ReviewBiochemistry2014
RB69 DNA polymerase structure, kinetics, and fidelity.
Review in Biochemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
35 citing papers in PubMed.
- Dual cytosine modification through hydroxylation and arabinofuranosylation in phages.Nature chemical biology · 2026Article
- The bacteriophage T4 replisome: a model system for understanding DNA replication mechanisms.EcoSal Plus · 2025Review
- Structural insights into the exchange mechanism of a replicative DNA polymerase.Nucleic acids research · 2025Article
- The A, B, C, D's of replicative DNA polymerase fidelity: utilizing high-throughput single-molecule sequencing to understand the molecular basis for DNA polymerase accuracy.Nucleic acids research · 2025Article
- Structural basis for processive daughter-strand synthesis and proofreading by the human leading-strand DNA polymerase Pol ε.Nature structural & molecular biology · 2024Article
- Repair and DNA Polymerase Bypass of Clickable Pyrimidine Nucleotides.Biomolecules · 2024Article
- Sequencing by avidity enables high accuracy with low reagent consumption.Nature biotechnology · 2024Article
- Recognition of a Clickable Abasic Site Analog by DNA Polymerases and DNA Repair Enzymes.International journal of molecular sciences · 2022Article
- Host translesion polymerases are required for viral genome integrity.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Review
- Article
- Cryo-EM structure of translesion DNA synthesis polymerase ζ with a base pair mismatch.Nature communications · 2022Article
- Article
- Two-Metal-Ion Catalysis: Inhibition of DNA Polymerase Activity by a Third Divalent Metal Ion.Frontiers in molecular biosciences · 2022Review
- Twisting and swiveling domain motions in Cas9 to recognize target DNA duplexes, make double-strand breaks, and release cleaved duplexes.Frontiers in molecular biosciences · 2022Review
- Review
- Mechanism of Inhibition of the Reproduction of SARS-CoV-2 andBiochemistry · 2021Article
- Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Article
- Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
This review will summarize our structural and kinetic studies of RB69 DNA polymerase (RB69pol) as well as selected variants of the wild-type enzyme that were undertaken to obtain a deeper understanding of the exquisitely high fidelity of B family replicative DNA polymerases. We discuss how the structures of the various RB69pol ternary complexes can be used to rationalize the results obtained from pre-steady-state kinetic assays. Our main findings can be summarized as follows. (i) Interbase hydrogen bond interactions can increase catalytic efficiency by 5000-fold; meanwhile, base selectivity is not solely determined by the number of hydrogen bonds between the incoming dNTP and the templating base. (ii) Minor-groove hydrogen bond interactions at positions n - 1 and n - 2 of the primer strand and position n - 1 of the template strand in RB69pol ternary complexes are essential for efficient primer extension and base selectivity. (iii) Partial charge interactions among the incoming dNTP, the penultimate base pair, and the hydration shell surrounding the incoming dNTP modulate nucleotide insertion efficiency and base selectivity. (iv) Steric clashes between mismatched incoming dNTPs and templating bases with amino acid side chains in the nascent base pair binding pocket (NBP) as well as weak interactions and large gaps between the incoming dNTPs and the templating base are some of the reasons that incorrect dNTPs are incorporated so inefficiently by wild-type RB69pol. In addition, we developed a tC°-tCnitro Förster resonance energy transfer assay to monitor partitioning of the primer terminus between the polymerase and exonuclease subdomains.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.