ArticleProceedings of the National Academy of Sciences of the United States of America2010
DNA conformational changes at the primer-template junction regulate the fidelity of replication by DNA polymerase.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. 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, 37 citations in OpenAlex.
- Impacts of sequence and structure on pyrrolocytosine fluorescence in RNA.Nucleic acids research · 2025Article
- Modifying the Basicity of the dNTP Leaving Group Modulates Precatalytic Conformational Changes of DNA Polymerase β.Biochemistry · 2024Article
- Article
- A pre-catalytic non-covalent step governs DNA polymerase β fidelity.Nucleic acids research · 2019Article
- Calcium-driven DNA synthesis by a high-fidelity DNA polymerase.Nucleic acids research · 2017Article
- Switching between Exonucleolysis and Replication by T7 DNA Polymerase Ensures High Fidelity.Biophysical journal · 2017Article
- Increased duplex stabilization in porphyrin-LNA zipper arrays with structure dependent exciton coupling.Organic & biomolecular chemistry · 2016Article
- Mapping the interactions of the single-stranded DNA binding protein of bacteriophage T4 (gp32) with DNA lattices at single nucleotide resolution: polynucleotide binding and cooperativity.Nucleic acids research · 2015Article
- Fifty years of DNA "breathing": Reflections on old and new approaches.Biopolymers · 2013Review
- Observation of unpaired substrate DNA in the flap endonuclease-1 active site.Nucleic acids research · 2013Article
- Alteration in the cavity size adjacent to the active site of RB69 DNA polymerase changes its conformational dynamics.Nucleic acids research · 2013Article
- Distance-dependent duplex DNA destabilization proximal to G-quadruplex/i-motif sequences.Nucleic acids research · 2013Article
- Temperature-dependent conformations of a membrane supported zinc porphyrin tweezer by 2D fluorescence spectroscopy.The journal of physical chemistry. A · 2013Article
- Electronic transition moments of 6-methyl isoxanthopterin--a fluorescent analogue of the nucleic acid base guanine.Nucleic acids research · 2013Article
- Single-molecule microscopy reveals new insights into nucleotide selection by DNA polymerase I.Nucleic acids research · 2012Article
- Active site opening and closure control translocation of multisubunit RNA polymerase.Nucleic acids research · 2012Article
- Single-molecule Förster resonance energy transfer reveals an innate fidelity checkpoint in DNA polymerase I.Journal of the American Chemical Society · 2012Article
- Characterization of dark quencher chromophores as nonfluorescent acceptors for single-molecule FRET.Biophysical journal · 2012Article
- Energy landscapes of dynamic ensembles of rolling triplet repeat bulge loops: implications for DNA expansion associated with disease states.Journal of the American Chemical Society · 2012Article
- Characterization of the 6-methyl isoxanthopterin (6-MI) base analog dimer, a spectroscopic probe for monitoring guanine base conformations at specific sites in nucleic acids.Nucleic acids research · 2012Article
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
Local conformational changes in primer-template (P/T) DNA are involved in the selective incorporation of dNTP by DNA polymerases (DNAP). Here we use near UV CD and fluorescence spectra of pairs of base analogue probes, substituted either at the primer terminus or in the coding region of the template strand, to monitor and interpret conformational changes at and near the coding base of the template in P/T DNA complexes with Klenow fragment (KF) DNAP as the polymerase moves through the nucleotide addition cycle. Incoming dNTPs and rNTPs encounter binary complexes in which the 3'-end of the primer shuttles between the polymerization (pol) and exonuclease (exo) sites of DNAPs, even for perfectly complementary P/T DNA sequences. We have used spectral changes of probes inserted in both strands to monitor this two-state distribution and determine how it depends on the formation of ternary complexes with both complementary ("correct") and noncomplementary ("incorrect") NTPs and on the local sequence of the P/T DNA. The results show that the relative occupancy of the exo and pol sites is coupled to conformational changes in the P/T DNA of the complex that are partially regulated by the incoming NTP. We find that the coding base on the template strand is unperturbed by the binding of incorrect dNTPs, while binding of complementary rNTPs induces a novel template conformation. We conclude that, in addition to its editing function, primer strand occupancy of the 3'-exo site may also serve as a regulatory checkpoint for accurate dNTP selection in DNA synthesis.
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