Nonequilibrium Work Fluctuations in Force-induced Melting of a Short B-DNA

TL;DR

This study investigates the nonequilibrium work fluctuations during force-induced melting of short B-DNA, using pulling experiments and the Jarzynski equality to determine free energy differences.

Contribution

It demonstrates how nonequilibrium work measurements can accurately estimate DNA melting free energies, validating the approach with experimental data.

Findings

Work distribution $P(W)$ characterized for DNA melting

Free energy difference $ riangle F$ matches equilibrium estimates

Method validates nonequilibrium work as a tool for biomolecular thermodynamics

Abstract

A system of a solvated canonical B-DNA of 12 base pairs with the specified sequence is initially equilibrated in a state of zero external force $f$ acting on it. After equilibration, a switching experiment is performed over the system by pulling one end of the DNA while restraining its other end. The finite time pulling process is performed at a constant rate of the applied force until a maximum value of 400 pN. The associated nonequilibrium work done $(W)$ during this process is determined by numerically integrating the force-extension curve as a function of the applied force. An ensemble of the work values, $P(W)$, is obtained by repeating the pulling experiment a large number of times. We determine the free energy difference $(\Delta F)$ between the equilibrium and force-induced melted states of the DNA by employing the Jarzynski equality. The value of $\Delta F$ is found to be in close agreement with the conventional equilibrium methods.