1nkb › Citations

Structures of mismatch replication errors observed in a DNA polymerase.

Johnson SJ, Beese LS
Cell 116 803-16 (2004)
Related entries: 1l3s, 1l3t, 1l3u, 1l3v, 1l5u, 1lv5, 1njw, 1njx, 1njy, 1njz, 1nk0, 1nk4, 1nk5, 1nk6, 1nk7, 1nk8, 1nk9, 1nkc, 1nke

Cited: 190 times
EuropePMC logo PMID: 15035983

Abstract

Accurate DNA replication is essential for genomic stability. One mechanism by which high-fidelity DNA polymerases maintain replication accuracy involves stalling of the polymerase in response to covalent incorporation of mismatched base pairs, thereby favoring subsequent mismatch excision. Some polymerases retain a "short-term memory" of replication errors, responding to mismatches up to four base pairs in from the primer terminus. Here we a present a structural characterization of all 12 possible mismatches captured at the growing primer terminus in the active site of a polymerase. Our observations suggest four mechanisms that lead to mismatch-induced stalling of the polymerase. Furthermore, we have observed the effects of extending a mismatch up to six base pairs from the primer terminus and find that long-range distortions in the DNA transmit the presence of the mismatch back to the enzyme active site, suggesting the structural basis for the short-term memory of replication errors.

Articles - 1nkb mentioned but not cited (1)

  1. Crystal Structures and Nuclear Magnetic Resonance Studies of the Apo Form of the c-MYC:MAX bHLHZip Complex Reveal a Helical Basic Region in the Absence of DNA. Sammak S, Hamdani N, Gorrec F, Allen MD, Freund SMV, Bycroft M, Zinzalla G. Biochemistry 58 3144-3154 (2019)


Reviews citing this publication (24)

  1. Structural insights into translational fidelity. Ogle JM, Ramakrishnan V. Annu Rev Biochem 74 129-177 (2005)
  2. The fidelity of DNA synthesis by eukaryotic replicative and translesion synthesis polymerases. McCulloch SD, Kunkel TA. Cell Res 18 148-161 (2008)
  3. DNA polymerases and human disease. Loeb LA, Monnat RJ. Nat Rev Genet 9 594-604 (2008)
  4. RNA polymerase fidelity and transcriptional proofreading. Sydow JF, Cramer P. Curr Opin Struct Biol 19 732-739 (2009)
  5. Entering the era of bacterial epigenomics with single molecule real time DNA sequencing. Davis BM, Chao MC, Chao MC, Waldor MK. Curr Opin Microbiol 16 192-198 (2013)
  6. DNA Replication-A Matter of Fidelity. Ganai RA, Johansson E. Mol Cell 62 745-755 (2016)
  7. DNA polymerase delta in DNA replication and genome maintenance. Prindle MJ, Loeb LA. Environ Mol Mutagen 53 666-682 (2012)
  8. Variations on a theme: eukaryotic Y-family DNA polymerases. Washington MT, Carlson KD, Freudenthal BD, Pryor JM. Biochim Biophys Acta 1804 1113-1123 (2010)
  9. Lesion processing: high-fidelity versus lesion-bypass DNA polymerases. Broyde S, Wang L, Rechkoblit O, Geacintov NE, Patel DJ. Trends Biochem Sci 33 209-219 (2008)
  10. Regulation of DNA repair fidelity by molecular checkpoints: "gates" in DNA polymerase beta's substrate selection. Radhakrishnan R, Arora K, Wang Y, Beard WA, Wilson SH, Schlick T. Biochemistry 45 15142-15156 (2006)
  11. The difluorotoluene debate--a decade later. Kool ET, Sintim HO. Chem Commun (Camb) 3665-3675 (2006)
  12. Multi-template polymerase chain reaction. Kalle E, Kubista M, Rensing C. Biomol Detect Quantif 2 11-29 (2014)
  13. Bunyaviridae RdRps: structure, motifs, and RNA synthesis machinery. Amroun A, Priet S, de Lamballerie X, Quérat G. Crit Rev Microbiol 43 753-778 (2017)
  14. RB69 DNA polymerase structure, kinetics, and fidelity. Xia S, Konigsberg WH. Biochemistry 53 2752-2767 (2014)
  15. NTP-driven translocation and regulation of downstream template opening by multi-subunit RNA polymerases. Burton ZF, Feig M, Gong XQ, Zhang C, Nedialkov YA, Xiong Y. Biochem Cell Biol 83 486-496 (2005)
  16. Inhibiting DNA Polymerases as a Therapeutic Intervention against Cancer. Berdis AJ. Front Mol Biosci 4 78 (2017)
  17. Antimutator variants of DNA polymerases. Herr AJ, Williams LN, Preston BD. Crit Rev Biochem Mol Biol 46 548-570 (2011)
  18. Mismatch repair system proteins in oral benign and malignant lesions. Amaral-Silva GK, Martins MD, Pontes HA, Fregnani ER, Lopes MA, Fonseca FP, Vargas PA. J Oral Pathol Med 46 241-245 (2017)
  19. Structure and function relationships in mammalian DNA polymerases. Hoitsma NM, Whitaker AM, Schaich MA, Smith MR, Fairlamb MS, Freudenthal BD. Cell Mol Life Sci 77 35-59 (2020)
  20. Translesion DNA synthesis: little fingers teach tolerance. Fleck O, Schär P. Curr Biol 14 R389-91 (2004)
  21. Bacterial DNA excision repair pathways. Wozniak KJ, Simmons LA. Nat Rev Microbiol 20 465-477 (2022)
  22. Targeting structural dynamics of the RNA-dependent RNA polymerase for anti-viral strategies. Boehr DD, Liu X, Yang X. Curr Opin Virol 9 194-200 (2014)
  23. A rescue act: Translesion DNA synthesis past N(2) -deoxyguanosine adducts. Nair DT, Kottur J, Sharma R. IUBMB Life 67 564-574 (2015)
  24. Conformational Dynamics of DNA Polymerases Revealed at the Single-Molecule Level. Millar DP. Front Mol Biosci 9 826593 (2022)

Articles citing this publication (165)

  1. Structure of the human MutSalpha DNA lesion recognition complex. Warren JJ, Pohlhaus TJ, Changela A, Iyer RR, Modrich PL, Beese LS. Mol Cell 26 579-592 (2007)
  2. Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase. Hsu GW, Ober M, Carell T, Beese LS. Nature 431 217-221 (2004)
  3. Structural basis of high-fidelity DNA synthesis by yeast DNA polymerase delta. Swan MK, Johnson RE, Prakash L, Prakash S, Aggarwal AK. Nat Struct Mol Biol 16 979-986 (2009)
  4. A new paradigm for DNA polymerase specificity. Tsai YC, Johnson KA. Biochemistry 45 9675-9687 (2006)
  5. Human DNA polymerase kappa encircles DNA: implications for mismatch extension and lesion bypass. Lone S, Townson SA, Uljon SN, Johnson RE, Brahma A, Nair DT, Prakash S, Prakash L, Aggarwal AK. Mol Cell 25 601-614 (2007)
  6. The effect of primer-template mismatches on the detection and quantification of nucleic acids using the 5' nuclease assay. Stadhouders R, Pas SD, Anber J, Voermans J, Mes TH, Schutten M. J Mol Diagn 12 109-117 (2010)
  7. Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA. Sydow JF, Brueckner F, Cheung AC, Damsma GE, Dengl S, Lehmann E, Vassylyev D, Cramer P. Mol Cell 34 710-721 (2009)
  8. Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis. Vaisman A, Ling H, Woodgate R, Yang W. EMBO J 24 2957-2967 (2005)
  9. Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis. Wang W, Hellinga HW, Beese LS. Proc Natl Acad Sci U S A 108 17644-17648 (2011)
  10. Visualizing transient Watson-Crick-like mispairs in DNA and RNA duplexes. Kimsey IJ, Petzold K, Sathyamoorthy B, Stein ZW, Al-Hashimi HM. Nature 519 315-320 (2015)
  11. Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation. Batra VK, Beard WA, Shock DD, Pedersen LC, Wilson SH. Mol Cell 30 315-324 (2008)
  12. Automated electron-density sampling reveals widespread conformational polymorphism in proteins. Lang PT, Ng HL, Fraser JS, Corn JE, Echols N, Sales M, Holton JM, Alber T. Protein Sci 19 1420-1431 (2010)
  13. Stepwise translocation of Dpo4 polymerase during error-free bypass of an oxoG lesion. Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde S, Geacintov NE, Patel DJ. PLoS Biol 4 e11 (2006)
  14. Replication infidelity via a mismatch with Watson-Crick geometry. Bebenek K, Pedersen LC, Kunkel TA. Proc Natl Acad Sci U S A 108 1862-1867 (2011)
  15. Probing the active site tightness of DNA polymerase in subangstrom increments. Kim TW, Delaney JC, Essigmann JM, Kool ET. Proc Natl Acad Sci U S A 102 15803-15808 (2005)
  16. Structural basis of viral RNA-dependent RNA polymerase catalysis and translocation. Shu B, Gong P. Proc Natl Acad Sci U S A 113 E4005-14 (2016)
  17. The structural basis for the mutagenicity of O(6)-methyl-guanine lesions. Warren JJ, Forsberg LJ, Beese LS. Proc Natl Acad Sci U S A 103 19701-19706 (2006)
  18. Thinking Outside the Triangle: Replication Fidelity of the Largest RNA Viruses. Smith EC, Sexton NR, Denison MR. Annu Rev Virol 1 111-132 (2014)
  19. Adaptive ligand binding by the purine riboswitch in the recognition of guanine and adenine analogs. Gilbert SD, Reyes FE, Edwards AL, Batey RT. Structure 17 857-868 (2009)
  20. Coupling of N7-methyltransferase and 3'-5' exoribonuclease with SARS-CoV-2 polymerase reveals mechanisms for capping and proofreading. Yan L, Yang Y, Li M, Zhang Y, Zheng L, Ge J, Huang YC, Liu Z, Wang T, Gao S, Zhang R, Huang YY, Guddat LW, Gao Y, Rao Z, Lou Z. Cell 184 3474-3485.e11 (2021)
  21. Proofreading dynamics of a processive DNA polymerase. Ibarra B, Chemla YR, Plyasunov S, Smith SB, Lázaro JM, Salas M, Bustamante C. EMBO J 28 2794-2802 (2009)
  22. Structural analysis of strand misalignment during DNA synthesis by a human DNA polymerase. Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC, Kunkel TA. Cell 124 331-342 (2006)
  23. Directed evolution of DNA polymerase, RNA polymerase and reverse transcriptase activity in a single polypeptide. Ong JL, Loakes D, Jaroslawski S, Too K, Holliger P. J Mol Biol 361 537-550 (2006)
  24. Structural insights into DNA polymerase beta deterrents for misincorporation support an induced-fit mechanism for fidelity. Krahn JM, Beard WA, Wilson SH. Structure 12 1823-1832 (2004)
  25. Structure of PolC reveals unique DNA binding and fidelity determinants. Evans RJ, Davies DR, Bullard JM, Christensen J, Green LS, Guiles JW, Pata JD, Ribble WK, Janjic N, Jarvis TC. Proc Natl Acad Sci U S A 105 20695-20700 (2008)
  26. Motif D of viral RNA-dependent RNA polymerases determines efficiency and fidelity of nucleotide addition. Yang X, Smidansky ED, Maksimchuk KR, Lum D, Welch JL, Arnold JJ, Cameron CE, Boehr DD. Structure 20 1519-1527 (2012)
  27. Multiple functions of DNA polymerases. Garcia-Diaz M, Bebenek K. CRC Crit Rev Plant Sci 26 105-122 (2007)
  28. Direct detection and sequencing of damaged DNA bases. Clark TA, Spittle KE, Turner SW, Korlach J. Genome Integr 2 10 (2011)
  29. A role for yeast and human translesion synthesis DNA polymerases in promoting replication through 3-methyl adenine. Johnson RE, Yu SL, Prakash S, Prakash L. Mol Cell Biol 27 7198-7205 (2007)
  30. The mechanism of the translocation step in DNA replication by DNA polymerase I: a computer simulation analysis. Golosov AA, Warren JJ, Beese LS, Karplus M. Structure 18 83-93 (2010)
  31. Base modifications affecting RNA polymerase and reverse transcriptase fidelity. Potapov V, Fu X, Dai N, Corrêa IR, Tanner NA, Ong JL. Nucleic Acids Res 46 5753-5763 (2018)
  32. Enzymatic synthesis of DNA on glycerol nucleic acid templates without stable duplex formation between product and template. Tsai CH, Chen J, Szostak JW. Proc Natl Acad Sci U S A 104 14598-14603 (2007)
  33. Fidelity discrimination in DNA polymerase beta: differing closing profiles for a mismatched (G:A) versus matched (G:C) base pair. Radhakrishnan R, Schlick T. J Am Chem Soc 127 13245-13252 (2005)
  34. Replicative DNA polymerase δ but not ε proofreads errors in Cis and in Trans. Flood CL, Rodriguez GP, Bao G, Shockley AH, Kow YW, Crouse GF. PLoS Genet 11 e1005049 (2015)
  35. Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides. Wang W, Wu EY, Hellinga HW, Beese LS. J Biol Chem 287 28215-28226 (2012)
  36. Selectivity and proofreading both contribute significantly to the fidelity of RNA polymerase III transcription. Alic N, Ayoub N, Landrieux E, Favry E, Baudouin-Cornu P, Riva M, Carles C. Proc Natl Acad Sci U S A 104 10400-10405 (2007)
  37. Insights into base selectivity from the 1.8 Å resolution structure of an RB69 DNA polymerase ternary complex. Wang M, Xia S, Blaha G, Steitz TA, Konigsberg WH, Wang J. Biochemistry 50 581-590 (2011)
  38. A unique error signature for human DNA polymerase nu. Arana ME, Takata K, Garcia-Diaz M, Wood RD, Kunkel TA. DNA Repair (Amst) 6 213-223 (2007)
  39. Does the tautomeric status of the adenine bases change upon the dissociation of the A*·A(syn) Topal-Fresco DNA mismatch? A combined QM and QTAIM atomistic insight. Brovarets' OO, Zhurakivsky RO, Hovorun DM. Phys Chem Chem Phys 16 3715-3725 (2014)
  40. Remarkable sensitivity to DNA base shape in the DNA polymerase active site. Sintim HO, Kool ET. Angew Chem Int Ed Engl 45 1974-1979 (2006)
  41. Vaccine-derived mutation in motif D of poliovirus RNA-dependent RNA polymerase lowers nucleotide incorporation fidelity. Liu X, Yang X, Lee CA, Moustafa IM, Smidansky ED, Lum D, Arnold JJ, Cameron CE, Boehr DD. J Biol Chem 288 32753-32765 (2013)
  42. A DinB variant reveals diverse physiological consequences of incomplete TLS extension by a Y-family DNA polymerase. Jarosz DF, Cohen SE, Delaney JC, Essigmann JM, Walker GC. Proc Natl Acad Sci U S A 106 21137-21142 (2009)
  43. Proofreading exonuclease activity of human DNA polymerase delta and its effects on lesion-bypass DNA synthesis. Fazlieva R, Spittle CS, Morrissey D, Hayashi H, Yan H, Matsumoto Y. Nucleic Acids Res 37 2854-2866 (2009)
  44. DNA polymerase catalysis in the absence of Watson-Crick hydrogen bonds: analysis by single-turnover kinetics. Potapova O, Chan C, DeLucia AM, Helquist SA, Kool ET, Grindley ND, Joyce CM. Biochemistry 45 890-898 (2006)
  45. Exploiting extension bias in polymerase chain reaction to improve primer specificity in ensembles of nearly identical DNA templates. Wright ES, Yilmaz LS, Ram S, Gasser JM, Harrington GW, Noguera DR. Environ Microbiol 16 1354-1365 (2014)
  46. Promiscuous mismatch extension by human DNA polymerase lambda. Picher AJ, García-Díaz M, Bebenek K, Pedersen LC, Kunkel TA, Blanco L. Nucleic Acids Res 34 3259-3266 (2006)
  47. Template misalignment in multisubunit RNA polymerases and transcription fidelity. Kashkina E, Anikin M, Brueckner F, Pomerantz RT, McAllister WT, Cramer P, Temiakov D. Mol Cell 24 257-266 (2006)
  48. Coarse-grained modeling of allosteric regulation in protein receptors. Balabin IA, Yang W, Beratan DN. Proc Natl Acad Sci U S A 106 14253-14258 (2009)
  49. DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase. Xia S, Wang J, Konigsberg WH. J Am Chem Soc 135 193-202 (2013)
  50. Mechano-chemical kinetics of DNA replication: identification of the translocation step of a replicative DNA polymerase. Morin JA, Cao FJ, Lázaro JM, Arias-Gonzalez JR, Valpuesta JM, Carrascosa JL, Salas M, Ibarra B. Nucleic Acids Res 43 3643-3652 (2015)
  51. Mutability of DNA polymerase I: implications for the creation of mutant DNA polymerases. Loh E, Loeb LA. DNA Repair (Amst) 4 1390-1398 (2005)
  52. Nucleotide-induced DNA polymerase active site motions accommodating a mutagenic DNA intermediate. Batra VK, Beard WA, Shock DD, Pedersen LC, Wilson SH. Structure 13 1225-1233 (2005)
  53. Ambivalent incorporation of the fluorescent cytosine analogues tC and tCo by human DNA polymerase alpha and Klenow fragment. Stengel G, Purse BW, Wilhelmsson LM, Urban M, Kuchta RD. Biochemistry 48 7547-7555 (2009)
  54. Atomistic understanding of the C·T mismatched DNA base pair tautomerization via the DPT: QM and QTAIM computational approaches. Brovarets' OO, Hovorun DM. J Comput Chem 34 2577-2590 (2013)
  55. A mechanism of nucleotide misincorporation during transcription due to template-strand misalignment. Pomerantz RT, Temiakov D, Anikin M, Vassylyev DG, McAllister WT. Mol Cell 24 245-255 (2006)
  56. DNA bending propensity in the presence of base mismatches: implications for DNA repair. Sharma M, Predeus AV, Mukherjee S, Feig M. J Phys Chem B 117 6194-6205 (2013)
  57. The L561A substitution in the nascent base-pair binding pocket of RB69 DNA polymerase reduces base discrimination. Zhang H, Rhee C, Bebenek A, Drake JW, Wang J, Konigsberg W. Biochemistry 45 2211-2220 (2006)
  58. Unexpected non-Hoogsteen-based mutagenicity mechanism of FaPy-DNA lesions. Gehrke TH, Lischke U, Gasteiger KL, Schneider S, Arnold S, Müller HC, Stephenson DS, Zipse H, Carell T. Nat Chem Biol 9 455-461 (2013)
  59. Impact of conformational heterogeneity of OxoG lesions and their pairing partners on bypass fidelity by Y family polymerases. Rechkoblit O, Malinina L, Cheng Y, Geacintov NE, Broyde S, Patel DJ. Structure 17 725-736 (2009)
  60. Loop 1 modulates the fidelity of DNA polymerase lambda. Bebenek K, Garcia-Diaz M, Zhou RZ, Povirk LF, Kunkel TA. Nucleic Acids Res 38 5419-5431 (2010)
  61. RB69 DNA polymerase mutants with expanded nascent base-pair-binding pockets are highly efficient but have reduced base selectivity. Zhang H, Beckman J, Wang J, Konigsberg W. Biochemistry 48 6940-6950 (2009)
  62. Self-correcting mismatches during high-fidelity DNA replication. Fernandez-Leiro R, Conrad J, Yang JC, Freund SM, Scheres SH, Lamers MH. Nat Struct Mol Biol 24 140-143 (2017)
  63. Mechanism of error-free and semitargeted mutagenic bypass of an aromatic amine lesion by Y-family polymerase Dpo4. Rechkoblit O, Kolbanovskiy A, Malinina L, Geacintov NE, Broyde S, Patel DJ. Nat Struct Mol Biol 17 379-388 (2010)
  64. Mismatched and matched dNTP incorporation by DNA polymerase beta proceed via analogous kinetic pathways. Roettger MP, Bakhtina M, Tsai MD. Biochemistry 47 9718-9727 (2008)
  65. How does the long G·G* Watson-Crick DNA base mispair comprising keto and enol tautomers of the guanine tautomerise? The results of a QM/QTAIM investigation. Brovarets' OO, Hovorun DM. Phys Chem Chem Phys 16 15886-15899 (2014)
  66. Switching between polymerase and exonuclease sites in DNA polymerase ε. Ganai RA, Bylund GO, Johansson E. Nucleic Acids Res 43 932-942 (2015)
  67. Synthetic polymers and their potential as genetic materials. Pinheiro VB, Loakes D, Holliger P. Bioessays 35 113-122 (2013)
  68. Directed DNA polymerase evolution: effects of mutations in motif C on the mismatch-extension selectivity of thermus aquaticus DNA polymerase. Strerath M, Gloeckner C, Liu D, Schnur A, Marx A. Chembiochem 8 395-401 (2007)
  69. Regulation of hetDNA Length during Mitotic Double-Strand Break Repair in Yeast. Guo X, Hum YF, Lehner K, Jinks-Robertson S. Mol Cell 67 539-549.e4 (2017)
  70. Structural and Kinetic Studies of the Effect of Guanine N7 Alkylation and Metal Cofactors on DNA Replication. Kou Y, Koag MC, Lee S. Biochemistry 57 5105-5116 (2018)
  71. Efforts towards expansion of the genetic alphabet: pyridone and methyl pyridone nucleobases. Leconte AM, Matsuda S, Hwang GT, Romesberg FE. Angew Chem Int Ed Engl 45 4326-4329 (2006)
  72. Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism. Batra VK, Beard WA, Pedersen LC, Wilson SH. Structure 24 1863-1875 (2016)
  73. Transition state in DNA polymerase β catalysis: rate-limiting chemistry altered by base-pair configuration. Oertell K, Chamberlain BT, Wu Y, Ferri E, Kashemirov BA, Beard WA, Wilson SH, McKenna CE, Goodman MF. Biochemistry 53 1842-1848 (2014)
  74. Crystal structures and repair studies reveal the identity and the base-pairing properties of the UV-induced spore photoproduct DNA lesion. Heil K, Kneuttinger AC, Schneider S, Lischke U, Carell T. Chemistry 17 9651-9657 (2011)
  75. Examination of the long-range effects of aminofluorene-induced conformational heterogeneity and its relevance to the mechanism of translesional DNA synthesis. Meneni S, Liang F, Cho BP. J Mol Biol 366 1387-1400 (2007)
  76. pH-Dependent mismatch discrimination of oligonucleotide duplexes containing 2'-deoxytubercidin and 2- or 7-substituted derivatives: protonated base pairs formed between 7-deazapurines and cytosine. Peng X, Li H, Seela F. Nucleic Acids Res 34 5987-6000 (2006)
  77. DNA polymerase from temperate phage Bam35 is endowed with processive polymerization and abasic sites translesion synthesis capacity. Berjón-Otero M, Villar L, de Vega M, Salas M, Redrejo-Rodríguez M. Proc Natl Acad Sci U S A 112 E3476-84 (2015)
  78. Mismatched base-pair simulations for ASFV Pol X/DNA complexes help interpret frequent G*G misincorporation. Sampoli Benítez BA, Arora K, Balistreri L, Schlick T. J Mol Biol 384 1086-1097 (2008)
  79. Mispairs with Watson-Crick base-pair geometry observed in ternary complexes of an RB69 DNA polymerase variant. Xia S, Konigsberg WH. Protein Sci 23 508-513 (2014)
  80. MsDpo4-a DinB Homolog from Mycobacterium smegmatis-Is an Error-Prone DNA Polymerase That Can Promote G:T and T:G Mismatches. Sharma A, Nair DT. J Nucleic Acids 2012 285481 (2012)
  81. Single gold-bridged nanoprobes for identification of single point DNA mutations. Ma X, Song S, Kim S, Kwon MS, Lee H, Park W, Sim SJ. Nat Commun 10 836 (2019)
  82. Switching between Exonucleolysis and Replication by T7 DNA Polymerase Ensures High Fidelity. Hoekstra TP, Depken M, Lin SN, Cabanas-Danés J, Gross P, Dame RT, Peterman EJG, Wuite GJL. Biophys J 112 575-583 (2017)
  83. A highly conserved Tyrosine residue of family B DNA polymerases contributes to dictate translesion synthesis past 8-oxo-7,8-dihydro-2'-deoxyguanosine. de Vega M, Salas M. Nucleic Acids Res 35 5096-5107 (2007)
  84. Hydrophobic amino acid and single-atom substitutions increase DNA polymerase selectivity. Rudinger NZ, Kranaster R, Marx A. Chem Biol 14 185-194 (2007)
  85. Probing minor groove hydrogen bonding interactions between RB69 DNA polymerase and DNA. Xia S, Christian TD, Wang J, Konigsberg WH. Biochemistry 51 4343-4353 (2012)
  86. The miscoding potential of 5-hydroxycytosine arises due to template instability in the replicative polymerase active site. Zahn KE, Averill A, Wallace SS, Doublié S. Biochemistry 50 10350-10358 (2011)
  87. Crystal structures of a natural DNA polymerase that functions as an XNA reverse transcriptase. Jackson LN, Chim N, Shi C, Chaput JC. Nucleic Acids Res 47 6973-6983 (2019)
  88. Differentiation of Salmonella strains from the SARA, SARB and SARC reference collections by using three genes PCR-RFLP and the 2100 Agilent Bioanalyzer. Soler-García AA, De Jesús AJ, Taylor K, Brown EW. Front Microbiol 5 417 (2014)
  89. Effects of mercury(II) on structural properties, electronic structure and UV absorption spectra of a duplex containing thymine-mercury(II)-thymine nucleobase pairs. Miyachi H, Matsui T, Shigeta Y, Hirao K. Phys Chem Chem Phys 12 909-917 (2010)
  90. Hydrogen-bonding capability of a templating difluorotoluene nucleotide residue in an RB69 DNA polymerase ternary complex. Xia S, Konigsberg WH, Wang J. J Am Chem Soc 133 10003-10005 (2011)
  91. Structural Insights into the Post-Chemistry Steps of Nucleotide Incorporation Catalyzed by a DNA Polymerase. Reed AJ, Vyas R, Raper AT, Suo Z. J Am Chem Soc 139 465-471 (2017)
  92. Mismatched dNTP incorporation by DNA polymerase beta does not proceed via globally different conformational pathways. Tang KH, Niebuhr M, Tung CS, Chan HC, Chou CC, Tsai MD. Nucleic Acids Res 36 2948-2957 (2008)
  93. Following an environmental carcinogen N2-dG adduct through replication: elucidating blockage and bypass in a high-fidelity DNA polymerase. Xu P, Oum L, Beese LS, Geacintov NE, Broyde S. Nucleic Acids Res 35 4275-4288 (2007)
  94. Triphosphate Reorientation of the Incoming Nucleotide as a Fidelity Checkpoint in Viral RNA-dependent RNA Polymerases. Yang X, Liu X, Musser DM, Moustafa IM, Arnold JJ, Cameron CE, Boehr DD. J Biol Chem 292 3810-3826 (2017)
  95. Visualizing sequence-governed nucleotide selectivities and mutagenic consequences through a replicative cycle: processing of a bulky carcinogen N2-dG lesion in a Y-family DNA polymerase. Xu P, Oum L, Lee YC, Geacintov NE, Broyde S. Biochemistry 48 4677-4690 (2009)
  96. Biomolecular detection with a thin membrane transducer. Cha M, Shin J, Kim JH, Kim I, Choi J, Lee N, Kim BG, Lee J. Lab Chip 8 932-937 (2008)
  97. Crystal structures of DNA polymerase I capture novel intermediates in the DNA synthesis pathway. Chim N, Jackson LN, Trinh AM, Chaput JC. Elife 7 e40444 (2018)
  98. Discrimination against the cytosine analog tC by Escherichia coli DNA polymerase IV DinB. Walsh JM, Bouamaied I, Brown T, Wilhelmsson LM, Beuning PJ. J Mol Biol 409 89-100 (2011)
  99. Discrimination between right and wrong purine dNTPs by DNA polymerase I from Bacillus stearothermophilus. Trostler M, Delier A, Beckman J, Urban M, Patro JN, Spratt TE, Beese LS, Kuchta RD. Biochemistry 48 4633-4641 (2009)
  100. Entropy involved in fidelity of DNA replication. Arias-Gonzalez JR. PLoS One 7 e42272 (2012)
  101. Formation of purine-purine mispairs by Sulfolobus solfataricus DNA polymerase IV. DeCarlo L, Gowda AS, Suo Z, Spratt TE. Biochemistry 47 8157-8164 (2008)
  102. Identification of a new motif required for the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I (Klenow fragment): the RRRY motif is necessary for the binding of single-stranded DNA substrate and the template strand of the mismatched duplex. Kukreti P, Singh K, Ketkar A, Modak MJ. J Biol Chem 283 17979-17990 (2008)
  103. Prediction of RNA multiloop and pseudoknot conformations from a lattice-based, coarse-grain tertiary structure model. Jost D, Everaers R. J Chem Phys 132 095101 (2010)
  104. Role of 6-Mercaptopurine in the potential therapeutic targets DNA base pairs and G-quadruplex DNA: insights from quantum chemical and molecular dynamics simulations. Radhika R, Shankar R, Vijayakumar S, Kolandaivel P. J Biomol Struct Dyn 36 1369-1401 (2018)
  105. Human DNA Polymerase ν Catalyzes Correct and Incorrect DNA Synthesis with High Catalytic Efficiency. Gowda AS, Moldovan GL, Spratt TE. J Biol Chem 290 16292-16303 (2015)
  106. Kinetic analysis of the unique error signature of human DNA polymerase ν. Arana ME, Potapova O, Kunkel TA, Joyce CM. Biochemistry 50 10126-10135 (2011)
  107. Polymorphic G:G mismatches act as hotspots for inducing right-handed Z DNA by DNA intercalation. Satange R, Chuang CY, Neidle S, Hou MH. Nucleic Acids Res 47 8899-8912 (2019)
  108. Probing DNA Base-Dependent Leaving Group Kinetic Effects on the DNA Polymerase Transition State. Oertell K, Kashemirov BA, Negahbani A, Minard C, Haratipour P, Alnajjar KS, Sweasy JB, Batra VK, Beard WA, Wilson SH, McKenna CE, Goodman MF. Biochemistry 57 3925-3933 (2018)
  109. Rational Control of Poliovirus RNA-Dependent RNA Polymerase Fidelity by Modulating Motif-D Loop Conformational Dynamics. Shi J, Perryman JM, Yang X, Liu X, Musser DM, Boehr AK, Moustafa IM, Arnold JJ, Cameron CE, Boehr DD. Biochemistry 58 3735-3743 (2019)
  110. Sequence determination of nucleic acids containing 5-methylisocytosine and isoguanine: identification and insight into polymerase replication of the non-natural nucleobases. Ahle JD, Barr S, Chin AM, Battersby TR. Nucleic Acids Res 33 3176-3184 (2005)
  111. Two-dimensional IR spectroscopy of the anti-HIV agent KP1212 reveals protonated and neutral tautomers that influence pH-dependent mutagenicity. Peng CS, Fedeles BI, Singh V, Li D, Amariuta T, Essigmann JM, Tokmakoff A. Proc Natl Acad Sci U S A 112 3229-3234 (2015)
  112. 3-Methyl-3-deazaadenine, a stable isostere of N3-methyl-adenine, is efficiently bypassed by replication in vivo and by transcription in vitro. Monti P, Broxson C, Inga A, Wang RW, Menichini P, Tornaletti S, Gold B, Fronza G. DNA Repair (Amst) 10 861-868 (2011)
  113. DNA replication studies of N-nitroso compound-induced O 6-alkyl-2'-deoxyguanosine lesions in Escherichia coli. Wang P, Leng J, Wang Y. J Biol Chem 294 3899-3908 (2019)
  114. Enzymatic polymerization of phosphonate nucleosides. Renders M, Lievrouw R, Krecmerová M, Holý A, Herdewijn P. Chembiochem 9 2883-2888 (2008)
  115. Impact of SARS-CoV-2 Variants on the Analytical Sensitivity of rRT-PCR Assays. Chen Y, Han Y, Yang J, Ma Y, Li J, Zhang R. J Clin Microbiol 60 e0237421 (2022)
  116. Insights into the effect of minor groove interactions and metal cofactors on mutagenic replication by human DNA polymerase β. Koag MC, Lee S. Biochem J 475 571-585 (2018)
  117. Substitution of a residue contacting the triphosphate moiety of the incoming nucleotide increases the fidelity of yeast DNA polymerase zeta. Howell CA, Kondratick CM, Washington MT. Nucleic Acids Res 36 1731-1740 (2008)
  118. Thermodynamics of translesion synthesis across a major DNA adduct of antitumor oxaliplatin: differential scanning calorimetric study. Florian J, Brabec V. Chemistry 18 1634-1639 (2012)
  119. Assessment of genetic mutation frequency induced by oxidative stress in Trypanosoma cruzi. Torres-Silva CF, Repolês BM, Ornelas HO, Macedo AM, Franco GR, Junho Pena SD, Tahara EB, Machado CR. Genet Mol Biol 41 466-474 (2018)
  120. Fluorous base-pairing effects in a DNA polymerase active site. Lai JS, Kool ET. Chemistry 11 2966-2971 (2005)
  121. The influence of base pair tautomerism on single point mutations in aqueous DNA. Gheorghiu A, Coveney PV, Arabi AA. Interface Focus 10 20190120 (2020)
  122. Computational delineation of the catalytic step of a high-fidelity DNA polymerase. Venkatramani R, Radhakrishnan R. Protein Sci 19 815-825 (2010)
  123. Cryo-EM structure of translesion DNA synthesis polymerase ζ with a base pair mismatch. Malik R, Johnson RE, Prakash L, Prakash S, Ubarretxena-Belandia I, Aggarwal AK. Nat Commun 13 1050 (2022)
  124. DNA Polymerase ν Rapidly Bypasses O6-Methyl-dG but Not O6-[4-(3-Pyridyl)-4-oxobutyl-dG and O2-Alkyl-dTs. Gowda AS, Spratt TE. Chem Res Toxicol 29 1894-1900 (2016)
  125. DNA ligase I fidelity mediates the mutagenic ligation of pol β oxidized and mismatch nucleotide insertion products in base excision repair. Kamble P, Hall K, Chandak M, Tang Q, Çağlayan M. J Biol Chem 296 100427 (2021)
  126. Implications for damage recognition during Dpo4-mediated mutagenic bypass of m1G and m3C lesions. Rechkoblit O, Delaney JC, Essigmann JM, Patel DJ. Structure 19 821-832 (2011)
  127. In crystallo observation of three metal ion promoted DNA polymerase misincorporation. Chang C, Lee Luo C, Gao Y. Nat Commun 13 2346 (2022)
  128. Information management in DNA replication modeled by directional, stochastic chains with memory. Arias-Gonzalez JR. J Chem Phys 145 185103 (2016)
  129. Molecular mechanism of substrate recognition and specificity of tRNAHis guanylyltransferase during nucleotide addition in the 3'-5' direction. Nakamura A, Wang D, Komatsu Y. RNA 24 1583-1593 (2018)
  130. Probing conformational transitions towards mutagenic Watson-Crick-like G·T mismatches using off-resonance sugar carbon R1ρ relaxation dispersion. Rangadurai A, Szymanski ES, Kimsey I, Shi H, Al-Hashimi HM. J Biomol NMR 74 457-471 (2020)
  131. Relationship between conformational changes in pol lambda's active site upon binding incorrect nucleotides and mismatch incorporation rates. Foley MC, Schlick T. J Phys Chem B 113 13035-13047 (2009)
  132. Rolling Circle Transcription-Amplified Hierarchically Structured Organic-Inorganic Hybrid RNA Flowers for Enzyme Immobilization. Wang Y, Kim E, Lin Y, Lin Y, Kim N, Kit-Anan W, Gopal S, Agarwal S, Howes PD, Stevens MM. ACS Appl Mater Interfaces 11 22932-22940 (2019)
  133. The roles of polymerases ν and θ in replicative bypass of O 6- and N 2-alkyl-2'-deoxyguanosine lesions in human cells. Du H, Wang P, Wu J, He X, Wang Y. J Biol Chem 295 4556-4562 (2020)
  134. A DNA-centered explanation of the DNA polymerase translocation mechanism. Arias-Gonzalez JR. Sci Rep 7 7566 (2017)
  135. Achieving fidelity in homologous recombination despite extreme complexity: informed decisions by molecular profiling. Rambo RP, Williams GJ, Tainer JA. Mol Cell 40 347-348 (2010)
  136. Conformational dynamics during misincorporation and mismatch extension defined using a DNA polymerase with a fluorescent artificial amino acid. Dangerfield TL, Kirmizialtin S, Johnson KA. J Biol Chem 298 101451 (2022)
  137. Effect of oxidatively damaged DNA on the active site preorganization during nucleotide incorporation in a high fidelity polymerase from Bacillus stearothermophilus. Venkatramani R, Radhakrishnan R. Proteins 71 1360-1372 (2008)
  138. Structural basis for promutagenicity of 8-halogenated guanine. Koag MC, Min K, Lee S. J Biol Chem 289 6289-6298 (2014)
  139. The effect of different divalent cations on the kinetics and fidelity of Bacillus stearothermophilus DNA polymerase. Vashishtha AK, Konigsberg WH. AIMS Biophys 5 125-143 (2018)
  140. Bending of DNA duplexes with mutation motifs. Růžička M, Souček P, Kulhánek P, Radová L, Fajkusová L, Réblová K. DNA Res 26 341-352 (2019)
  141. Dissecting and tuning primer editing by proofreading polymerases. Gohl DM, Auch B, Certano A, LeFrançois B, Bouevitch A, Doukhanine E, Fragel C, Macklaim J, Hollister E, Garbe J, Beckman KB. Nucleic Acids Res 49 e87 (2021)
  142. Effect of induced dNTP pool imbalance on HIV-1 reverse transcription in macrophages. Shepard C, Xu J, Holler J, Kim DH, Mansky LM, Schinazi RF, Kim B. Retrovirology 16 29 (2019)
  143. Evaluation of a real-time RT-PCR panel for detection of SARS-CoV-2 in bat guano. Anis E, Turner G, Ellis JC, Di Salvo A, Barnard A, Carroll S, Murphy L. J Vet Diagn Invest 33 331-335 (2021)
  144. Comment Flexibility promotes fidelity. Perry JJ, Hitomi K, Tainer JA. Structure 17 633-634 (2009)
  145. Mechanism of nucleotide discrimination by the translesion synthesis polymerase Rev1. Weaver TM, Click TH, Khoang TH, Todd Washington M, Agarwal PK, Freudenthal BD. Nat Commun 13 2876 (2022)
  146. Networked Communication between Polymerase and Exonuclease Active Sites in Human Mitochondrial DNA Polymerase. Sowers ML, Anderson APP, Wrabl JO, Yin YW. J Am Chem Soc 141 10821-10829 (2019)
  147. Within and Beyond the Nucleotide Addition Cycle of Viral RNA-dependent RNA Polymerases. Gong P. Front Mol Biosci 8 822218 (2021)
  148. A possible mechanism of processive nucleotide and repeat additions by the telomerase. Xie P. Biosystems 97 168-178 (2009)
  149. Covalent modification of primers improves PCR amplification specificity and yield. Schoenbrunner NJ, Gupta AP, Young KKY, Will SG. Biol Methods Protoc 2 bpx011 (2017)
  150. Steric constraints dependent on nucleobase pair orientation vary in different DNA polymerase active sites. Streckenbach F, Rangam G, Möller HM, Marx A. Chembiochem 10 1630-1633 (2009)
  151. The DNA polymerase of bacteriophage YerA41 replicates its T-modified DNA in a primer-independent manner. Gomez-Raya-Vilanova MV, Leskinen K, Bhattacharjee A, Virta P, Rosenqvist P, Smith JLR, Bayfield OW, Homberger C, Kerrinnes T, Vogel J, Pajunen MI, Skurnik M. Nucleic Acids Res 50 3985-3997 (2022)
  152. Unfaithful DNA polymerase caught in the act. Jiricny J. Mol Cell 13 768-769 (2004)
  153. Active Site Interactions Impact Phosphoryl Transfer during Replication of Damaged and Undamaged DNA by Escherichia coli DNA Polymerase I. Prakasha Gowda AS, Spratt TE. Chem Res Toxicol 30 2033-2043 (2017)
  154. An end for mismatch repair. Crouse GF. Proc Natl Acad Sci U S A 107 20851-20852 (2010)
  155. News Chemical biology: a broader take on DNA. Leconte AM, Romesberg FE. Nature 444 553-555 (2006)
  156. Crystal structure of DNA polymerase I from Thermus phage G20c. Ahlqvist J, Linares-Pastén JA, Jasilionis A, Welin M, Håkansson M, Svensson LA, Wang L, Watzlawick H, Ævarsson A, Friðjónsson ÓH, Hreggviðsson GÓ, Ketelsen Striberny B, Glomsaker E, Lanes O, Al-Karadaghi S, Nordberg Karlsson E. Acta Crystallogr D Struct Biol 78 1384-1398 (2022)
  157. Enzymatic Incorporation of Modified Purine Nucleotides in DNA. Abu El Asrar R, Margamuljana L, Abramov M, Bande O, Agnello S, Jang M, Herdewijn P. Chembiochem 18 2408-2415 (2017)
  158. Improving the Accuracy of Single-Nucleotide Variant Diagnosis Using On-Off Discriminating Primers. Shin J, Jung C. Biosensors (Basel) 13 380 (2023)
  159. In crystallo observation of active site dynamics and transient metal ion binding within DNA polymerases. Chang C, Zhou G, Gao Y. Struct Dyn 10 034702 (2023)
  160. Comment Infidelity out in the open. Doublié S. Structure 12 1749-1750 (2004)
  161. Polγ coordinates DNA synthesis and proofreading to ensure mitochondrial genome integrity. Park J, Herrmann GK, Mitchell PG, Sherman MB, Yin YW. Nat Struct Mol Biol 30 812-823 (2023)
  162. Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase η and reduces DNA synthesis fidelity. Chang C, Lee Luo C, Eleraky S, Lin A, Zhou G, Gao Y. J Biol Chem 299 102938 (2023)
  163. Rep protein accommodates together dsDNA and ssDNA which enables a loop-back mechanism to plasmid DNA replication initiation. Wegrzyn K, Oliwa M, Nowacka M, Zabrocka E, Bury K, Purzycki P, Czaplewska P, Pipka J, Giraldo R, Konieczny I. Nucleic Acids Res 51 10551-10567 (2023)
  164. Structural basis for DNA proofreading. Buchel G, Nayak AR, Herbine K, Sarfallah A, Sokolova VO, Zamudio-Ochoa A, Temiakov D. Nat Commun 14 8501 (2023)
  165. Structures of LIG1 that engage with mutagenic mismatches inserted by polβ in base excision repair. Tang Q, Gulkis M, McKenna R, Çağlayan M. Nat Commun 13 3860 (2022)


Related citations provided by authors (3)

  1. Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations.. Johnson SJ, Taylor JS, Beese LS Proc Natl Acad Sci U S A 100 3895-900 (2003)
  2. Visualizing DNA Replication in a Catalytically Active Bacillus DNA Polymerase Crystal. Kiefer JR, Mao C, Braman JC, Beese LS Nature 391 304-307 (1998)
  3. Crystal Structure of a Thermostable Bacillus DNA Polymerase I Large Fragment at 2.1 A Resolution. Kiefer JR, Mao C, Hansen CJ, Basehore SL, Hogrefe HH, Braman JC, Beese LS Structure 5 95-108 (1997)

Quick links