ArticlePloS one2013
Structures of an apo and a binary complex of an evolved archeal B family DNA polymerase capable of synthesising highly cy-dye labelled DNA.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 32 citations in OpenAlex.
- Semi-rational evolution of a recombinant DNA polymerase for modified nucleotide incorporation efficiency.PloS one · 2025Article
- Non-Covalent Interactions between dUTP C5-Substituents and DNA Polymerase Decrease PCR Efficiency.International journal of molecular sciences · 2023Article
- Thermally controlled intein splicing of engineered DNA polymerases provides a robust and generalizable solution for accurate and sensitive molecular diagnostics.Nucleic acids research · 2023Article
- Precise genomic mapping of 5-hydroxymethylcytosine via covalent tether-directed sequencing.PLoS biology · 2020Article
- Building better enzymes: Molecular basis of improved non-natural nucleobase incorporation by an evolved DNA polymerase.Protein science : a publication of the Protein Society · 2020Article
- A synthetic genetic polymer with an uncharged backbone chemistry based on alkyl phosphonate nucleic acids.Nature chemistry · 2019Article
- Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase ε.Nature communications · 2019Article
- Snapshots of an evolved DNA polymerase pre- and post-incorporation of an unnatural nucleotide.Nucleic acids research · 2018Article
- dUTPs conjugated with zwitterionic Cy3 or Cy5 fluorophore analogues are effective substrates for DNA amplification and labelling by Taq polymerase.Nucleic acids research · 2018Article
- Structural basis for TNA synthesis by an engineered TNA polymerase.Nature communications · 2017Article
- Comparative Study of Novel Fluorescent Cyanine Nucleotides: Hybridization Analysis of Labeled PCR Products Using a Biochip.Journal of fluorescence · 2017Article
- Article
- Secondary Interaction Interfaces with PCNA Control Conformational Switching of DNA Polymerase PolB from Polymerization to Editing.The journal of physical chemistry. B · 2016Article
- The Toolbox for Modified Aptamers.Molecular biotechnology · 2016Review
- DNA polymerases engineered by directed evolution to incorporate non-standard nucleotides.Frontiers in microbiology · 2014Review
- PCR performance of a thermostable heterodimeric archaeal DNA polymerase.Frontiers in microbiology · 2014Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Thermophilic DNA polymerases of the polB family are of great importance in biotechnological applications including high-fidelity PCR. Of particular interest is the relative promiscuity of engineered versions of the exo- form of polymerases from the Thermo- and Pyrococcales families towards non-canonical substrates, which enables key advances in Next-generation sequencing. Despite this there is a paucity of structural information to guide further engineering of this group of polymerases. Here we report two structures, of the apo form and of a binary complex of a previously described variant (E10) of Pyrococcus furiosus (Pfu) polymerase with an ability to fully replace dCTP with Cyanine dye-labeled dCTP (Cy3-dCTP or Cy5-dCTP) in PCR and synthesise highly fluorescent "CyDNA" densely decorated with cyanine dye heterocycles. The apo form of Pfu-E10 closely matches reported apo form structures of wild-type Pfu. In contrast, the binary complex (in the replicative state with a duplex DNA oligonucleotide) reveals a closing movement of the thumb domain, increasing the contact surface with the nascent DNA duplex strand. Modelling based on the binary complex suggests how bulky fluorophores may be accommodated during processive synthesis and has aided the identification of residues important for the synthesis of unnatural nucleic acid polymers.
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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.