ArticleNature communications2013
Conformational landscapes of DNA polymerase I and mutator derivatives establish fidelity checkpoints for nucleotide insertion.
Article in Nature communications, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
What it found
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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
52 citing papers in PubMed, 103 citations in OpenAlex.
- A Thymine Dimer Stalls a High-Fidelity DNA Polymerase by Providing No Template Information in the Same Manner as an Abasic Site.Biochemistry · 2026Article
- Understanding the Fidelity and Specificity of DNA Polymerase I.ACS omega · 2025Article
- Structural basis of multitasking by the apicoplast DNA polymerase from Plasmodium falciparum.Nucleic acids research · 2025Article
- Precise mapping of single-stranded DNA breaks by sequence-templated erroneous DNA polymerase end-labelling.Nature communications · 2025Article
- Invention, innovation, and commercialisation in British biophysics.Biophysical reviews · 2025Review
- Labelizer: systematic selection of protein residues for covalent fluorophore labeling.Nature communications · 2025Article
- Structural basis for processive daughter-strand synthesis and proofreading by the human leading-strand DNA polymerase Pol ε.Nature structural & molecular biology · 2024Article
- Single-Molecule FRET Analyses of NMDA Receptors.Methods in molecular biology (Clifton, N.J.) · 2024Article
- smFRET Detection of Cis and Trans DNA Interactions by the BfiI Restriction Endonuclease.The journal of physical chemistry. B · 2023Article
- Polγ coordinates DNA synthesis and proofreading to ensure mitochondrial genome integrity.Nature structural & molecular biology · 2023Article
- Molecular Characterization of a DNA Polymerase fromInternational journal of molecular sciences · 2022Article
- The Rate-limiting Step of DNA Synthesis by DNA Polymerase Occurs in the Fingers-closed Conformation.Journal of molecular biology · 2022Article
- Conformational Dynamics of DNA Polymerases Revealed at the Single-Molecule Level.Frontiers in molecular biosciences · 2022Review
- Following replicative DNA synthesis by time-resolved X-ray crystallography.Nature communications · 2021Article
- FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices.eLife · 2021Review
- Article
- DNA replication machinery: Insights fromComputational and structural biotechnology journal · 2021Review
- Extracting Transition Rates in Particle Tracking Using Analytical Diffusion Distribution Analysis.Biophysical journal · 2020Article
- The smfBox is an open-source platform for single-molecule FRET.Nature communications · 2020Article
- Using single-molecule FRET to probe the nucleotide-dependent conformational landscape of polymerase β-DNA complexes.The Journal of biological chemistry · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
Abstract
The fidelity of DNA polymerases depends on conformational changes that promote the rejection of incorrect nucleotides before phosphoryl transfer. Here, we combine single-molecule FRET with the use of DNA polymerase I and various fidelity mutants to highlight mechanisms by which active-site side chains influence the conformational transitions and free-energy landscape that underlie fidelity decisions in DNA synthesis. Ternary complexes of high fidelity derivatives with complementary dNTPs adopt mainly a fully closed conformation, whereas a conformation with a FRET value between those of open and closed is sparsely populated. This intermediate-FRET state, which we attribute to a partially closed conformation, is also predominant in ternary complexes with incorrect nucleotides and, strikingly, in most ternary complexes of low-fidelity derivatives for both correct and incorrect nucleotides. The mutator phenotype of the low-fidelity derivatives correlates well with reduced affinity for complementary dNTPs and highlights the partially closed conformation as a primary checkpoint for nucleotide selection.
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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.