Theoretical study of sequence dependent nanopore
unzipping of DNA
Ulrich Bockelmann 1* and Virgile Viasnoff 1
1 ESPCI
* To whom correspondence should be addressed. E-mail: ulrich.bockelmann{at}espci.fr.
Submitted on April 30, 2007
Revised on July 18, 2007
Accepted on 12 November 2007
 |
Abstract |
|---|
We theoretically investigate the unzipping of DNA electrically driven through a nanometer size pore. Taking the DNA base sequence explicitely 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 behaviour 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.
Key Words:
Alpha-hemolysin, Biased diffusion, Monte Carlo simulation, Nucleic acids, Single molecule, Translocation through pores
