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The effect of hydrodynamic interactions on the dynamics of DNA translocation through pores

J. Chem. Phys. 128, 085102 (2008); doi:10.1063/1.2831777

Published 25 February 2008

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Aslin Izmitli, David C. Schwartz, Michael D. Graham, and Juan J. de Pablo
Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706-1691, USA
In this work, we investigate the effect of hydrodynamic interactions on the dynamics of DNA translocation through micropores. We simulate DNA as a bead-spring chain and use a lattice Boltzmann method to simulate the flow field that arises from the motion of the molecule. We investigate the free-draining entrance of DNA to the pore by diffusion and find that, consistent with experiments, molecules have a higher probability of entering the pore from one end. We then consider the electric-field driven translocation of 21–210  µm DNA with and without hydrodynamic interactions. Consistent with experiments, we study translocation events that are much shorter than the relaxation time of DNA. We find that the effect of hydrodynamic interactions on this process is to cause different regions of a molecule, other than the ones pulled by voltage or chain connectivity into the pore, to move toward the pore. We quantify this effect and show that it is smaller than the difference in the translocation dynamics of chains that arises from different initial configurations of the molecules. A power-law scaling of translocation time with chain length is observed, with exponents of 1.28±0.03 and 1.31±0.03 in simulations with and without hydrodynamic interactions, respectively. Our results are in good agreement with recent translocation experiments conducted in small pores and show that, for the regime considered in this work, hydrodynamic interactions play a minor role in the relation of the translocation time to chain length. For fast translocation processes, the effect of hydrodynamic interactions is local and the main factor determining the dynamics of DNA is the initial configuration of the molecules. ©2008 American Institute of Physics
History: Received 4 May 2007; accepted 13 December 2007; published 25 February 2008
Permalink: http://link.aip.org/link/?JCPSA6/128/085102/1
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KEYWORDS and PACS

Keywords
PACS
  • 87.15.Vv
    Diffusion (molecular biophysics)
  • 87.15.hg
    Dynamics of intermolecular interactions in biomolecules
  • 87.10.-e
    General theory and mathematical aspects (biological/medical physics)
  • YEAR: 2008

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PUBLICATION DATA

ISSN:
0021-9606 (print)   1089-7690 (online)
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