ArticleNucleic acids research2017
Calcium-driven DNA synthesis by a high-fidelity DNA polymerase.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 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
15 citing papers in PubMed, 33 citations in OpenAlex.
- Thermodynamic Profiling Reveals DNA Polymerase Template Binding, Substrate Incorporation, and Exonuclease Function.International journal of molecular sciences · 2025Article
- Zebrafish Polymerase Theta and human Polymerase Theta: Orthologues with homologous function.PloS one · 2025Article
- Identification of a novel family B DNA polymerase from Enterococcus phage IME199 and its overproduction in Escherichia coli BL21(DE3).Microbial cell factories · 2023Article
- Direct Enzyme Engineering of B Family DNA Polymerases for Biotechnological Approaches.Bioengineering (Basel, Switzerland) · 2023Review
- Genotoxic effects of the major alkylation damage N7-methylguanine and methyl formamidopyrimidine.The Biochemical journal · 2023Article
- Interaction of human HelQ with DNA polymerase delta halts DNA synthesis and stimulates DNA single-strand annealing.Nucleic acids research · 2023Article
- Mg-based materials diminish tumor spreading and cancer metastases.Bioactive materials · 2023Article
- Bst polymerase - a humble relative of Taq polymerase.Computational and structural biotechnology journal · 2023Review
- Mechanistic Insights into the Phase Separation Behavior and Pathway-Directed Information Exchange in all-DNA Droplets.Angewandte Chemie (International ed. in English) · 2022Article
- Peptide Aptamer PA3 Attenuates the Viability ofFrontiers in microbiology · 2022Article
- E. coli RNase I exhibits a strong Ca2+-dependent inherent double-stranded RNase activity.Nucleic acids research · 2021Article
- Liquid drop of DNA libraries reveals total genome information.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Role of RadA and DNA Polymerases in Recombination-Associated DNA Synthesis in Hyperthermophilic Archaea.Biomolecules · 2020Article
- Synthesis of phosphoramidate-linked DNA by a modified DNA polymerase.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Article
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 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Divalent metal ions, usually Mg2+, are required for both DNA synthesis and proofreading functions by DNA polymerases (DNA Pol). Although used as a non-reactive cofactor substitute for binding and crystallographic studies, Ca2+ supports DNA polymerization by only one DNA Pol, Dpo4. Here, we explore whether Ca2+-driven catalysis might apply to high-fidelity (HiFi) family B DNA Pols. The consequences of replacing Mg2+ by Ca2+ on base pairing at the polymerase active site as well as the editing of terminal nucleotides at the exonuclease active site of the archaeal Pyrococcus abyssi DNA Pol (PabPolB) are characterized and compared to other (families B, A, Y, X, D) DNA Pols. Based on primer extension assays, steady-state kinetics and ion-chased experiments, we demonstrate that Ca2+ (and other metal ions) activates DNA synthesis by PabPolB. While showing a slower rate of phosphodiester bond formation, nucleotide selectivity is improved over that of Mg2+. Further mechanistic studies show that the affinities for primer/template are higher in the presence of Ca2+ and reinforced by a correct incoming nucleotide. Conversely, no exonuclease degradation of the terminal nucleotides occurs with Ca2+. Evolutionary and mechanistic insights among DNA Pols are thus discussed.
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.