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Watching DNA polymerase η make a phosphodiester bond.

Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W
Nature 487 196-201 (2012)
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Cited: 157 times
EuropePMC logo PMID: 22785315

Abstract

DNA synthesis has been extensively studied, but the chemical reaction itself has not been visualized. Here we follow the course of phosphodiester bond formation using time-resolved X-ray crystallography. Native human DNA polymerase η, DNA and dATP were co-crystallized at pH 6.0 without Mg(2+). The polymerization reaction was initiated by exposing crystals to 1 mM Mg(2+) at pH 7.0, and stopped by freezing at desired time points for structural analysis. The substrates and two Mg(2+) ions are aligned within 40 s, but the bond formation is not evident until 80 s. From 80 to 300 s structures show a mixture of decreasing substrate and increasing product of the nucleotidyl-transfer reaction. Transient electron densities indicate that deprotonation and an accompanying C2'-endo to C3'-endo conversion of the nucleophile 3'-OH are rate limiting. A third Mg(2+) ion, which arrives with the new bond and stabilizes the intermediate state, may be an unappreciated feature of the two-metal-ion mechanism.

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Reviews citing this publication (31)

  1. An overview of Y-Family DNA polymerases and a case study of human DNA polymerase η. Yang W. Biochemistry 53 2793-2803 (2014)
  2. Eukaryotic Base Excision Repair: New Approaches Shine Light on Mechanism. Beard WA, Horton JK, Prasad R, Wilson SH. Annu Rev Biochem 88 137-162 (2019)
  3. Mechanisms of DNA Transposition. Hickman AB, Dyda F. Microbiol Spectr 3 MDNA3-0034-2014 (2015)
  4. The social fabric of the RNA degradosome. Bandyra KJ, Bouvier M, Carpousis AJ, Luisi BF. Biochim Biophys Acta 1829 514-522 (2013)
  5. Poly(A)-specific ribonuclease (PARN): an allosterically regulated, processive and mRNA cap-interacting deadenylase. Virtanen A, Henriksson N, Nilsson P, Nissbeck M. Crit Rev Biochem Mol Biol 48 192-209 (2013)
  6. Different Divalent Cations Alter the Kinetics and Fidelity of DNA Polymerases. Vashishtha AK, Wang J, Konigsberg WH. J Biol Chem 291 20869-20875 (2016)
  7. Targets for Combating the Evolution of Acquired Antibiotic Resistance. Culyba MJ, Mo CY, Kohli RM. Biochemistry 54 3573-3582 (2015)
  8. Structure-function studies of DNA polymerase λ. Bebenek K, Pedersen LC, Kunkel TA. Biochemistry 53 2781-2792 (2014)
  9. Nucleophilic Substitution (SN 2): Dependence on Nucleophile, Leaving Group, Central Atom, Substituents, and Solvent. Hamlin TA, Swart M, Bickelhaupt FM. Chemphyschem 19 1315-1330 (2018)
  10. A new paradigm of DNA synthesis: three-metal-ion catalysis. Yang W, Weng PJ, Gao Y. Cell Biosci 6 51 (2016)
  11. Basic mechanism of transcription by RNA polymerase II. Svetlov V, Nudler E. Biochim Biophys Acta 1829 20-28 (2013)
  12. RB69 DNA polymerase structure, kinetics, and fidelity. Xia S, Konigsberg WH. Biochemistry 53 2752-2767 (2014)
  13. Structural comparison of DNA polymerase architecture suggests a nucleotide gateway to the polymerase active site. Wu S, Beard WA, Pedersen LG, Wilson SH. Chem Rev 114 2759-2774 (2014)
  14. The cyclopurine deoxynucleosides: DNA repair, biological effects, mechanistic insights, and unanswered questions. Brooks PJ. Free Radic Biol Med 107 90-100 (2017)
  15. Preventive DNA repair by sanitizing the cellular (deoxy)nucleoside triphosphate pool. Nagy GN, Leveles I, Vértessy BG. FEBS J 281 4207-4223 (2014)
  16. dUTPase: the frequently overlooked enzyme encoded by many retroviruses. Hizi A, Herzig E. Retrovirology 12 70 (2015)
  17. 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)
  18. Two-Metal-Ion Catalysis: Inhibition of DNA Polymerase Activity by a Third Divalent Metal Ion. Wang J, Konigsberg WH. Front Mol Biosci 9 824794 (2022)
  19. Computational simulation strategies for analysis of multisubunit RNA polymerases. Wang B, Feig M, Cukier RI, Burton ZF. Chem Rev 113 8546-8566 (2013)
  20. New structural snapshots provide molecular insights into the mechanism of high fidelity DNA synthesis. Freudenthal BD, Beard WA, Wilson SH. DNA Repair (Amst) 32 3-9 (2015)
  21. Catalytic mechanism of DNA polymerases-Two metal ions or three? Tsai MD. Protein Sci 28 288-291 (2019)
  22. History of DNA polymerase β X-ray crystallography. Whitaker AM, Freudenthal BD. DNA Repair (Amst) 93 102928 (2020)
  23. Structural and Molecular Kinetic Features of Activities of DNA Polymerases. Kuznetsova AA, Fedorova OS, Kuznetsov NA. Int J Mol Sci 23 6373 (2022)
  24. The Role of Natural Polymorphic Variants of DNA Polymerase β in DNA Repair. Kladova OA, Fedorova OS, Kuznetsov NA. Int J Mol Sci 23 2390 (2022)
  25. Mechanism of the nucleotidyl-transfer reaction in DNA polymerase revealed by time-resolved protein crystallography. Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W. Biophysics (Nagoya-shi) 9 31-36 (2013)
  26. Emerging Time-Resolved X-Ray Diffraction Approaches for Protein Dynamics. Hekstra DR. Annu Rev Biophys 52 255-274 (2023)
  27. Recent Advances in Understanding the Structures of Translesion Synthesis DNA Polymerases. Ling JA, Frevert Z, Washington MT. Genes (Basel) 13 915 (2022)
  28. New insights into DNA polymerase mechanisms provided by time-lapse crystallography. Weaver TM, Washington MT, Freudenthal BD. Curr Opin Struct Biol 77 102465 (2022)
  29. Repair and tolerance of DNA damage at the replication fork: A structural perspective. Eichman BF. Curr Opin Struct Biol 81 102618 (2023)
  30. Watching the bacterial RNA polymerase transcription reaction by time-dependent soak-trigger-freeze X-ray crystallography. Shin Y, Murakami KS. Enzymes 49 305-314 (2021)
  31. Nucleoside Analogs: A Review of Its Source and Separation Processes. Wang P, Cheng T, Pan J. Molecules 28 7043 (2023)

Articles citing this publication (125)

  1. Observing a DNA polymerase choose right from wrong. Freudenthal BD, Beard WA, Shock DD, Wilson SH. Cell 154 157-168 (2013)
  2. Structural basis for processive DNA synthesis by yeast DNA polymerase ɛ. Hogg M, Osterman P, Bylund GO, Ganai RA, Lundström EB, Sauer-Eriksson AE, Johansson E. Nat Struct Mol Biol 21 49-55 (2014)
  3. Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide. Freudenthal BD, Beard WA, Perera L, Shock DD, Kim T, Schlick T, Wilson SH. Nature 517 635-639 (2015)
  4. Capture of a third Mg²⁺ is essential for catalyzing DNA synthesis. Gao Y, Yang W. Science 352 1334-1337 (2016)
  5. 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)
  6. Structure and mechanism of DNA polymerase β. Beard WA, Wilson SH. Biochemistry 53 2768-2780 (2014)
  7. Capturing snapshots of APE1 processing DNA damage. Freudenthal BD, Beard WA, Cuneo MJ, Dyrkheeva NS, Wilson SH. Nat Struct Mol Biol 22 924-931 (2015)
  8. Aprataxin resolves adenylated RNA-DNA junctions to maintain genome integrity. Tumbale P, Williams JS, Schellenberg MJ, Kunkel TA, Williams RS. Nature 506 111-115 (2014)
  9. Kinetics, structure, and mechanism of 8-Oxo-7,8-dihydro-2'-deoxyguanosine bypass by human DNA polymerase η. Patra A, Nagy LD, Zhang Q, Su Y, Müller L, Guengerich FP, Egli M. J Biol Chem 289 16867-16882 (2014)
  10. Parametrization of DFTB3/3OB for magnesium and zinc for chemical and biological applications. Lu X, Gaus M, Elstner M, Cui Q. J Phys Chem B 119 1062-1082 (2015)
  11. Mechanism of somatic hypermutation at the WA motif by human DNA polymerase η. Zhao Y, Gregory MT, Biertümpfel C, Hua YJ, Hanaoka F, Yang W. Proc Natl Acad Sci U S A 110 8146-8151 (2013)
  12. Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability. Tsutakawa SE, Thompson MJ, Arvai AS, Neil AJ, Shaw SJ, Algasaier SI, Kim JC, Finger LD, Jardine E, Gotham VJB, Sarker AH, Her MZ, Rashid F, Hamdan SM, Mirkin SM, Grasby JA, Tainer JA. Nat Commun 8 15855 (2017)
  13. Cracking the DNA Code for V(D)J Recombination. Kim MS, Chuenchor W, Chen X, Cui Y, Zhang X, Zhou ZH, Gellert M, Yang W. Mol Cell 70 358-370.e4 (2018)
  14. Structural basis for DNA 5´-end resection by RecJ. Cheng K, Xu H, Chen X, Wang L, Tian B, Zhao Y, Hua Y. Elife 5 e14294 (2016)
  15. Structures of dNTP intermediate states during DNA polymerase active site assembly. Freudenthal BD, Beard WA, Wilson SH. Structure 20 1829-1837 (2012)
  16. Structural and mechanistic studies of polymerase η bypass of phenanthriplatin DNA damage. Gregory MT, Park GY, Johnstone TC, Lee YS, Yang W, Lippard SJ. Proc Natl Acad Sci U S A 111 9133-9138 (2014)
  17. Viewing Human DNA Polymerase β Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography. Vyas R, Reed AJ, Tokarsky EJ, Suo Z. J Am Chem Soc 137 5225-5230 (2015)
  18. Time-lapse crystallography snapshots of a double-strand break repair polymerase in action. Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF, Krahn JM, Bebenek K, Kunkel TA, Wilson SH. Nat Commun 8 253 (2017)
  19. Amino acid substitution in the active site of DNA polymerase β explains the energy barrier of the nucleotidyl transfer reaction. Batra VK, Perera L, Lin P, Shock DD, Beard WA, Pedersen LC, Pedersen LG, Wilson SH. J Am Chem Soc 135 8078-8088 (2013)
  20. Requirement for transient metal ions revealed through computational analysis for DNA polymerase going in reverse. Perera L, Freudenthal BD, Beard WA, Shock DD, Pedersen LG, Wilson SH. Proc Natl Acad Sci U S A 112 E5228-36 (2015)
  21. A conformational switch in PRP8 mediates metal ion coordination that promotes pre-mRNA exon ligation. Schellenberg MJ, Wu T, Ritchie DB, Fica S, Staley JP, Atta KA, LaPointe P, MacMillan AM. Nat Struct Mol Biol 20 728-734 (2013)
  22. Cation trafficking propels RNA hydrolysis. Samara NL, Yang W. Nat Struct Mol Biol 25 715-721 (2018)
  23. Calcium inhibition of ribonuclease H1 two-metal ion catalysis. Rosta E, Yang W, Hummer G. J Am Chem Soc 136 3137-3144 (2014)
  24. A synthetic genetic polymer with an uncharged backbone chemistry based on alkyl phosphonate nucleic acids. Arangundy-Franklin S, Taylor AI, Porebski BT, Genna V, Peak-Chew S, Vaisman A, Woodgate R, Orozco M, Holliger P. Nat Chem 11 533-542 (2019)
  25. Structural insights into catalysis and dimerization enhanced exonuclease activity of RNase J. Zhao Y, Lu M, Zhang H, Hu J, Zhou C, Xu Q, Ul Hussain Shah AM, Xu H, Wang L, Hua Y. Nucleic Acids Res 43 5550-5559 (2015)
  26. DPT tautomerisation of the G·A(syn) and A*·G*(syn) DNA mismatches: a QM/QTAIM combined atomistic investigation. Brovarets' OO, Hovorun DM. Phys Chem Chem Phys 16 9074-9085 (2014)
  27. 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)
  28. Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction. Kottur J, Nair DT. Nucleic Acids Res 46 5875-5885 (2018)
  29. Watching the bacteriophage N4 RNA polymerase transcription by time-dependent soak-trigger-freeze X-ray crystallography. Basu RS, Murakami KS. J Biol Chem 288 3305-3311 (2013)
  30. Exploring the Role of the Third Active Site Metal Ion in DNA Polymerase η with QM/MM Free Energy Simulations. Stevens DR, Hammes-Schiffer S. J Am Chem Soc 140 8965-8969 (2018)
  31. Structures of intermediates along the catalytic cycle of terminal deoxynucleotidyltransferase: dynamical aspects of the two-metal ion mechanism. Gouge J, Rosario S, Romain F, Beguin P, Delarue M. J Mol Biol 425 4334-4352 (2013)
  32. Roles of Residues Arg-61 and Gln-38 of Human DNA Polymerase η in Bypass of Deoxyguanosine and 7,8-Dihydro-8-oxo-2'-deoxyguanosine. Su Y, Patra A, Harp JM, Egli M, Guengerich FP. J Biol Chem 290 15921-15933 (2015)
  33. Structure and function of TatD exonuclease in DNA repair. Chen YC, Li CL, Hsiao YY, Duh Y, Yuan HS. Nucleic Acids Res 42 10776-10785 (2014)
  34. Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase. Wu J, Samara NL, Kuraoka I, Yang W. Mol Cell 76 44-56.e3 (2019)
  35. Revealing the role of the product metal in DNA polymerase β catalysis. Perera L, Freudenthal BD, Beard WA, Pedersen LG, Wilson SH. Nucleic Acids Res 45 2736-2745 (2017)
  36. Capturing a mammalian DNA polymerase extending from an oxidized nucleotide. Whitaker AM, Smith MR, Schaich MA, Freudenthal BD. Nucleic Acids Res 45 6934-6944 (2017)
  37. Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-η. Genna V, Gaspari R, Dal Peraro M, De Vivo M. Nucleic Acids Res 44 2827-2836 (2016)
  38. Crystal structures of ternary complexes of archaeal B-family DNA polymerases. Kropp HM, Betz K, Wirth J, Diederichs K, Marx A. PLoS One 12 e0188005 (2017)
  39. Crystallographic observation of nonenzymatic RNA primer extension. Zhang W, Walton T, Li L, Szostak JW. Elife 7 e36422 (2018)
  40. Fluorescence resonance energy transfer studies of DNA polymerase β: the critical role of fingers domain movements and a novel non-covalent step during nucleotide selection. Towle-Weicksel JB, Dalal S, Sohl CD, Doublié S, Anderson KS, Sweasy JB. J Biol Chem 289 16541-16550 (2014)
  41. Metal-dependent conformational activation explains highly promutagenic replication across O6-methylguanine by human DNA polymerase β. Koag MC, Lee S. J Am Chem Soc 136 5709-5721 (2014)
  42. Modulating the DNA polymerase β reaction equilibrium to dissect the reverse reaction. Shock DD, Freudenthal BD, Beard WA, Wilson SH. Nat Chem Biol 13 1074-1080 (2017)
  43. Visualizing phosphodiester-bond hydrolysis by an endonuclease. Molina R, Stella S, Redondo P, Gomez H, Marcaida MJ, Orozco M, Prieto J, Montoya G. Nat Struct Mol Biol 22 65-72 (2015)
  44. Crystallographic Snapshots of Class A β-Lactamase Catalysis Reveal Structural Changes That Facilitate β-Lactam Hydrolysis. Pan X, He Y, Lei J, Huang X, Zhao Y. J Biol Chem 292 4022-4033 (2017)
  45. DNA synthesis from diphosphate substrates by DNA polymerases. Burke CR, Lupták A. Proc Natl Acad Sci U S A 115 980-985 (2018)
  46. Simulating the fidelity and the three Mg mechanism of pol η and clarifying the validity of transition state theory in enzyme catalysis. Yoon H, Warshel A. Proteins 85 1446-1453 (2017)
  47. Visualizing Rev1 catalyze protein-template DNA synthesis. Weaver TM, Cortez LM, Khoang TH, Washington MT, Agarwal PK, Freudenthal BD. Proc Natl Acad Sci U S A 117 25494-25504 (2020)
  48. Detection of Reaction Intermediates in Mg2+-Dependent DNA Synthesis and RNA Degradation by Time-Resolved X-Ray Crystallography. Samara NL, Gao Y, Wu J, Yang W. Methods Enzymol 592 283-327 (2017)
  49. The E295K cancer variant of human polymerase β favors the mismatch conformational pathway during nucleotide selection. Eckenroth BE, Towle-Weicksel JB, Sweasy JB, Doublié S. J Biol Chem 288 34850-34860 (2013)
  50. Calcium-driven DNA synthesis by a high-fidelity DNA polymerase. Ralec C, Henry E, Lemor M, Killelea T, Henneke G. Nucleic Acids Res 45 12425-12440 (2017)
  51. Enhancement of human DNA polymerase η activity and fidelity is dependent upon a bipartite interaction with the Werner syndrome protein. Maddukuri L, Ketkar A, Eddy S, Zafar MK, Griffin WC, Eoff RL. J Biol Chem 287 42312-42323 (2012)
  52. Leukotriene biosynthesis inhibitor MK886 impedes DNA polymerase activity. Ketkar A, Zafar MK, Maddukuri L, Yamanaka K, Banerjee S, Egli M, Choi JY, Lloyd RS, Eoff RL. Chem Res Toxicol 26 221-232 (2013)
  53. Polymerase/DNA interactions and enzymatic activity: multi-parameter analysis with electro-switchable biosurfaces. Langer A, Schräml M, Strasser R, Daub H, Myers T, Heindl D, Rant U. Sci Rep 5 12066 (2015)
  54. Protein Kinase A Catalytic Subunit Primed for Action: Time-Lapse Crystallography of Michaelis Complex Formation. Das A, Gerlits O, Parks JM, Langan P, Kovalevsky A, Heller WT. Structure 23 2331-2340 (2015)
  55. 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)
  56. Extensive free-energy simulations identify water as the base in nucleotide addition by DNA polymerase. Roston D, Demapan D, Cui Q. Proc Natl Acad Sci U S A 116 25048-25056 (2019)
  57. Five checkpoints maintaining the fidelity of transcription by RNA polymerases in structural and energetic details. Wang B, Opron K, Burton ZF, Cukier RI, Feig M. Nucleic Acids Res 43 1133-1146 (2015)
  58. Structural basis of DNA synthesis opposite 8-oxoguanine by human PrimPol primase-polymerase. Rechkoblit O, Johnson RE, Gupta YK, Prakash L, Prakash S, Aggarwal AK. Nat Commun 12 4020 (2021)
  59. Catalytic mechanism of α-phosphate attack in dUTPase is revealed by X-ray crystallographic snapshots of distinct intermediates, 31P-NMR spectroscopy and reaction path modelling. Barabás O, Németh V, Bodor A, Perczel A, Rosta E, Kele Z, Zagyva I, Szabadka Z, Grolmusz VI, Wilmanns M, Vértessy BG. Nucleic Acids Res 41 10542-10555 (2013)
  60. Computational Simulations of DNA Polymerases: Detailed Insights on Structure/Function/Mechanism from Native Proteins to Cancer Variants. Walker AR, Cisneros GA. Chem Res Toxicol 30 1922-1935 (2017)
  61. Molecular events during translocation and proofreading extracted from 200 static structures of DNA polymerase. Ren Z. Nucleic Acids Res 44 7457-7474 (2016)
  62. Second-Shell Basic Residues Expand the Two-Metal-Ion Architecture of DNA and RNA Processing Enzymes. Genna V, Colombo M, De Vivo M, Marcia M. Structure 26 40-50.e2 (2018)
  63. Structural basis for proficient oxidized ribonucleotide insertion in double strand break repair. Jamsen JA, Sassa A, Perera L, Shock DD, Beard WA, Wilson SH. Nat Commun 12 5055 (2021)
  64. Crystallographic evidence for two-metal-ion catalysis in human pol η. Wang J, Smithline ZB. Protein Sci 28 439-447 (2019)
  65. Divalent ions attenuate DNA synthesis by human DNA polymerase α by changing the structure of the template/primer or by perturbing the polymerase reaction. Zhang Y, Baranovskiy AG, Tahirov ET, Tahirov TH, Pavlov YI. DNA Repair (Amst) 43 24-33 (2016)
  66. Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction. Gregory MT, Gao Y, Cui Q, Yang W. Proc Natl Acad Sci U S A 118 e2103990118 (2021)
  67. 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)
  68. Quantum mechanical analysis of nonenzymatic nucleotidyl transfer reactions: kinetic and thermodynamic effects of β-γ bridging groups of dNTP substrates. Zhang Z, Eloge J, Florián J. Biochemistry 53 4180-4191 (2014)
  69. Structural and dynamic characterization of polymerase κ's minor groove lesion processing reveals how adduct topology impacts fidelity. Lior-Hoffmann L, Ding S, Geacintov NE, Zhang Y, Broyde S. Biochemistry 53 5683-5691 (2014)
  70. 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)
  71. "Gate-keeper" residues and active-site rearrangements in DNA polymerase μ help discriminate non-cognate nucleotides. Li Y, Schlick T. PLoS Comput Biol 9 e1003074 (2013)
  72. Conformational changes in motif D of RdRPs as fidelity determinant. Verdaguer N, Ferrer-Orta C. Structure 20 1448-1450 (2012)
  73. Following replicative DNA synthesis by time-resolved X-ray crystallography. Chim N, Meza RA, Trinh AM, Yang K, Chaput JC. Nat Commun 12 2641 (2021)
  74. Regulation of adenylyl cyclase 5 in striatal neurons confers the ability to detect coincident neuromodulatory signals. Bruce NJ, Narzi D, Trpevski D, van Keulen SC, Nair AG, Röthlisberger U, Wade RC, Carloni P, Hellgren Kotaleski J. PLoS Comput Biol 15 e1007382 (2019)
  75. Structural basis for polymerase η-promoted resistance to the anticancer nucleoside analog cytarabine. Rechkoblit O, Choudhury JR, Buku A, Prakash L, Prakash S, Aggarwal AK. Sci Rep 8 12702 (2018)
  76. The mechanism of the nucleo-sugar selection by multi-subunit RNA polymerases. Mäkinen JJ, Shin Y, Vieras E, Virta P, Metsä-Ketelä M, Murakami KS, Belogurov GA. Nat Commun 12 796 (2021)
  77. Comment Watching a DNA polymerase in action. Freudenthal BD, Beard WA, Wilson SH. Cell Cycle 13 691-692 (2014)
  78. Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide. Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH. Nat Commun 12 2059 (2021)
  79. 2.0 Å resolution crystal structure of human polκ reveals a new catalytic function of N-clasp in DNA replication. Jha V, Ling H. Sci Rep 8 15125 (2018)
  80. A cyclobutane thymine-N4-methylcytosine dimer is resistant to hydrolysis but strongly blocks DNA synthesis. Yamamoto J, Oyama T, Kunishi T, Masutani C, Hanaoka F, Iwai S. Nucleic Acids Res 42 2075-2084 (2014)
  81. Determination of chemical identity and occupancy from experimental density maps. Wang J. Protein Sci 27 411-420 (2018)
  82. How Mg2+ ions lower the SN2@P barrier in enzymatic triphosphate hydrolysis. van Bochove MA, Roos G, Fonseca Guerra C, Hamlin TA, Bickelhaupt FM. Chem Commun (Camb) 54 3448-3451 (2018)
  83. In crystallo observation of three metal ion promoted DNA polymerase misincorporation. Chang C, Lee Luo C, Gao Y. Nat Commun 13 2346 (2022)
  84. Optimal and variant metal-ion routes in DNA polymerase β's conformational pathways. Li Y, Freudenthal BD, Beard WA, Wilson SH, Schlick T. J Am Chem Soc 136 3630-3639 (2014)
  85. Comparative Molecular Dynamics Studies of Human DNA Polymerase η. Ucisik MN, Hammes-Schiffer S. J Chem Inf Model 55 2672-2681 (2015)
  86. Ectopic suicide inhibition of thioredoxin glutathione reductase. Silvestri I, Lyu H, Fata F, Banta PR, Mattei B, Ippoliti R, Bellelli A, Pitari G, Ardini M, Petukhova V, Thatcher GRJ, Petukhov PA, Williams DL, Angelucci F. Free Radic Biol Med 147 200-211 (2020)
  87. Intrinsic Cleavage of RNA Polymerase II Adopts a Nucleobase-independent Mechanism Assisted by Transcript Phosphate. Ka Man Tse C, Xu J, Xu L, Sheong FK, Wang S, Chow HY, Gao X, Li X, Cheung PP, Wang D, Zhang Y, Huang X. Nat Energy 2 228-235 (2019)
  88. Isothermal multiple displacement amplification of DNA templates in minimally buffered conditions using phi29 polymerase. Tenaglia E, Imaizumi Y, Miyahara Y, Guiducci C. Chem Commun (Camb) 54 2158-2161 (2018)
  89. Kinetic and thermodynamic analysis defines roles for two metal ions in DNA polymerase specificity and catalysis. Gong S, Kirmizialtin S, Chang A, Mayfield JE, Zhang YJ, Zhang YJ, Johnson KA. J Biol Chem 296 100184 (2021)
  90. Role of the LEXE motif of protein-primed DNA polymerases in the interaction with the incoming nucleotide. Santos E, Lázaro JM, Pérez-Arnaiz P, Salas M, de Vega M. J Biol Chem 289 2888-2898 (2014)
  91. Structural and Enzymatic Characterization of a Nucleoside Diphosphate Sugar Hydrolase from Bdellovibrio bacteriovorus. de la Peña AH, Suarez A, Duong-Ly KC, Schoeffield AJ, Pizarro-Dupuy MA, Zarr M, Pineiro SA, Amzel LM, Gabelli SB. PLoS One 10 e0141716 (2015)
  92. Structures of DNA duplexes containing O6-carboxymethylguanine, a lesion associated with gastrointestinal cancer, reveal a mechanism for inducing pyrimidine transition mutations. Zhang F, Tsunoda M, Suzuki K, Kikuchi Y, Wilkinson O, Millington CL, Margison GP, Williams DM, Czarina Morishita E, Takénaka A. Nucleic Acids Res 41 5524-5532 (2013)
  93. Differential furanose selection in the active sites of archaeal DNA polymerases probed by fixed-conformation nucleotide analogues. Ketkar A, Zafar MK, Banerjee S, Marquez VE, Egli M, Eoff RL. Biochemistry 51 9234-9244 (2012)
  94. Gαi1 inhibition mechanism of ATP-bound adenylyl cyclase type 5. Narzi D, van Keulen SC, Röthlisberger U. PLoS One 16 e0245197 (2021)
  95. Interlocking activities of DNA polymerase β in the base excision repair pathway. Kumar A, Reed AJ, Zahurancik WJ, Daskalova SM, Hecht SM, Suo Z. Proc Natl Acad Sci U S A 119 e2118940119 (2022)
  96. Computational insights into the mutagenicity of two tobacco-derived carcinogenic DNA lesions. Wilson KA, Garden JL, Wetmore NT, Wetmore SD. Nucleic Acids Res 46 11858-11868 (2018)
  97. Controlled Trafficking of Multiple and Diverse Cations Prompts Nucleic Acid Hydrolysis. Manigrasso J, De Vivo M, Palermo G. ACS Catal 11 8786-8797 (2021)
  98. Following DNA chain extension and protein conformational changes in crystals of a Y-family DNA polymerase via Raman crystallography. Espinoza-Herrera SJ, Gaur V, Suo Z, Carey PR. Biochemistry 52 4881-4890 (2013)
  99. Insights into DNA polymerase δ's mechanism for accurate DNA replication. Foley MC, Couto L, Rauf S, Boyke A. J Mol Model 25 80 (2019)
  100. Visualization of mutagenic nucleotide processing by Escherichia coli MutT, a Nudix hydrolase. Nakamura T, Yamagata Y. Proc Natl Acad Sci U S A 119 e2203118119 (2022)
  101. Watching right and wrong nucleotide insertion captures hidden polymerase fidelity checkpoints. Jamsen JA, Shock DD, Wilson SH. Nat Commun 13 3193 (2022)
  102. Comment Biochemistry: DNA replication caught in the act. Johnson KA. Nature 487 177-178 (2012)
  103. Combining Evolutionary Conservation and Quantum Topological Analyses To Determine Quantum Mechanics Subsystems for Biomolecular Quantum Mechanics/Molecular Mechanics Simulations. Hix MA, Leddin EM, Cisneros GA. J Chem Theory Comput 17 4524-4537 (2021)
  104. HIV Reverse Transcriptase Pre-Steady-State Kinetic Analysis of Chain Terminators and Translocation Inhibitors Reveals Interactions between Magnesium and Nucleotide 3'-OH. Dilmore CR, DeStefano JJ. ACS Omega 6 14621-14628 (2021)
  105. Observation of the Unbiased Conformers of Putative DNA-Scaffold Ribosugars. Calabrese C, Uriarte I, Insausti A, Vallejo-López M, Basterretxea FJ, Cochrane SA, Davis BG, Corzana F, Cocinero EJ. ACS Cent Sci 6 293-303 (2020)
  106. Photo-activatable Ub-PCNA probes reveal new structural features of the Saccharomyces cerevisiae Polη/PCNA complex. Shen S, Davidson GA, Yang K, Zhuang Z. Nucleic Acids Res 49 9374-9388 (2021)
  107. A static magnetic field inhibits the expression of platelet-derived growth factor-AA in human oral squamous cell carcinoma. Obayashi-Ishii M, Saito S, Omagari D, Asano M, Ishigami T. J Oral Sci 60 374-380 (2018)
  108. Altered Nucleotide Insertion Mechanisms of Disease-Associated TERT Variants. Welfer GA, Borin VA, Cortez LM, Opresko PL, Agarwal PK, Freudenthal BD. Genes (Basel) 14 281 (2023)
  109. An uncommon [K+(Mg2+)2] metal ion triad imparts stability and selectivity to the Guanidine-I riboswitch. Trachman RJ, Ferré-D'Amaré AR. RNA 27 1257-1264 (2021)
  110. Insight into the mechanism of DNA synthesis by human terminal deoxynucleotidyltransferase. Kuznetsova AA, Tyugashev TE, Alekseeva IV, Timofeyeva NA, Fedorova OS, Kuznetsov NA. Life Sci Alliance 5 e202201428 (2022)
  111. Molecular Characterization of a DNA Polymerase from Thermus thermophilus MAT72 Phage vB_Tt72: A Novel Type-A Family Enzyme with Strong Proofreading Activity. Dorawa S, Werbowy O, Plotka M, Kaczorowska AK, Makowska J, Kozlowski LP, Fridjonsson OH, Hreggvidsson GO, Aevarsson A, Kaczorowski T. Int J Mol Sci 23 7945 (2022)
  112. Monovalent metal ion binding promotes the first transesterification reaction in the spliceosome. Aupič J, Borišek J, Fica SM, Galej WP, Magistrato A. Nat Commun 14 8482 (2023)
  113. 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)
  114. The Electronic Structure of Genome Editors from the First Principles. Nierzwicki Ł, Ahsan M, Palermo G. Electron Struct 5 014003 (2023)
  115. The active site residues Gln55 and Arg73 play a key role in DNA damage bypass by S. cerevisiae Pol η. Boldinova EO, Ignatov A, Kulbachinskiy A, Makarova AV. Sci Rep 8 10314 (2018)
  116. "Catch and Release": A Variation of the Archetypal Nucleotidyl Transfer Reaction. Selvaraj B, Kocaman S, Trifas M, Serpersu EH, Cuneo MJ. ACS Catal 10 3548-3555 (2020)
  117. Advances in Structural and Single-Molecule Methods for Investigating DNA Lesion Bypass and Repair Polymerases. Raper AT, Reed AJ, Gadkari VV, Suo Z. Chem Res Toxicol 30 260-269 (2017)
  118. Editorial Editorial: Nucleic Acid Polymerases: The Two-Metal-Ion Mechanism and Beyond. Pata JD, Yin YW, Lahiri I. Front Mol Biosci 9 948326 (2022)
  119. Human telomerase protein: Understanding how the catalytic activity is suppressed under single substitutions of some conserved residues. A computational study. Herrera FE, Sferco SJ. Proteins 86 1020-1036 (2018)
  120. 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)
  121. Mechanism of Deoxyguanosine Diphosphate Insertion by Human DNA Polymerase β. Varela FA, Freudenthal BD. Biochemistry 60 373-380 (2021)
  122. Molecular Mechanism of Thymidylate Synthase Inhibition by N4-Hydroxy-dCMP in View of Spectrophotometric and Crystallographic Studies. Maj P, Jarmuła A, Wilk P, Prokopowicz M, Rypniewski W, Zieliński Z, Dowierciał A, Bzowska A, Rode W. Int J Mol Sci 22 4758 (2021)
  123. Quantification of cyclic DNA polymerization with lanthanide coordination nanomaterials for liquid biopsy. Zhou W, Wang L, Liu C, Teng Q, Wang Z, Dai Z. Chem Sci 11 3745-3751 (2020)
  124. Structural Insight into Polymerase Mechanism via a Chiral Center Generated with a Single Selenium Atom. Qin T, Hu B, Zhao Q, Wang Y, Wang S, Luo D, Lyu J, Chen Y, Gan J, Huang Z. Int J Mol Sci 24 15758 (2023)
  125. Visualizing the three-metal-ion-dependent cleavage of a mutagenic nucleotide. Samara NL. Proc Natl Acad Sci U S A 119 e2207180119 (2022)


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