ArticleThe Journal of biological chemistry2009
Mechanistic studies of the bypass of a bulky single-base lesion catalyzed by a Y-family DNA polymerase.
Article in The Journal of biological chemistry, 2009. 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, 38 citations in OpenAlex.
- Conformational gating governs nucleotide incorporation by a DNA-crosslinked polymerase.Nucleic acids research · 2026Article
- Investigating the Conformational Dynamics of a Y-Family DNA Polymerase during Its Folding and Binding to DNA and a Nucleotide.JACS Au · 2022Article
- A hand-off of DNA between archaeal polymerases allows high-fidelity replication to resume at a discrete intermediate three bases past 8-oxoguanine.Nucleic acids research · 2020Article
- Investigating the trade-off between folding and function in a multidomain Y-family DNA polymerase.eLife · 2020Article
- A Unique B-Family DNA Polymerase Facilitating Error-Prone DNA Damage Tolerance in Crenarchaeota.Frontiers in microbiology · 2020Article
- Uncovering a unique approach for damaged DNA replication: A computational investigation of a mutagenic tobacco-derived thymine lesion.Nucleic acids research · 2019Article
- Computational insights into the mutagenicity of two tobacco-derived carcinogenic DNA lesions.Nucleic acids research · 2018Article
- Advances in Structural and Single-Molecule Methods for Investigating DNA Lesion Bypass and Repair Polymerases.Chemical research in toxicology · 2017Article
- Pre-steady-state kinetic investigation of bypass of a bulky guanine lesion by human Y-family DNA polymerases.DNA repair · 2016Article
- Mechanism of aromatic amine carcinogen bypass by the Y-family polymerase, Dpo4.Nucleic acids research · 2015Article
- Mechanistic Basis for the Bypass of a Bulky DNA Adduct Catalyzed by a Y-Family DNA Polymerase.Journal of the American Chemical Society · 2015Article
- Dynamic conformational change regulates the protein-DNA recognition: an investigation on binding of a Y-family polymerase to its target DNA.PLoS computational biology · 2014Article
- Mechanistic investigation of the bypass of a bulky aromatic DNA adduct catalyzed by a Y-family DNA polymerase.DNA repair · 2014Article
- Recent insight into the kinetic mechanisms and conformational dynamics of Y-Family DNA polymerases.Biochemistry · 2014Review
- Conformational dynamics of a Y-family DNA polymerase during substrate binding and catalysis as revealed by interdomain Förster resonance energy transfer.Biochemistry · 2014Article
- Structural mechanism of replication stalling on a bulky amino-polycyclic aromatic hydrocarbon DNA adduct by a y family DNA polymerase.Journal of molecular biology · 2013Article
- Replication of a carcinogenic nitropyrene DNA lesion by human Y-family DNA polymerase.Nucleic acids research · 2013Article
- Differential temperature-dependent multimeric assemblies of replication and repair polymerases on DNA increase processivity.Biochemistry · 2012Article
- Quantitative analysis of the mutagenic potential of 1-aminopyrene-DNA adduct bypass catalyzed by Y-family DNA polymerases.Mutation research · 2012Article
- Identification of an unfolding intermediate for a DNA lesion bypass polymerase.Chemical research in toxicology · 2012Article
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
1-nitropyrene, the most abundant nitro polycyclic aromatic hydrocarbon in diesel emissions, has been found to react with DNA to form predominantly N-(deoxyguanosin-8-yl)-1-aminopyrene (dGAP). This bulky adduct has been shown to induce genetic mutations, which may implicate Y-family DNA polymerases in its bypass in vivo. To establish a kinetic mechanism for the bypass of such a prototype single-base lesion, we employed pre-steady-state kinetic methods to investigate individual nucleotide incorporations upstream, opposite, and downstream from a site-specifically placed dGAP lesion catalyzed by Sulfolobus solfataricus DNA polymerase IV (Dpo4), a model Y-family DNA polymerase. Dpo4 was able to bypass dGAP but paused strongly at two sites: opposite the lesion and immediately downstream from the lesion. Both nucleotide incorporation efficiency and fidelity decreased significantly at the pause sites, especially during extension of the bypass product. Interestingly, a 4-fold tighter binding affinity of damaged DNA to Dpo4 promoted catalysis through putative interactions between the active site residues of Dpo4 and 1-aminopyrene moiety at the first pause site. In the presence of a DNA trap, the kinetics of nucleotide incorporation at these sites was biphasic in which a small, fast phase preceded a larger, slow phase. In contrast, only a large, fast phase was observed during nucleotide incorporation at non-pause sites. Our kinetic studies support a general kinetic mechanism for lesion bypass catalyzed by numerous DNA polymerases.
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