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

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$_α$ (from an incoming dCTP), in response, O3$_α$ (bonded to P$_α$) 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.

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