Nonequilibrium Thermodynamics of DNA Nanopore Unzipping
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.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2023 |
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| Erschienen: |
2023 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:130 |
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| Enthalten in: |
Physical review letters - 130(2023), 4 vom: 27. Jan., Seite 048101 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Suma, Antonio [VerfasserIn] |
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Date Completed 14.02.2023 Date Revised 14.02.2023 published: Print Citation Status MEDLINE |
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| doi: |
10.1103/PhysRevLett.130.048101 |
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| Förderinstitution / Projekttitel: |
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| 520 | |a 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 | ||
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| 700 | 1 | |a Micheletti, Cristian |e verfasserin |4 aut | |
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