Article

Theoretical study of sequence-dependent nanopore unzipping of DNA.

Nanobiophysique, Ecole Superieure Physique et Chimie Industrielles, Centre National de Recherche Scientifique, Paris, France.
Biophysical Journal (impact factor: 3.65). 05/2008; 94(7):2716-24. DOI:10.1529/biophysj.107.111732 pp.2716-24
Source: PubMed

ABSTRACT 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.

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Keywords

biased random walk
 
diffusive behavior
 
Distributions
 
DNA base sequence
 
DNA electrically
 
dynamics
 
one-dimensional energy landscape
 
statistical distribution
 
translocation process
 
two parameters changes
 
unpairing
 

U Bockelmann