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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Structure of a Covalently Trapped Catalytic Complex of HIV-1 Reverse Transcriptase: Implications for Drug Resistance

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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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Thermodynamics of DNA Binding by DNA Polymerase I and RecA Recombinase from Deinococcus radiodurans

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Computational Simulations of Cancer and Disease-Related Enzymatic Systems Using Molecular Dynamics and Combined Quantum Methods

Walker, A. R. (2018) · doi:10.12794/metadc1157647

Formation, Degradation, and Bypass of DNA-Protein Crosslinks

Sedgeman, C. A. (2018)

Computational Investigations of Biomolecular Mechanisms in Genomic Replication, Repair and Transcription

Dodd, T. (2022) · Digital Archive @ GSU · doi:10.57709/20345880

Bacterial DNA Replicases

McHenry, C. S. (2014) · Springer eBooks · doi:10.1007/978-1-4614-1531-2_54

DNA Dependent DNA Polymerases as Targets for Low-Weight Molecular Inhibitors: State of Art and Prospects of Rational Design

Nyporko, A. Y. (2014) · Challenges and advances in computational chemistry and physics · doi:10.1007/978-94-017-9257-8_4

DNA Polymerase

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Base Excision Repair

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Introduction to Mutagenesis

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Bacterial DNA Polymerase I

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Engineering Escherichia coli DNA polymerase III α for translesion synthesis

Sharma, R. (2010) · doi:10.17760/d20000331

Yeast mtDNA transcription initiation in single nucleotide addition stepsPreprint

Goovaerts, Q., Shen, J., Wijngaert, B. D., Basu, U., Patel, S. S., & Das, K. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.09.27.509796

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DNA replication machineries: Structural insights from crystallography and electron microscopy

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Phylogeny comparison based on conserved sequence of 16S rRNA, DNA polymerase I, and lipase genes from PLS 80 isolate

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Zn 2+ ions improve the fidelity of metal-mediated primer extension while suppressing intrinsic and Mn 2+ -induced mutagenic effects by DNA polymerases

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Computational Modeling of Cancer-Related Mutations in DNA Repair Enzymes Using Molecular Dynamics and Quantum Mechanics/Molecular Mechanics

Leddin, E. M. (2022) · University of North Texas Digital Library (University of North Texas) · doi:10.12794/metadc1944361

Predictive Modeling of Novel Mutations to DNA-Editing Metalloenzymes and Development of Improved QM/MM Methods

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The Role of AZT (Azidothymidine) in the Treatment of HIV and AIDS

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Y-family DNA polymerases : mechanism of single-base deletion and effect of PCNA interaction

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Introducing Favorable Mutations of Polymerase Orthologs in Human DNA PolymerasePreprint

Manavala, K. (2025) · doi:10.58445/rars.2658

A Web-Based Experimental Biochemistry Virtual Laboratory for Science and Engineering Education

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Structural basis of multitasking by the apicoplast DNA polymerase from Plasmodium falciparum

Kumari, A., Enache, T., Craggs, T. D., Pata, J. D., & Lahiri, I. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf1005

The Natural history of the transition between RNA to DNA in the early stages of life

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Multiequilibria of oligomeric thermophilic DNA replication polymerases

Lin, H.-K. (2013) · D-Scholarship@Pitt (University of Pittsburgh)

Regulation of Mammalian Poly(A) Polymerase Activity

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The S180R Human Germline Variant of DNA Polymerase β Is a Low Fidelity Enzyme with Reduced Flexibility of the Fingers Domain

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AlphaFold modeling of the white spot syndrome virus polymerase

Skern, T., & Oakey, J. (2026) · Virology · doi:10.1016/j.virol.2026.110818

Taxonomy of Family: Partitiviridae

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Real-Time Visualization of G2L4 Reverse Transcriptase in DNA Repair via Microhomology-Mediated End JoiningPreprint

Lin, Y., Zhang, P., Guo, M., Zhang, Y. J., & Lambowitz, A. M. (2026) · Research Square · doi:10.21203/rs.3.rs-8780377/v1

Strand Displacement Increases the Fidelity of DNA Polymerases

Yudkina, A. V., Yakovlev, A. O., Rychkov, D. A., Golyshev, V. M., & Zharkov, D. O. (2026) · Biochemistry · doi:10.1021/acs.biochem.6c00115

The study of susceptibility and resistance of HIV integrases to integrase strand transfer inhibitors and the development of novel single domain antibody targeting HIV integrase

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A thumb-domain insertion balances processivity and fidelity in DNA polymerase ε

Singh, N. I., Bylund, G. O., & Johansson, E. (2026) · Nucleic Acids Research · doi:10.1093/nar/gkag282

Influence de la variation de la concentration intracellulaire des désoxyribonucléotides et rubbonucléotides sur la stabilité génomique chez Pyrococcus abyssi

Lemor, M. (2017) · theses.fr (ABES) · doi:10.70675/c008e746z3c84z45e6zb8f1z9f96609cbe22

Rôle des 2'-O-méthylations internes du génome ARN du VIH-1 dans la réplication virale

Decombe, A. (2023) · theses.fr (ABES) · doi:10.70675/82535ee7z2ed0z457ezb976za900d3f7241a

Recombinant Taq DNA polymerase

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O4-Modified thymidine analogues with photolabile o-nitrobenzyl group derivatives for modulating polymerase primer extension reaction

Sugiura, R., Okamura, H., Yonezawa, N., & Taniguchi, Y. (2026) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2026.118712

Preorganized RdRp-Thumb Dynamics Drives SARS-CoV-2 Polymerase FunctionPreprint

Gibbs, H., Butuc, A., Moore, P. B., & Gianti, E. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.29.728794

Consecutive catalytic steps of viral RNA polymerase and exonuclease suggest a way to overcome intrinsic nucleotide analogue resistance

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An autocatalytic DNA circuit via polymerase mediated strand displacement

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Insights into Genotype-Phenotype Mapping and Evolvability: A Perspective of Neutral EvolutionPreprint

Deng, S. (2026) · SSRN Electronic Journal · doi:10.2139/ssrn.7308264

Structural biology of retron-mediated immunity against phage

Jasnauskaitė, M., & Pausch, P. (2026) · Biological Chemistry · doi:10.1515/hsz-2026-0145

DNA polymerase I and DnaE mediate RNA-templated DNA synthesis over embedded ribonucleotides

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Computational screening of bacterial and fungal natural compounds targeting monkeypox virus DNA polymerase (F8) holoenzyme

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Structural basis for coupled DNA replication and uracil repair by a family of DNA polymerases from phages with T-modified genomes

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BindingDB Entry 50014672: Rational design and synthesis of novel dimeric diketoacid-containing inhibitors of HIV-1 integrase: implication for binding to two metal ions on the active site of integrase.

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BindingDB Entry 50018059: From ligand to complexes: inhibition of human immunodeficiency virus type 1 integrase by beta-diketo acid metal complexes.

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BindingDB Entry 50006022: Inhibiting the HIV integration process: past, present, and the future.

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BindingDB Entry 50037487: Control of hepatitis C: a medicinal chemistry perspective.

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BindingDB Entry 50013042: Use of a pharmacophore model to discover a new class of influenza endonuclease inhibitors.

BindingDB (2009) · UC San Diego · doi:10.7270/q22j6b6v

BindingDB Entry 50032405: Mechanism of hepatitis C virus RNA polymerase inhibition with dihydroxypyrimidines.

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Modelo cinético estocástico para a transcrição considerando colisões entre as moléculas de RNA polimerase

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MODULATION OF HIV-1 REVERSE TRANSCRIPTASE AND FAMILY A DNA POLYMERASE PRIMER-TEMPLATE BINDING

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Processivity and thermostability of archaeal DNA polymerases; application in PCR

Kinsman, T. S. (2014)

Structural Studies of Klenow Fragment: An Enzyme with Two Active SitesPreprint

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DNA Polymerase Structure and Mechanisms of Action

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DNA Replication Fidelity

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DNA-polimeraza: mehanizami kojima se ostvaruje visoka vjernost replikacije

Poljak, K. (2009)

Getting a grip on how DNA polymerases function.

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