Nonequilibrium Thermodynamics of DNA Nanopore Unzipping

Phys Rev Lett. 2023 Jan 27;130(4):048101. doi: 10.1103/PhysRevLett.130.048101.

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<17 pN), (ii) normal (17 pN<f<60 pN), and (iii) anomalous (f>60 pN) drift-diffusive behavior. We show that the normal drift-diffusion regime can be effectively modeled 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-pair 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.

MeSH terms

  • Base Pairing
  • DNA / genetics
  • Nanopores*
  • Nucleic Acid Conformation
  • Thermodynamics

Substances

  • DNA