Molecular dynamics and quantum simulations of conformational changes of dGTP and oxo-dGTP based on study of Dpo4 polymerase

Kotulic Bunta, J.*; Pinak, M.; Saito, Kimiaki  

DNA polymerase IV (Dpo4) is the crucial enzyme in the process of DNA recombination, being responsible for extending primer by incorporating new nucleotides. This study is focused on the incoming nucleotide which is primarily in a form of Guanosinetriphosphate (dGTP) molecule. Oxidation of the dGTP molecule to 8-OH-dGTP state can cause mutation in the process of recombination, enabled by precedent conformational change of 8-OH-dGTP molecule from -anti to -syn conformation. This work describes important aspects of this change as well as relation of the oxidized 8-OH-dGTP to surrounding amino acids in the polymerase.