Journal
JOURNAL OF PHYSICAL CHEMISTRY C
Volume 116, Issue 5, Pages 3376-3393Publisher
AMER CHEMICAL SOC
DOI: 10.1021/jp210641j
Keywords
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Funding
- National Science Foundation [DMR-0955959]
- National Institutes of Health [R01-HG005115, P41-RR005969]
- TeraGrid [MCA05S028]
- Direct For Mathematical & Physical Scien
- Division Of Materials Research [955959] Funding Source: National Science Foundation
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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.
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