Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution brownian dynamics

Jeffrey Comer, Aleksei Aksimentiev

Research output: Contribution to journalArticlepeer-review


It has become possible to distinguish DNA molecules of different nucleotide sequences by measuring ion current passing through a narrow pore containing DNA. To assist experimentalists in interpreting the results of such measurements and to improve the DNA sequence detection method, we have developed a computational approach that has both the atomic-scale accuracy and the computational efficiency required to predict DNA sequence-specific differences in the nanopore ion current. In our Brownian dynamics method, the interaction between the ions and DNA is described by three-dimensional potential of mean force maps determined to a 0.03 nm resolution from all-atom molecular dynamics simulations. While this atomic-resolution Brownian dynamics method produces results with orders of magnitude less computational effort than all-atom molecular dynamics requires, we show here that the ion distributions and ion currents predicted by the two methods agree. Finally, using our Brownian dynamics method, we find that a small change in the sequence of DNA within a pore can cause a large change in the ion current and validate this result with all-atom molecular dynamics.

Original languageEnglish (US)
Pages (from-to)3376-3393
Number of pages18
JournalJournal of Physical Chemistry C
Issue number5
StatePublished - Feb 9 2012

ASJC Scopus subject areas

  • Electronic, Optical and Magnetic Materials
  • Energy(all)
  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films


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