Statistical Theory of Force Induced Unzipping of DNA

TL;DR

This paper develops a statistical physics model to analyze the force-induced unzipping transition of DNA, revealing how force depends on molecular parameters and how mismatches affect unzipping behavior.

Contribution

It introduces a Peyrard-Bishop Hamiltonian-based framework to study DNA unzipping, including effects of mismatches and specific structural formations like loops and bubbles.

Findings

Critical force depends on DNA stiffness and potential depth.

Force required varies with base pair location along DNA.

Mismatches alter unzipping peak characteristics.

Abstract

The unzipping transition under the influence of external force of a dsDNA molecule has been studied using the Peyrard-Bishop Hamiltonian. The critical force $F_c(T)$ is found to depend on the potential parameters $k$, represents the stiffness of single strand of DNA and the potential depth $D$. We used constant extension ensemble to calculate the average force needed to stretch a base pair $y$ distance apart. A very large peak around $y = 1 {\rm \AA}$ is found. The value of $F(y)$ needed to stretch a base pair located far away from the ends of a dsDNA molecule is found twice the value of the force needed to stretch a base pair located at one of the ends to the same distance. The effect of mismatching in the base pairs on the peak height and position is investigated. The formation and behaviour of a loop of Y shape when one of the ends base pair is stretched and a bubble of ssDNA with the shape of "an eye" when a base pair far from ends is stretched are investigated.