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arXiv · 2212.05882

Nonequilibrium thermodynamics of DNA nanopore unzipping

Antonio Suma·Vincenzo Carnevale·Cristian Micheletti
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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.

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Antonio Suma, Vincenzo Carnevale, Cristian Micheletti. 2022-12-12. Nonequilibrium thermodynamics of DNA nanopore unzipping. https://doi.org/10.1103/physrevlett.130.048101

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