DNA Polymerases: Structural Diversity and Common Mechanisms

Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor

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Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution

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A general two-metal-ion mechanism for catalytic RNA

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Crystal structure of human immunodeficiency virus type 1 reverse transcriptase complexed with double-stranded DNA at 3.0 A resolution shows bent DNA

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Structural basis for the 3′‐5′ exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism.

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Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP

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STRUCTURES OF TERNARY COMPLEXES OF RAT DNA POLYMERASE BETA, A DNA TEMPLATE-PRIMER, AND DDCTP

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An attempt to unify the structure of polymerases

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FUNCTION AND STRUCTURE RELATIONSHIPS IN DNA POLYMERASES

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Molecular events during translocation and proofreading extracted from 200 static structures of DNA polymerase

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Compartmentalized Self-Replication: A Novel Method for the Directed Evolution of Polymerases and Other Enzymes

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Mechanisms of nucleotide selection by telomerase

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Building better polymerases: Engineering the replication of expanded genetic alphabets

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The Nature of the Last Common Ancestor

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Differing Conformational Pathways Before and After Chemistry for Insertion of dATP versus dCTP Opposite 8-OxoG in DNA Polymerase β

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Multiple solutions to inefficient lesion bypass by T7 DNA polymerase

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Biological and Therapeutic Relevance of Nonreplicative DNA Polymerases to Cancer

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The crystal structure of XC847 from Xanthomonas campestris: A 3′–5′ oligoribonuclease of DnaQ fold family with a novel opposingly shifted helix

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A Group II Intron-Type Open Reading Frame from the Thermophile Bacillus ( Geobacillus ) stearothermophilus Encodes a Heat-Stable Reverse Transcriptase

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Microbial alkaline phosphatases in bioprocessing

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Cofactors as Molecular Fossils To Trace the Origin and Evolution of Proteins

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Mechanism and Dynamics of Translesion DNA Synthesis Catalyzed by the Escherichia coli Klenow Fragment

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Molecular Basis for Chiral Selection in RNA Aminoacylation

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Polymerization behavior of Klenow fragment and Taq DNA polymerase in short primer extension reactions

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Expanding the repertoire of DNA polymerase substrates: template-instructed incorporation of non-nucleoside triphosphate analogues by DNA polymerases and

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RNA-dependent RNA polymerase encoded by hepatitis C virus: biomedical applications

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Inhibition of DNA polymerases and DNA topoisomerase II by triterpenes produced by plant callus

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DNA polymerases β and λ and their roles in cell

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Translesion DNA Synthesis

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Mismatched Base-Pair Simulations for ASFV Pol X/DNA Complexes Help Interpret Frequent G•G Misincorporation

Benitez, B. A. S., Arora, K., Balistreri, L., & Tamar Schlick, A. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.10.025 · Cited by 21

Comparison of the π-stacking properties of purine versus pyrimidine residues. Some generalizations regarding selectivity

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Mechanism of Error-Free DNA Replication Past Lucidin-Derived DNA Damage by Human DNA Polymerase κ

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Cryo-EM Structures Reveal Transcription Initiation Steps by Yeast Mitochondrial RNA Polymerase

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A Light‐Activated DNA Polymerase

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Molecular dynamics study of HIV‐1 RT‐DNA‐nevirapine complexes explains NNRTI inhibition and resistance by connection mutations

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Thermal stability landscape for Klenow DNA polymerase as a function of pH and salt concentration

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Quasispecies Dynamics and Evolution of Foot-and-Mouth Disease Virus

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Mechanism of error-free replication across benzo[a]pyrene stereoisomers by Rev1 DNA polymerase

Rechkoblit, O., Kolbanovskiy, A., Landes, H., Geacintov, N. E., & Aggarwal, A. K. (2017) · Nature Communications · doi:10.1038/s41467-017-01013-5 · Cited by 20

Kinetic and thermodynamic analysis defines roles for two metal ions in DNA polymerase specificity and catalysis

Gong, S., Kırmızıaltın, S., Chang, A., Mayfield, J. E., Zhang, Y. J., & Johnson, K. A. (2020) · Journal of Biological Chemistry · doi:10.1074/jbc.ra120.016489 · Cited by 20

Inhibition of Monkeypox Virus DNA Polymerase Using Moringa oleifera Phytochemicals: Computational Studies of Drug-Likeness, Molecular Docking, Molecular Dynamics Simulation and Density Functional Theory

Yousaf, M. A., Basheera, S., & Sivanandan, S. (2024) · Indian Journal of Microbiology · doi:10.1007/s12088-024-01244-3 · Cited by 20

Mutagenic nucleotide incorporation and hindered translocation by a food carcinogen C8-dG adduct in Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): modeling and dynamics studies

Zhang, L. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl425 · Cited by 20

Cloning, purification, crystallization and preliminary X-ray crystallographic analysis of XC847, a 3′-5′ oligoribonuclease fromXanthomonas campestris

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Thermodynamics of the DNA Structural Selectivity of the Pol I DNA Polymerases from Escherichia coli and Thermus aquaticus

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A highly conserved Tyrosine residue of family B DNA polymerases contributes to dictate translesion synthesis past 8-oxo-7,8-dihydro-2′-deoxyguanosine

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Iminodiacetic-phosphoramidates as metabolic prototypes for diversifying nucleic acid polymerization in vivo

Giraut, A., Song, X., Froeyen, M., Marlière, P., & Herdewijn, P. A. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp1246 · Cited by 20

An update on small molecule inhibitors of the HCV NS5B polymerase: effects on RNA synthesis in vitro and in cultured cells, and potential resistance in viral quasispecies

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Detection of Reaction Intermediates in Mg 2+ -Dependent DNA Synthesis and RNA Degradation by Time-Resolved X-Ray Crystallography

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Two forms of human DNA polymerase δ: Who does what and why?

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Herpes Simplex Virus-1 Helicase−Primase: Roles of Each Subunit in DNA Binding and Phosphodiester Bond Formation

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3‘-5‘ Exonuclease of Klenow Fragment: Role of Amino Acid Residues within the Single-Stranded DNA Binding Region in Exonucleolysis and Duplex DNA Melting

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Terminal RNA uridylyltransferases of trypanosomes

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New high fidelity polymerases from Thermococcus species

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Thermodynamic Dissection of the Polymerizing and Editing Modes of a DNA Polymerase

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Characterization of catalytic carboxylate triad in non-replicative DNA polymerase III (pol E) of Geobacillus kaustophilus HTA.

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Cryo-EM structure of translesion DNA synthesis polymerase ζ with a base pair mismatch

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Dynamics of the Herpes simplex virus DNA polymerase holoenzyme during DNA synthesis and proof-reading revealed by Cryo-EM

Gustavsson, E., Grünewald, K., Elias, P., & Hällberg, B. M. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae374 · Cited by 19

Novel mechanism of gene regulation: the protein Rv1222 ofMycobacterium tuberculosisinhibits transcription by anchoring the RNA polymerase onto DNA

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Exploiting Polymerase Promiscuity: A Simple Colorimetric RNA Polymerase Assay

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O 6 -Alkylguanine Postlesion DNA Synthesis Is Correct with the Right Complement of Hydrogen Bonding

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A Viral T7 RNA Polymerase Ratcheting Along DNA With Fidelity Control

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AtREV1, a Y-Family DNA Polymerase in Arabidopsis, Has Deoxynucleotidyl Transferase Activity in Vitro

Takahashi, S., Sakamoto, A. N., Tanaka, A., & Shimizu, K. (2007) · PLANT PHYSIOLOGY · doi:10.1104/pp.107.101980 · Cited by 20

Distinct Function of Conserved Amino Acids in the Fingers of Saccharomyces cerevisiae DNA Polymerase α

Ogawa, M., Limsirichaikul, S., Niimi, A., Iwai, S., Yoshida, S., & Suzuki, M. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m208605200 · Cited by 19

Inactivation of the 3′-5′ Exonuclease of the Replicative T4 DNA Polymerase Allows Translesion DNA Synthesis at an Abasic Site

Gac, N. T. L., Delagoutte, E., Germain, M., & Villani, G. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.01.005 · Cited by 19

A Ty1 Reverse Transcriptase Active-Site Aspartate Mutation Blocks Transposition but Not Polymerization

Uzun, O., & Gabriel, A. (2001) · Journal of Virology · doi:10.1128/jvi.75.14.6337-6347.2001 · Cited by 19

Discrimination against the Cytosine Analog tC by Escherichia coli DNA Polymerase IV DinB

Walsh, J. M., Bouamaïed, I., Brown, T. P., Wilhelmsson, L. M., & Beuning, P. J. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.03.069 · Cited by 18

Dynamics on multiple timescales in the RNA-directed RNA polymerase from the cystovirus ϕ6

Ren, Z., Wang, H., & Ghose, R. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq210 · Cited by 18

Phi29 DNA polymerase residues Tyr59, His61 and Phe69 of the highly conserved ExoII motif are essential for interaction with the terminal protein

Eisenbrandt, R. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.6.1379 · Cited by 18

A trimeric DNA polymerase complex increases the native replication processivity

Mikheikin, A. L., Lin, H.-K., Mehta, P., Jen‐Jacobson, L., & Trakselis, M. A. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp767 · Cited by 18

Sequential Side-Chain Residue Motions Transform the Binary into the Ternary State of DNA Polymerase λ

Foley, M. C., Arora, K., & Tamar Schlick, A. (2006) · Biophysical Journal · doi:10.1529/biophysj.106.092080 · Cited by 18

Utilization of a Deoxynucleoside Diphosphate Substrate by HIV Reverse Transcriptase

Garforth, S., Parniak, M. A., & Prasad, V. R. (2008) · PLoS ONE · doi:10.1371/journal.pone.0002074 · Cited by 18

Directed evolution as a tool for understanding and optimizing nucleic acid polymerase function

Brakmann, S. (2005) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-005-5165-5 · Cited by 18

Arg660Ser mutation in Thermus aquaticus DNA polymerase I suppresses T->C transitions: implication of wobble base pair formation at the nucleotide incorporation step

Yoshida, K. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.20.4206 · Cited by 18

5. Prebiotic Chemistry – Biochemistry – Emergence of Life (4.4–2 Ga)

Pascal, R., Boiteau, L., Forterre, P., Gargaud, M., Lazcano, A., López‐García, P., Maurel, M., Moreira, D., Peretó, J. G., Prieur, D., et al. (2006) · Earth Moon and Planets · doi:10.1007/s11038-006-9089-3 · Cited by 20

Primus inter pares (first among equals).

Berger, J. M., & Keck, J. L. (2001) · Nature Structural Biology · doi:10.1038/82996 · Cited by 18

Sulfolobus shibatae CCA-adding enzyme forms a tetramer upon binding two tRNA molecules: a scrunching-shuttling model of CCA specificity

Li, F., Wang, J., & Steitz, T. A. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.4189 · Cited by 18

Structures illustrate step-by-step mitochondrial transcription initiation

Goovaerts, Q., Shen, J., De Wijngaert, B., Basu, U., Patel, S. S., & Das, K. (2023) · Nature · doi:10.1038/s41586-023-06643-y · Cited by 16

Discovering autoinhibition as a design principle for the control of biological mechanisms

Bollhagen, A., & Bechtel, W. (2022) · Studies in History and Philosophy of Science Part A · doi:10.1016/j.shpsa.2022.08.008 · Cited by 17

Chemical, Biochemical, and Structural Similarities and Differences of Dermatological cAMP Phosphodiesterase-IV Inhibitors

Wang, J., Ho, M., & Bunick, C. G. (2024) · Journal of Investigative Dermatology · doi:10.1016/j.jid.2024.10.597 · Cited by 17

Molecular Basis of Genetic Variation of Viruses

Domingo, E. (2015) · Elsevier eBooks · doi:10.1016/b978-0-12-800837-9.00002-2 · Cited by 18

Investigation of sliding DNA clamp dynamics by single-molecule fluorescence, mass spectrometry and structure-based modeling

Gadkari, V. V., Harvey, S. R., Raper, A. T., Chu, W., Wang, J., Wysocki, V. H., & Suo, Z. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky125 · Cited by 17

Structural Studies of a Bacterial tRNAHIS Guanylyltransferase (Thg1)-Like Protein, with Nucleotide in the Activation and Nucleotidyl Transfer Sites

Hyde, S. J., Rao, B. S., Eckenroth, B. E., Jackman, J. E., & Doublié, S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0067465 · Cited by 17

Purification and crystallization ofEscherichia colioligoribonuclease

Fiedler, T. J., Vincent, H. A., Zuo, Y., Gavrialov, O., & Malhotra, A. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904002252 · Cited by 17

Functional roles of carboxylate residues comprising the DNA polymerase active site triad of Ty3 reverse transcriptase

Bibiłło, A. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki150 · Cited by 17

One‐step purification of Taq DNA polymerase using nucleotide‐mimetic affinity chromatography

Melissis, S., Labrou, N. E., & Clonis, Y. D. (2006) · Biotechnology Journal · doi:10.1002/biot.200600191 · Cited by 17

Pre-Steady-State Kinetics of RB69 DNA Polymerase and Its Exo Domain Mutants: Effect of pH and Thiophosphoryl Linkages on 3‘−5‘ Exonuclease Activity

Wang, C. X., Zakharova, E., Li, J., Joyce, C. M., Wang, J., & Konigsberg, W. H. (2004) · Biochemistry · doi:10.1021/bi0302292 · Cited by 17

Human Immunodeficiency Virus Reverse Transcriptase

Wendeler, M., Miller, J. T., & Grice, S. F. J. L. (2009) · Springer eBooks · doi:10.1007/b135974_19 · Cited by 17

Mimivirus encodes a multifunctional primase with DNA/RNA polymerase, terminal transferase and translesion synthesis activities

Gupta, A., Lad, S. B., Ghodke, P. P., Pradeepkumar, P. I., & Kondabagil, K. R. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz236 · Cited by 16

Combining Evolutionary Conservation and Quantum Topological Analyses To Determine Quantum Mechanics Subsystems for Biomolecular Quantum Mechanics/Molecular Mechanics Simulations

Hix, M. A., Leddin, E. M., & Cisneros, G. A. (2021) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.1c00313 · Cited by 17

pIT3, a cryptic plasmid isolated from the hyperthermophilic crenarchaeon Sulfolobus solfataricus IT3

Prato, S., Cannio, R., Klenk, H., Contursi, P., Rossi, M., & Bartolucci, S. (2006) · Plasmid · doi:10.1016/j.plasmid.2006.02.002 · Cited by 16

From Quasispecies Theory to Viral Quasispecies: How Complexity has Permeated Virology

Domingo, E., & Perales, C. (2012) · Mathematical Modelling of Natural Phenomena · doi:10.1051/mmnp/20127508 · Cited by 16

Common Structural Core of Three-Dozen Residues Reveals Intersuperfamily Relationships

Mönttinen, H. A. M., Ravantti, J., & Poranen, M. M. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw047 · Cited by 17

Enzymatic hydrolysis by transition-metal-dependent nucleophilic aromatic substitution

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A Conformational Change in E. coli DNA Polymerase I (Klenow Fragment) Is Induced in the Presence of a dNTP Complementary to the Template Base in the Active Site

Dzantiev, L., & Romano, L. J. (1999) · Biochemistry · doi:10.1021/bi991952o · Cited by 16

Purifying Selection Masks the Mutational Flexibility of HIV-1 Reverse Transcriptase

Smith, R. A., Anderson, D. J., & Preston, B. D. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m314038200 · Cited by 16

1,2-GG intrastrand cross-link of antitumor dinuclear bifunctional platinum compound with spermidine linker inhibits DNA polymerization more effectively than the cross-link of conventional cisplatin

Moriarity, B. S., Nováková, O., Farrell, N. P., Brabec, V., & Kašpárková, J. (2006) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2006.11.022 · Cited by 16

Noncognate DNA damage prevents the formation of the active conformation of the Y‐family DNA polymerases DinB and DNA polymerase κ

Nevin, P., Lu, X., Zhang, K., Engen, J. R., & Beuning, P. J. (2015) · FEBS Journal · doi:10.1111/febs.13304 · Cited by 16

Enzyme active sites: bioinformatics, architecture, and mechanisms of action

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Nucleotide modification at the -phosphate leads to the improved fidelity of HIV-1 reverse transcriptase

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