Nonequilibrium thermodynamics of DNA nanopore unzipping

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.

6 pages, 4 figures

References in corpus (4)

• Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA
• Single-molecule derivation of salt dependent base-pair free energies in DNA
• Nonequilibrium dynamics of polymer translocation and straightening
• Stem-loop formation drives RNA folding in mechanical unzipping experiments

Cited by in corpus (4)

• Coarse-grained modelling of DNA-RNA hybrids
• Fluctuation theorems with optical tweezers: theory and practice
• Inverse thermodynamic uncertainty relation and entropy production
• Hotter isn't faster for a melting RNA hairpin