ArticleNucleic acids research2014
Nucleotide selection by the Y-family DNA polymerase Dpo4 involves template translocation and misalignment.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 34 citations in OpenAlex.
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- Stabilization of the hexasome intermediate during histone exchange by yeast SWR1 complex.Molecular cell · 2024Article
- DNA-directed termination of RNA polymerase II transcription.Molecular cell · 2023Article
- Investigating the Conformational Dynamics of a Y-Family DNA Polymerase during Its Folding and Binding to DNA and a Nucleotide.JACS Au · 2022Article
- Insights into the mismatch discrimination mechanism of Y-family DNA polymerase Dpo4.The Biochemical journal · 2021Article
- Investigating the trade-off between folding and function in a multidomain Y-family DNA polymerase.eLife · 2020Article
- Template-switching mechanism of a group II intron-encoded reverse transcriptase and its implications for biological function and RNA-Seq.The Journal of biological chemistry · 2019Article
- Bulky Lesion Bypass Requires Dpo4 Binding in Distinct Conformations.Scientific reports · 2017Article
- Increased Processivity, Misincorporation, and Nucleotide Incorporation Efficiency in Sulfolobus solfataricus Dpo4 Thumb Domain Mutants.Applied and environmental microbiology · 2017Article
- Characterization of a coupled DNA replication and translesion synthesis polymerase supraholoenzyme from archaea.Nucleic acids research · 2017Article
- Advances in Structural and Single-Molecule Methods for Investigating DNA Lesion Bypass and Repair Polymerases.Chemical research in toxicology · 2017Article
- Investigation of Intradomain Motions of a Y-Family DNA Polymerase during Substrate Binding and Catalysis.Biochemistry · 2016Article
- Computational Evaluation of Nucleotide Insertion Opposite Expanded and Widened DNA by the Translesion Synthesis Polymerase Dpo4.Molecules (Basel, Switzerland) · 2016Article
- Single-Molecule Investigation of Response to Oxidative DNA Damage by a Y-Family DNA Polymerase.Biochemistry · 2016Article
- Mechanism of aromatic amine carcinogen bypass by the Y-family polymerase, Dpo4.Nucleic acids research · 2015Article
- Local DNA dynamics shape mutational patterns of mononucleotide repeats in human genomes.Nucleic acids research · 2015Article
- An underlying mechanism for the increased mutagenesis of lagging-strand genes in Bacillus subtilis.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
Y-family DNA polymerases play a crucial role in translesion DNA synthesis. Here, we have characterized the binding kinetics and conformational dynamics of the Y-family polymerase Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) using single-molecule fluorescence. We find that in the absence of dNTPs, the binary complex shuttles between two different conformations within ∼1 s. These data are consistent with prior crystal structures in which the nucleotide binding site is either occupied by the terminal base pair (preinsertion conformation) or empty following Dpo4 translocation by 1 base pair (insertion conformation). Most interestingly, on dNTP binding, only the insertion conformation is observed and the correct dNTP stabilizes this complex compared with the binary complex, whereas incorrect dNTPs destabilize it. However, if the n+1 template base is complementary to the incoming dNTP, a structure consistent with a misaligned template conformation is observed, in which the template base at the n position loops out. This structure provides evidence for a Dpo4 mutagenesis pathway involving a transient misalignment mechanism.
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