Talk abstracts

Talk on Saturday 10:35-10:50am submitted by Shanen Sherrer

Mechanistic studies of the bypass of a bulky single-base lesion catalyzed by a Y-family DNA polymerase

Shanen M. Sherrer (Department of Biochemistry, The Ohio State University), Jessica A. Brown, Lindsey R. Pack (Department of Biochemistry, The Ohio State University), Vijay P. Jasati (Department of Chemistry, University of Connecticut), Jason D. Fowler (Department of Biochemistry, The Ohio State University), Ashis K. Basu (Department of Chemistry, University of Connecticut), Zucai Suo (Department of Biochemistry, The Ohio State University)

Abstract:
1-Nitropyrene, the most abundant nitro polyaromatic hydrocarbon in gasoline/diesel emissions, reacts with DNA via nitro reduction to form predominantly N-(deoxyguanosin-8-yl)-1-aminopyrene (dG-AP). This DNA lesion stalls replicative DNA polymerases and causes genetic mutations in vivo, which may implicate the involvement of Y-family DNA polymerases. To elucidate a bypass mechanism for such a bulky lesion catalyzed by a Y-family DNA polymerase, a pre-steady state kinetic study was initiated. For this study, model Y-family enzyme Sulfolobus solfataricus DNA polymerase IV (Dpo4) was chosen to investigate nucleotide incorporation upstream, opposite and downstream of the dG-AP lesion. It was demonstrated that Dpo4 bypassed dG-AP with significant pausing during the incorporation opposite the lesion and the extension of the bypass products. At the first pause site, Dpo4 decreased 9-fold in catalytic efficiency and up to 42-fold in fidelity. At the second pause site, Dpo4 decreased 88-fold in catalytic efficiency and up to 100-fold in fidelity. Interestingly, DNA binding affinity increased 4-fold only at the first pause site, suggesting hydrophobic interactions between DNA adduct and amino acid residues within the active site. Thus, the extension of the dG-AP bypass product was more problematic than the insertion opposite the dG-AP lesion. During single-turnover incorporation in the presence of DNA trap, the kinetics at the pause sites were determined to be biphasic with total product less than 70 percent. In contrast, the corresponding control DNA substrates are monophasic with total product 90 percent. Understanding how a Y-family polymerase bypasses dG-AP mechanistically will provide valuable insight into the mutagenic effects of nitro PAHs.

Keywords: Dpo4, 1-nitropyrene, translesion DNA synthesis