Sunday, January 29, 2012

Slowing down DNA Translocation through a Nanopore in Lithium Chloride

Stefan W. Kowalczyk, David B. Wells, Aleksei Aksimentiev, and Cees Dekker*
Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
Department of Physics and Beckman Institute for Advances Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
Nano Lett., Article ASAP
DOI: 10.1021/nl204273h
Publication Date (Web): January 9, 2012
Copyright © 2012 American Chemical Society
 
 The charge of a DNA molecule is a crucial parameter in many DNA detection and manipulation schemes such as gel electrophoresis and lab-on-a-chip applications. Here, we study the partial reduction of the DNA charge due to counterion binding by means of nanopore translocation experiments and all-atom molecular dynamics (MD) simulations. Surprisingly, we find that the translocation time of a DNA molecule through a solid-state nanopore strongly increases as the counterions decrease in size from K+ to Na+ to Li+, both for double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA). MD simulations elucidate the microscopic origin of this effect: Li+ and Na+ bind DNA stronger than K+. These fundamental insights into the counterion binding to DNA also provide a practical method for achieving at least 10-fold enhanced resolution in nanopore applications.

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