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.