Slowing down DNA translocation through a nanopore in lithium chloride

  • Kowalczyk S
  • Wells D
  • Aksimentiev A
 et al. 
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Abstract

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.

Author-supplied keywords

  • DNA
  • Nanopore
  • effective charge
  • lithium chloride
  • molecular dynamics
  • single molecule

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Authors

  • Stefan W. Kowalczyk

  • David B. Wells

  • Aleksei Aksimentiev

  • Cees Dekker

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