Theoretical study of sequence-dependent nanopore unzipping of DNA.
We theoretically investigate the unzipping of DNA electrically driven through a nanometer-size pore. Taking the DNA base sequence explicitly into account, the unpairing and translocation process is described by a biased random walk in a one-dimensional energy landscape determined by the sequential basepair opening. Distributions of translocation times are numerically calculated as a function of applied voltage and temperature. We show that varying these two parameters changes the dynamics from a predominantly diffusive behavior to a dynamics governed by jumps over local energy barriers. The work suggests experimentally studying sequence effects, by comparing the average value and standard deviation of the statistical distribution of translocation times.
Bockelmann
U
U
Nanobiophysique, Ecole Superieure Physique et Chimie Industrielles, Centre National de Recherche Scientifique, Paris, France. ulrich.bockelmann@espci.fr
Viasnoff
V
V
D001483:Base Sequence; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000528:radiation effects / Q000648:ultrastructure*; D018274:Electroporation / Q000379:methods*; D008051:Lipid Bilayers / Q000737:chemistry* / Q000528:radiation effects; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D049329:Nanostructures / Q000737:chemistry / Q000528:radiation effects / Q000648:ultrastructure; D009690:Nucleic Acid Conformation; D016062:Porosity
D008051:Lipid Bilayers; D004247:DNA