Nonequilibrium thermodynamics of DNA nanopore unzipping

TL;DR

This paper systematically characterizes DNA unzipping via nanopore translocation using theory and simulations, revealing three force-dependent regimes and modeling the process as a stochastic system to recover free-energy landscapes.

Contribution

It introduces a novel theoretical framework to analyze DNA unzipping dynamics and extract free-energy landscapes from nonequilibrium trajectories.

Findings

Identified three distinct force regimes affecting DNA unzipping behavior.

Modeled the normal drift-diffusion regime as a stochastic process in a tilted periodic potential.

Demonstrated the ability to recover free-energy landscapes from unzipping trajectories.

Abstract

Using theory and simulations, we carried out a first systematic characterization of DNA unzipping via nanopore translocation. Starting from partially unzipped states, we found three dynamical regimes depending on the applied force, f: (i) heterogeneous DNA retraction and rezipping (f < 17pN), (ii) normal (17pN < f < 60pN) and (iii) anomalous (f > 60pN) drift-diffusive behavior. We show that the normal drift-diffusion regime can be effectively modelled as a one-dimensional stochastic process in a tilted periodic potential. We use the theory of stochastic processes to recover the potential from nonequilibrium unzipping trajectories and show that it corresponds to the free-energy landscape for single base-pairs unzipping. Applying this general approach to other single-molecule systems with periodic potentials ought to yield detailed free-energy landscapes from out-of-equilibrium trajectories.