title: Diffusive dynamics of DNA unzipping in a nanopore.
abstract: When an electric field is applied to an insulating membrane, movement of charged particles through a nanopore is induced. The measured ionic current reports on biomolecules passing through the nanopore. In this work, we explored the kinetics of DNA unzipping in a nanopore using our coarse-grained model (Stachiewicz and Molski, J. Comput. Chem. 2015, 36, 947). Coarse graining allowed a more detailed analysis for a wider range of parameters than all-atom simulations. Dependence of the translocation mode (unzipping or distortion) on the pore diameter was examined, and the threshold voltages were estimated. We determined the potential of mean force, position-dependent diffusion coefficient, and position-dependent effective charge for the DNA unzipping. The three molecular profiles were correlated with the ionic current and molecular events. On the unzipping/translocation force profile, two energy maxima were found, one of them corresponding to the unzipping, and the other to the translocation barriers. The unzipping kinetics were further explored using Brownian dynamics.
authors.affiliation: Department of Chemistry, Adam Mickiewicz University, Poznań, Poland.
authors.forename: Anna
authors.initials: A
authors.lastname: Stachiewicz
authors.affiliation: Department of Chemistry, Adam Mickiewicz University, Poznań, Poland.
authors.forename: Andrzej
authors.initials: A
authors.lastname: Molski
mesh_terms: D004247:DNA / Q000737:chemistry*; D004058:Diffusion; D004560:Electricity; D007700:Kinetics; D008567:Membranes, Artificial; D056004:Molecular Dynamics Simulation; D058608:Nanopores; D009690:Nucleic Acid Conformation; D009994:Osmolar Concentration; D013816:Thermodynamics
chemical_list: D008567:Membranes, Artificial; D004247:DNA
keywords: Brownian dynamics; DNA; molecular dynamics; nanopores; unzipping kinetics