Molecular dynamics study of MspA arginine mutants predicts slow DNA translocations and ion current blockades indicative of DNA sequence

Academic Article

Abstract

  • The protein nanopore Mycobacteria smegmatis porin A (MspA), can be used to sense individual nucleotides within DNA, potentially enabling a technique known as nanopore sequencing. In this technique, single-stranded DNA electrophoretically moves through the nanopore and results in an ionic current that is nucleotide-specific. However, with a high transport velocity of the DNA within the nanopore, the ionic current cannot be used to distinguish signals within noise. Through extensive (∼100 μs in total) all-atom molecular dynamics simulations, we examine the effect of positively charged residues on DNA translocation rate and the ionic current blockades in MspA. Simulation of several arginine mutations show a ∼10-30 fold reduction of DNA translocation speed without eliminating the nucleotide induced current blockages. Comparison of our results with similar engineering efforts on a different nanopore (α-hemolysin) reveals a nontrivial effect of nanopore geometry on the ionic current blockades in mutant nanopores. © 2012 American Chemical Society.
  • Published In

  • ACS Nano  Journal
  • Digital Object Identifier (doi)

    Author List

  • Bhattacharya S; Derrington IM; Pavlenok M; Niederweis M; Gundlach JH; Aksimentiev A
  • Start Page

  • 6960
  • End Page

  • 6968
  • Volume

  • 6
  • Issue

  • 8