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J Phys Chem C Nanomater Interfaces. 2012 Feb 9;116(5):3376-3393. Epub 2012 Jan 9.

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

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1
Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.

Abstract

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.

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