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Theoretical Study of Sequence-Dependent Nanopore Unzipping of DNA

Nanobiophysique, Ecole Superieure Physique et Chimie Industrielles, Centre National de la Recherche Scientifique, Paris, France

Correspondence: Address reprint requests to Ulrich Bockelmann, Tel.: 33-1-4079-4761; E-mail: ulrich.bockelmann{at}espci.fr.

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.