Nucleotide insertion initiated by van der Waals interaction during polymerase beta DNA replication

Abstract

We give unambiguous theoretical analyses and show that the exclusive biochemical reaction involved in a single nucleotide insertion into the DNA primer can be efficiently tracked using the renormalized van der Waals (vdW) interaction of a stronger type, the Hermansson blue-shifting hydrogen bond effect, and the Arunan composite hydrogen-vdW bond. We find that there are two biochemical steps involved to complete the insertion of a single base (cytosine) into the 3$'$ end of a DNA primer. First, the O3$'$ (from a DNA primer) initiates the nucleophilic attack on P$_{\alpha}$ (from an incoming dCTP), in response, O3$_{\alpha}$ (bonded to P$_{\alpha}$) interacts with H$'$ (bonded to O3$'$). These interactions are shown to be strongly interdependent and require the forming and breaking of P---O and H---O covalent bonds, which in turn imply that we do not need any external energy supply.