Molecular dynamics studies of polymerase X/DNA complexes in the presence of OxoG on the templating strand

Abstract

The African Swine Fever Virus (ASFV) is an encapsulated deoxyvirus known to induce a lethal infection in domestic pigs. The double‐stranded DNA viral genome encodes a total of 151 proteins, including a minimal DNA repair system, with a repair polymerase, pol X, which catalyses a single‐nucleotide filling in gapped DNA. Pol X, is the smallest naturally occurring DNA‐directed DNA polymerase described so far. It belongs to the X family of polymerases and shares sequence and structure similarity with human DNA polymerase β (pol β). However, where pol β is a moderate fidelity enzyme, pol X is much more error tolerant. In this study, we are exploring several pol X/DNA complexes in which the templating base pair opposite to the incoming nucleotide contains the damaged base 7,8‐Dihydro‐8‐oxoguanine (oxoG). OxoG is one of the major known products of oxidation of DNA by reactive oxygen species (ROS). Since the African swine fever virus's components are in an active state of respiration, it is conceivable that the virus may encounter this common ROS‐induced DNA lesion. Kinetics data have shown that pol X accommodates A opposite to oxoG, with efficiency even higher than the non‐damaged G:C base pair. Thus, the goal of this molecular dynamics study is to explore combinations of oxoG:A, oxoG:G and oxoG:C systems to elucidate, at an atomistic level, the kinetics data. Research was supported by the Rose M. Badgeley Charitable Trust.