Computational insights into the molecular basis for the replication of flexible tobacco-derived DNA lesions

Abstract

DNA is damaged by many agents in the environment and this affects many cellular processes, including DNA replication. The present thesis uses a multiscale computational modeling approach to study the intrinsic conformational and base-pairing preferences of flexible O6-G and O2-T alkyl DNA lesions, and the corresponding properties within DNA duplexes and polymerase active sites. Specifically, the replication of O6-benzylguanine (Bz-G) by a prototypical DNA polymerase, DNA polymerase IV, as well as the replication of the tobacco-derived carcinogens, O6-[4-oxo-4-(3-pyridyl)butyl]guanine (POB-G), O6-[4-hydroxy-4-(3-pyridyl)butyl]guanine (PHB-G), and O2-[4-oxo-4-(3-pyridyl)butyl] thymine (POB-T), by human DNA polymerases η and κ, were investigated. This work uncovers structural bases for the reported lesion mutagenicity and biological processing. Additionally, a consistent theoretical framework was used to provide insight into the previously unidentified general base for the nucleotidyl transfer reaction catalyzed by polymerase η. Overall, this thesis emphasizes the complex interplay between many factors that are required to replicate damaged DNA.