Slowing down DNA translocation through a nanopore in lithium chloride

Stefan W. Kowalczyk, David B. Wells, Aleksei Aksimentiev, Cees Dekker

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Pages (from-to)1038-1044
Number of pages7
JournalNano letters
Issue number2
StatePublished - Feb 8 2012


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

ASJC Scopus subject areas

  • Bioengineering
  • Chemistry(all)
  • Materials Science(all)
  • Condensed Matter Physics
  • Mechanical Engineering


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