ArticleBiochemistry2012
Contribution of partial charge interactions and base stacking to the efficiency of primer extension at and beyond abasic sites in DNA.
Article in Biochemistry, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- A Thymine Dimer Stalls a High-Fidelity DNA Polymerase by Providing No Template Information in the Same Manner as an Abasic Site.Biochemistry · 2026Article
- Structural basis for processive daughter-strand synthesis and proofreading by the human leading-strand DNA polymerase Pol ε.Nature structural & molecular biology · 2024Article
- Error-Prone DNA Synthesis on Click-Ligated Templates.Doklady. Biochemistry and biophysics · 2024Article
- Probing the Conformational Restraints of DNA Damage Recognition with β-L-Nucleotides.International journal of molecular sciences · 2024Article
- Abasic site-peptide cross-links are blocking lesions repaired by AP endonucleases.Nucleic acids research · 2023Article
- Recognition of a Clickable Abasic Site Analog by DNA Polymerases and DNA Repair Enzymes.International journal of molecular sciences · 2022Article
- Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- The effect of different divalent cations on the kinetics and fidelity ofAIMS biophysics · 2018Article
- Mismodeled purines: implicit alternates and hidden Hoogsteens.Acta crystallographica. Section D, Structural biology · 2017Article
- Molecular events during translocation and proofreading extracted from 200 static structures of DNA polymerase.Nucleic acids research · 2016Article
- Effect of Different Divalent Cations on the Kinetics and Fidelity of RB69 DNA Polymerase.Biochemistry · 2016Article
- Article
- Polymerase and exonuclease activities in herpes simplex virus type 1 DNA polymerase are not highly coordinated.Biochemistry · 2015Article
- RB69 DNA polymerase structure, kinetics, and fidelity.Biochemistry · 2014Review
- Alteration in the cavity size adjacent to the active site of RB69 DNA polymerase changes its conformational dynamics.Nucleic acids research · 2013Article
- DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase.Journal of the American Chemical Society · 2013Article
- Probing minor groove hydrogen bonding interactions between RB69 DNA polymerase and DNA.Biochemistry · 2012Article
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6 authors.
Funding
Abstract
During DNA synthesis, base stacking and Watson-Crick (WC) hydrogen bonding increase the stability of nascent base pairs when they are in a ternary complex. To evaluate the contribution of base stacking to the incorporation efficiency of dNTPs when a DNA polymerase encounters an abasic site, we varied the penultimate base pairs (PBs) adjacent to the abasic site using all 16 possible combinations. We then determined pre-steady-state kinetic parameters with an RB69 DNA polymerase variant and solved nine structures of the corresponding ternary complexes. The efficiency of incorporation for incoming dNTPs opposite an abasic site varied between 2- and 210-fold depending on the identity of the PB. We propose that the A rule can be extended to encompass the fact that DNA polymerase can bypass dA/abasic sites more efficiently than other dN/abasic sites. Crystal structures of the ternary complexes show that the surface of the incoming base was stacked against the PB's interface and that the kinetic parameters for dNMP incorporation were consistent with specific features of base stacking, such as surface area and partial charge-charge interactions between the incoming base and the PB. Without a templating nucleotide residue, an incoming dNTP has no base with which it can hydrogen bond and cannot be desolvated, so that these surrounding water molecules become ordered and remain on the PB's surface in the ternary complex. When these water molecules are on top of a hydrophobic patch on the PB, they destabilize the ternary complex, and the incorporation efficiency of incoming dNTPs is reduced.
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