Paper Citing NAMD - Abstract
Comer, Jeffrey; Aksimentiev, Aleksei
Predicting the DNA Sequence Dependence of Nanopore Ion Current Using Atomic-Resolution Brownian Dynamics
JOURNAL OF PHYSICAL CHEMISTRY C, 116:3376-3393, FEB 9 2012
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 resu(l)t with all-atom molecular dynamics.
