ArticleNucleic acids research2015
Real-time single-molecule studies of the motions of DNA polymerase fingers illuminate DNA synthesis mechanisms.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
24 citing papers in PubMed, 52 citations in OpenAlex.
- Non-enzymatic error correction in self-replicators without extraneous energy supply.Scientific reports · 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
- Structural basis for processive daughter-strand synthesis and proofreading by the human leading-strand DNA polymerase Pol ε.Nature structural & molecular biology · 2024Article
- Sequential requirements for distinct Polθ domains during theta-mediated end joining.Molecular cell · 2024Article
- Entropic control of the free-energy landscape of an archetypal biomolecular machine.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Cooperative action of separate interaction domains promotes high-affinity DNA binding ofProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Cytosine methylation regulates DNA bendability depending on the curvature.Chemical science · 2022Article
- Single-molecule Taq DNA polymerase dynamics.Science advances · 2022Article
- The Rate-limiting Step of DNA Synthesis by DNA Polymerase Occurs in the Fingers-closed Conformation.Journal of molecular biology · 2022Article
- DNA Polymerase-Parental DNA Interaction Is Essential for Helicase-Polymerase Coupling during Bacteriophage T7 DNA Replication.International journal of molecular sciences · 2022Article
- Conformational Dynamics of DNA Polymerases Revealed at the Single-Molecule Level.Frontiers in molecular biosciences · 2022Review
- Can DyeCycling break the photobleaching limit in single-molecule FRET?Nano research · 2022Article
- DNA replication machinery: Insights fromComputational and structural biotechnology journal · 2021Review
- Using single-molecule FRET to probe the nucleotide-dependent conformational landscape of polymerase β-DNA complexes.The Journal of biological chemistry · 2020Article
- Design principles of a minimal auxin response system.Nature plants · 2020Article
- Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase.Nucleic acids research · 2019Article
- I260Q DNA polymerase β highlights precatalytic conformational rearrangements critical for fidelity.Nucleic acids research · 2018Article
- The RNA polymerase clamp interconverts dynamically among three states and is stabilized in a partly closed state by ppGpp.Nucleic acids research · 2018Article
- Efficient use of single molecule time traces to resolve kinetic rates, models and uncertainties.The Journal of chemical physics · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
DNA polymerases maintain genomic integrity by copying DNA with high fidelity. A conformational change important for fidelity is the motion of the polymerase fingers subdomain from an open to a closed conformation upon binding of a complementary nucleotide. We previously employed intra-protein single-molecule FRET on diffusing molecules to observe fingers conformations in polymerase-DNA complexes. Here, we used the same FRET ruler on surface-immobilized complexes to observe fingers-opening and closing of individual polymerase molecules in real time. Our results revealed the presence of intrinsic dynamics in the binary complex, characterized by slow fingers-closing and fast fingers-opening. When binary complexes were incubated with increasing concentrations of complementary nucleotide, the fingers-closing rate increased, strongly supporting an induced-fit model for nucleotide recognition. Meanwhile, the opening rate in ternary complexes with complementary nucleotide was 6 s(-1), much slower than either fingers closing or the rate-limiting step in the forward direction; this rate balance ensures that, after nucleotide binding and fingers-closing, nucleotide incorporation is overwhelmingly likely to occur. Our results for ternary complexes with a non-complementary dNTP confirmed the presence of a state corresponding to partially closed fingers and suggested a radically different rate balance regarding fingers transitions, which allows polymerase to achieve high fidelity.
Indexed as
Identifiers
What OpenQuestion holds
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.