A new approach to microscopic modeling of a hole transfer in heteropolymer DNA

TL;DR

This paper introduces a stochastic microscopic model for hole transfer in heteropolymer DNA, incorporating thermal oscillations and base overlap fluctuations, achieving good agreement with experimental kinetics.

Contribution

It presents a novel stochastic approach to model base overlap fluctuations affecting hole transfer in DNA, extending previous deterministic models.

Findings

Stochastic fluctuations significantly influence hole transfer kinetics.

Model reproduces experimental data across various parameters.

Thermal oscillations are effectively simulated by stochastic base overlap fluctuations.

Abstract

Thermal oscillations of base pairs in the Peyrard-Bishop-Holstein model are simulated by stochastic fluctuations of base overlap integrals. Numerical investigation of the model is carried out for a hole transfer in $G_1A_2G_3G_4$ sequence which was previously studied experimentally by F. Lewis et al. A hole migration between $G_1$ and $G_3G_4$ is determined by the matrix elements of the charge transition, but presence and amplitude of their stochastic fluctuations proved to play a key role in reproduction of the experimental kinetics. Good agreement with the experimental data was obtained for a wide range of the model parameters' combinations.