Dynamics of a bubble formed in double stranded DNA

TL;DR

This paper models the fluctuational dynamics of a specific base-pair in double-stranded DNA, deriving a drift force and autocorrelation functions that align well with experimental data, providing insights into DNA base-pair motion.

Contribution

It introduces a potential model at the base-pair level to calculate drift forces and autocorrelation functions, matching experimental observations.

Findings

Displacement autocorrelation function agrees with experimental data

Calculated most probable displacements highlight dominant motion contributions

Half-time displacement history provides dynamic insights

Abstract

We study the fluctuational dynamics of a tagged base-pair in double stranded DNA. We calculate the drift force which acts on the tagged base-pair using a potential model that describes interactions at base pairs level and use it to construct a Fokker-Planck equation.The calculated displacement autocorrelation function is found to be in very good agreement with the experimental result of Altan-Bonnet {\it et. al.} Phys. Rev. Lett. {\bf 90}, 138101 (2003) over the entire time range of measurement. We calculate the most probable displacements which predominately contribute to the autocorrelation function and the half-time history of these displacements.