMBO Journal · doi:10.1038/sj.emboj.7600354 · Cited by 210 · see citing works
Not breathing is not an option: How to deal with oxidative DNA damage
Markkanen, E. (2017) · DNA repair · doi:10.1016/j.dnarep.2017.09.007 · Cited by 192 · see citing works
The X family portrait: Structural insights into biological functions of X family polymerases
Moon, A. F., García–Díaz, M., Batra, V. K., Beard, W. A., Bębenek, K., Kunkel, T. A., Wilson, S. H., & Pedersen, L. C. (2007) · DNA repair · doi:10.1016/j.dnarep.2007.05.009 · Cited by 185 · see citing works
Self-citationFoster, P. L., Lee, H., Popodi, E. M., Townes, J. P., & Tang, H. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1512136112 · Cited by 171 · see citing works
DNA polymerase Family X: Function, structure, and cellular roles
Yamtich, J., & Sweasy, J. B. (2009) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2009.07.008 · Cited by 173 · see citing works
Structure and Mechanism of DNA Polymerase β
Beard, W. A., & Wilson, S. H. (2014) · Biochemistry · doi:10.1021/bi500139h · Cited by 164 · see citing works
Self-citationBeard, B. C., Wilson, S. H., & Smerdon, M. J. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1330328100 · Cited by 161 · see citing works
Self-citationStepwise Translocation of Dpo4 Polymerase during Error-Free Bypass of an oxoG Lesion
Rechkoblit, O., Malinina, L. V., Cheng, Y., Kuryavyi, V., Broyde, S. B., Geacintov, N. E., & Patel, D. J. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0040011 · Cited by 148 · see citing works
Kalam, M. A. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl099 · Cited by 141 · see citing works
Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site
Hogg, M., Wallace, S. S., & Doublié, S. (2004) · The EMBO Journal · doi:10.1038/sj.emboj.7600150 · Cited by 139 · see citing works
Lesion (in)tolerance reveals insights into DNA replication fidelity
Freisinger, E., Grollman, A. P., Miller, H., & Kisker, C. (2004) · The EMBO Journal · doi:10.1038/sj.emboj.7600158 · Cited by 131 · see citing works
Self-citationZang, H., Irimia, A., Choi, J., Angel, K. C., Loukachevitch, L. V., Egli, M., & Guengerich, F. P. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m510889200 · Cited by 129 · see citing works
Batra, V. K., Beard, W. A., Shock, D. D., Pedersen, L. C., & Wilson, S. H. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.02.025 · Cited by 125 · see citing works
Self-citationMultiple Functions of DNA Polymerases
García–Díaz, M., & Bębenek, K. (2007) · Critical Reviews in Plant Sciences · doi:10.1080/07352680701252817 · Cited by 116 · see citing works
Greenberg, M. M. (2013) · Accounts of Chemical Research · doi:10.1021/ar400229d · Cited by 107 · see citing works
Sources of spontaneous mutagenesis in bacteria
Schroeder, J. W., Yeesin, P., Simmons, L. A., & Wang, J. D. (2017) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409238.2017.1394262 · Cited by 101 · see citing works
The efficiency and fidelity of 8-oxo-guanine bypass by DNA polymerases δ and η
McCulloch, S. D., Kokoska, R., Garg, P., Burgers, P., & Kunkel, T. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp103 · Cited by 97 · see citing works
Biological Properties of Single Chemical−DNA Adducts: A Twenty Year Perspective
Delaney, J. C., & Essigmann, J. M. (2007) · Chemical Research in Toxicology · doi:10.1021/tx700292a · Cited by 102 · see citing works
Interactions of Carcinogen-Bound DNA with Individual DNA Polymerases
Guengerich, F. P. (2006) · Chemical Reviews · doi:10.1021/cr0404693 · Cited by 99 · see citing works
Graziewicz, M. A., Bienstock, R. J., & Copeland, W. C. (2007) · Human Molecular Genetics · doi:10.1093/hmg/ddm227 · Cited by 94 · see citing works
DNA polymerase structure-based insight on the mutagenic properties of 8-oxoguanine
Beard, W. A., Batra, V. K., & Wilson, S. H. (2010) · Mutation Research/Genetic Toxicology and Environmental Mutagenesis · doi:10.1016/j.mrgentox.2010.07.013 · Cited by 92 · see citing works
Self-citationEnergy analysis of chemistry for correct insertion by DNA polymerase β
Lin, P., Pedersen, L. C., Batra, V. K., Beard, W. A., Wilson, S. H., & Pedersen, L. G. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0606006103 · Cited by 92 · see citing works
Self-citationVariations on a theme: Eukaryotic Y-family DNA polymerases
Washington, M. T., Carlson, K. D., Freudenthal, B., & Pryor, J. M. (2009) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2009.07.004 · Cited by 87 · see citing works
Trace amounts of 8-oxo-dGTP in mitochondrial dNTP pools reduce DNA polymerase replication fidelity
Pursell, Z. F., McDonald, J., Mathews, C. K., & Kunkel, T. A. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn062 · Cited by 86 · see citing works
Incorporation and Replication of 8-Oxo-deoxyguanosine by the Human Mitochondrial DNA Polymerase
Hanes, J. W., Thal, D. M., & Johnson, K. A. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m607965200 · Cited by 85 · see citing works
MUTYH DNA glycosylase: the rationale for removing undamaged bases from the DNA
Markkanen, E., Dorn, J., & Hübscher, U. (2013) · Frontiers in Genetics · doi:10.3389/fgene.2013.00018 · Cited by 77 · see citing works
Krahn, J. M., Beard, W. A., & Wilson, S. H. (2004) · Structure · doi:10.1016/j.str.2004.08.001 · Cited by 75 · see citing works
Self-citationBatra, V. K., Shock, D. D., Beard, W. A., McKenna, C. E., & Wilson, S. H. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1112235108 · Cited by 75 · see citing works
Self-citationMolecular Basis of Transcriptional Mutagenesis at 8-Oxoguanine
Damsma, G. E., & Cramer, P. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.022764 · Cited by 74 · see citing works
Kirouac, K. N., & Ling, H. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1013909108 · Cited by 71 · see citing works
Isolation, Characterization, and Independent Synthesis of Guanine Oxidation Products
Gimisis, T., & Cismaş, C. (2006) · European Journal of Organic Chemistry · doi:10.1002/ejoc.200500581 · Cited by 71 · see citing works
DNA Polymerase β Substrate Specificity
Beard, W. A., Shock, D. D., Batra, V. K., Pedersen, L. C., & Wilson, S. H. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.029843 · Cited by 70 · see citing works
Self-citationStructural insight into the DNA polymerase β deoxyribose phosphate lyase mechanism
Prasad, R., Batra, V. K., Yang, X.-P., Krahn, J. M., Pedersen, L. C., Beard, W. A., & Wilson, S. H. (2005) · DNA repair · doi:10.1016/j.dnarep.2005.08.009 · Cited by 69 · see citing works
Self-citationBrown, J. A., Duym, W. W., Fowler, J. D., & Suo, Z. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.01.069 · Cited by 65 · see citing works
Carlson, K. D., & Washington, M. (2005) · Molecular and Cellular Biology · doi:10.1128/mcb.25.6.2169-2176.2005 · Cited by 70 · see citing works
Vyas, R., Reed, A. J., Tokarsky, E. J., & Suo, Z. (2015) · Journal of the American Chemical Society · doi:10.1021/jacs.5b02109 · Cited by 60 · see citing works
Structure of Human DNA Polymerase κ Inserting dATP Opposite an 8-OxoG DNA Lesion
Carpio, R. V., Silverstein, T. D., Lone, S., Swan, M. K., Choudhury, J. R., Johnson, R. E., Prakash, S., Prakash, L., & Aggarwal, A. K. (2009) · PLoS ONE · doi:10.1371/journal.pone.0005766 · Cited by 60 · see citing works
Bumps in the road: how replicative DNA polymerases see DNA damage
Hogg, M., Wallace, S. S., & Doublié, S. (2005) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2005.01.014 · Cited by 58 · see citing works
Mutagenic conformation of 8-oxo-7,8-dihydro-2′-dGTP in the confines of a DNA polymerase active site
Batra, V. K., Beard, W. A., Hou, E. W., Pedersen, L. C., Prasad, R., & Wilson, S. H. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1852 · Cited by 56 · see citing works
Self-citationArora, K., Beard, W. A., Wilson, S. H., & Tamar Schlick, A. (2005) · Biochemistry · doi:10.1021/bi0507682 · Cited by 55 · see citing works
Self-citationDynamic Conformational Heterogeneities of Carcinogen-DNA Adducts and their Mutagenic Relevance
Cho, B. P. (2004) · Journal of Environmental Science and Health Part C · doi:10.1081/lesc-200038217 · Cited by 55 · see citing works
Li, J., Braganza, A., & Sobol, R. W. (2013) · Antioxidants and Redox Signaling · doi:10.1089/ars.2012.5107 · Cited by 50 · see citing works
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Freudenthal, B., Beard, W. A., & Wilson, S. H. (2012) · Structure · doi:10.1016/j.str.2012.08.008 · Cited by 50 · see citing works
Self-citationFreudenthal, B., Beard, W. A., & Wilson, S. H. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1276 · Cited by 44 · see citing works
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Yudkina, A., Shilkin, E., Endutkin, A. V., Makarova, A., & Zharkov, D. (2019) · Crystals · doi:10.3390/cryst9050269 · Cited by 41 · see citing works
Wang, H., Chen, T., Weng, C.-W., Yang, C.-H., & Tang, M. (2016) · Oncotarget · doi:10.18632/oncotarget.12608 · Cited by 43 · see citing works
Hold Tight (but Not Too Tight) to Get It Right
Brieba, L. G., & Ellenberger, T. (2003) · Structure · doi:10.1016/s0969-2126(02)00917-6 · Cited by 41 · see citing works
Brieba, L. G., Kokoska, R. J., Bębenek, K., Kunkel, T. A., & Ellenberger, T. (2005) · Structure · doi:10.1016/j.str.2005.07.020 · Cited by 41 · see citing works
Base excision repair and design of small molecule inhibitors of human DNA polymerase β
Wilson, S. H., Beard, W. A., Shock, D. D., Batra, V. K., Cavanaugh, N. A., Prasad, R., Hou, E. W., Liu, Y., Asagoshi, K., Horton, J. K., et al. (2010) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-010-0489-1 · Cited by 39 · see citing works
Self-citationReactive Oxygen Species Play an Important Role in the Bactericidal Activity of Quinolone Antibiotics
Kottur, J., & Nair, D. T. (2016) · Angewandte Chemie International Edition · doi:10.1002/anie.201509340 · Cited by 38 · see citing works
Nucleotide-Induced DNA Polymerase Active Site Motions Accommodating a Mutagenic DNA Intermediate
Batra, V. K., Beard, W. A., Shock, D. D., Pedersen, L. C., & Wilson, S. H. (2005) · Structure · doi:10.1016/j.str.2005.05.010 · Cited by 37 · see citing works
Self-citationRechkoblit, O., Malinina, L., Cheng, Y., Geacintov, N., Broyde, S., & Patel, D. (2009) · Structure · doi:10.1016/j.str.2009.03.011 · Cited by 35 · see citing works
A fidelity mechanism in DNA polymerase lambda promotes error‐free bypass of 8‐oxo‐dG
Burak, M. J., Guja, K. E., Hambardjieva, E., Derkunt, B., & García–Díaz, M. (2016) · The EMBO Journal · doi:10.15252/embj.201694332 · Cited by 35 · see citing works
Zahn, K. E., Wallace, S. S., & Doublié, S. (2011) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2011.03.008 · Cited by 34 · see citing works
Unexpected non-Hoogsteen–based mutagenicity mechanism of FaPy-DNA lesions
Gehrke, T. H., Lischke, U., Gasteiger, K. L., Schneider, S., Arnold, S., Müller, H. C., Stephenson, D. S., Zipse, H., & Carell, T. (2013) · Nature Chemical Biology · doi:10.1038/nchembio.1254 · Cited by 34 · see citing works
Structural Basis for Error-free Replication of Oxidatively Damaged DNA by Yeast DNA Polymerase η
Silverstein, T. D., Jain, R., Johnson, R. E., Prakash, L., Prakash, S., & Aggarwal, A. K. (2010) · Structure · doi:10.1016/j.str.2010.08.019 · Cited by 33 · see citing works
Hang, B., Chenna, A., Guliaev, A. B., & Singer, B. (2003) · Mutation research. Fundamental and molecular mechanisms of mutagenesis · doi:10.1016/j.mrfmmm.2003.07.006 · Cited by 31 · see citing works
Nonpolar Isosteres of Damaged DNA Bases: Effective Mimicry of Mutagenic Properties of 8-Oxopurines
Taniguchi, Y., & Kool, E. T. (2007) · Journal of the American Chemical Society · doi:10.1021/ja071970q · Cited by 29 · see citing works
Choi, J., Lim, S., Eoff, R. L., & Guengerich, F. P. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.04.023 · Cited by 28 · see citing works
Kamble, P., Hall, K., Chandak, M. S., Tang, Q., & Çağlayan, M. (2021) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2021.100427 · Cited by 26 · see citing works
Wang, Y., & Tamar Schlick, A. (2007) · BMC Structural Biology · doi:10.1186/1472-6807-7-7 · Cited by 26 · see citing works
Maxwell, B. A., & Suo, Z. (2012) · Biochemistry · doi:10.1021/bi300246r · Cited by 25 · see citing works
Variable termination sites of DNA polymerases encountering a DNA–protein cross-link
Yudkina, A. V., Dvornikova, A. P., & Zharkov, D. O. (2018) · PLoS ONE · doi:10.1371/journal.pone.0198480 · Cited by 24 · see citing works
Efficient Primer Strand Extension beyond Oxadiazole Carboxamide Nucleobases
Adelfinskaya, O., Nashine, V. C., Bergstrom, D. E., & Davisson, V. J. (2005) · Journal of the American Chemical Society · doi:10.1021/ja054226j · Cited by 24 · see citing works
Enhanced cytarabine-induced killing in OGG1-deficient acute myeloid leukemia cells
Owen, N. M., Minko, I. G., Moellmer, S. A., Cammann, S. K., Lloyd, R. S., & McCullough, A. K. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2016833118 · Cited by 23 · see citing works
Processing oxidatively damaged bases at DNA strand breaks by APE1
Whitaker, A. M., Stark, W. J., & Freudenthal, B. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac695 · Cited by 23 · see citing works
Biochemical analysis of active site mutations of human polymerase η
Suarez, S. C., Beardslee, R. A., Toffton, S. M., & McCulloch, S. D. (2013) · Mutation research · doi:10.1016/j.mrfmmm.2013.03.001 · Cited by 22 · see citing works
Batra, V. K., Shock, D. D., Prasad, R., Beard, W. A., Hou, E. W., Pedersen, L. C., Sayer, J. M., Yagi, H., Kumar, S., Jerina, D. M., et al. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0605069103 · Cited by 23 · see citing works
Self-citationWang, Y., Reddy, S., Beard, W. A., Wilson, S. H., & Tamar Schlick, A. (2007) · Biophysical Journal · doi:10.1529/biophysj.106.092106 · Cited by 23 · see citing works
Self-citationDNA Lesion Alters Global Conformational Dynamics of Y-family DNA Polymerase during Catalysis
Maxwell, B. A., Xu, C., & Suo, Z. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.345835 · Cited by 22 · see citing works
Beckman, J. W., Wang, M., Blaha, G. M., Wang, J., & Konigsberg, W. H. (2010) · Biochemistry · doi:10.1021/bi100102s · Cited by 22 · see citing works
Tsutakawa, S. E., & Tainer, J. A. (2012) · Mechanisms of Ageing and Development · doi:10.1016/j.mad.2011.11.009 · Cited by 21 · see citing works
Impact of Ribonucleotide Backbone on Translesion Synthesis and Repair of 7,8-Dihydro-8-oxoguanine
Sassa, A., Çağlayan, M., Rodriguez, Y., Beard, W. A., Wilson, S. H., Nohmi, T., Honma, M., & Yasui, M. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.m116.738732 · Cited by 21 · see citing works
Self-citationInitiating base excision repair in chromatin
Kennedy, E. E., Caffrey, P. J., & Delaney, S. (2018) · DNA repair · doi:10.1016/j.dnarep.2018.08.011 · Cited by 21 · see citing works
Crystal structure analysis of DNA lesion repair and tolerance mechanisms
Schneider, S., Kath‐Schorr, S., & Carell, T. (2009) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2009.01.005 · Cited by 20 · see citing works
Hogg, M., Rudnicki, J., Midkiff, J., Reha-Krantz, L. J., Doublié, S., & Wallace, S. S. (2010) · Biochemistry · doi:10.1021/bi901488d · Cited by 20 · see citing works
Eckenroth, B. E., Fleming, A. M., Sweasy, J. B., Burrows, C. J., & Doublié, S. (2014) · Biochemistry · doi:10.1021/bi500270e · Cited by 19 · see citing works
Burak, M. J., Guja, K. E., & García–Díaz, M. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv760 · Cited by 19 · see citing works
Maddukuri, L., Ketkar, A. D., Eddy, S., Zafar, M. K., & Eoff, R. L. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku913 · Cited by 19 · see citing works
Yadav, S., Kumbhar, N., Jan, R., Roy, R., & Satsangi, P. G. (2018) · Environmental Geochemistry and Health · doi:10.1007/s10653-018-0199-4 · Cited by 19 · see citing works
Reynisson, J., & Steenken, S. (2005) · Journal of Molecular Structure THEOCHEM · doi:10.1016/j.theochem.2004.12.014 · Cited by 19 · see citing works
Obstacles and opportunities for base excision repair in chromatin
Biechele-Speziale, D., Sutton, T. B., & Delaney, S. (2022) · DNA repair · doi:10.1016/j.dnarep.2022.103345 · Cited by 17 · see citing works
Belousova, E. A., Rechkunova, N. I., & Lavrik, O. I. (2005) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2005.11.001 · Cited by 17 · see citing works
Oka, N. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki305 · Cited by 17 · see citing works
Chemical Synthesis of Oligonucleotides Containing Damaged Bases for Biological Studies
Iwai, S. (2006) · Nucleosides Nucleotides & Nucleic Acids · doi:10.1080/15257770600685826 · Cited by 17 · see citing works
Single-Molecule Investigation of Response to Oxidative DNA Damage by a Y-Family DNA Polymerase
Raper, A. T., Gadkari, V. V., Maxwell, B. A., & Suo, Z. (2016) · Biochemistry · doi:10.1021/acs.biochem.6b00166 · Cited by 16 · see citing works
Raper, A. T., Maxwell, B. A., & Suo, Z. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.166811 · Cited by 16 · see citing works
Jena, N. R., Bansal, M., & Mishra, P. (2016) · Physical Chemistry Chemical Physics · doi:10.1039/c6cp02212j · Cited by 16 · see citing works
Nagpal, S., & Nair, D. T. (2021) · Scientific Reports · doi:10.1038/s41598-021-83498-1 · Cited by 15 · see citing works
- Authors
- Krahn, J. M., Beard, W. A., Miller, H., Grollman, A. P., & Wilson, S. H.
- Affiliations
- National Institutes of Health (US)
- State University of New York (US)
- Corresponding author
- Wilson, Samuel H
- Venue
- Structure
- Publisher
- Elsevier BV
- Published
- 2003-01
- Volume
- 11
- Issue
- 1
- Pages
- 121-127
- ISSN
- 0969-2126 (ISSN-L)
- OpenAlex
- W2082963155
- Cited by
- 138
- References
- 46
- Citations by year
- 2025: 2 · 2022: 4 · 2021: 7 · 2020: 2 · 2019: 2 · 2018: 6 · 2017: 5 · 2016: 9 · 2015: 3 · 2014: 5 · 2013: 8 · 2012: 7
- FWCI
- 4.03
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Structure (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Cancer Institute (CA 47995, P01CA047995)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- DNA polymerase beta, oxidative DNA damage, polymerase active site, Watson-Crick hydrogen bonding, DNA replication, DNA repair synthesis, crystal structure
- MeSH terms
- Binding Sites, Deoxyadenine Nucleotides, DNA Damage, DNA Repair, DNA Replication, Guanine, Humans, Models, Molecular, Nucleic Acid Conformation, Molecular Structure, Protein Structure, Tertiary, DNA Polymerase beta
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