@article {26,
	title = {Molecular dynamics study of MspA arginine mutants predicts slow DNA translocations and ion current blockades indicative of DNA sequence},
	journal = {ACS Nano},
	volume = {6},
	year = {2012},
	month = {2012 Aug 28},
	pages = {6960-8},
	abstract = {<p>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.</p>
},
	keywords = {Arginine, Base Sequence, Biosensing Techniques, Computer Simulation, Conductometry, DNA, Electric Conductivity, Ion Channel Gating, Models, Chemical, Models, Genetic, Models, Molecular, Molecular Sequence Data, Mutation, Porins, Sequence Analysis, DNA, Translocation, Genetic},
	issn = {1936-086X},
	doi = {10.1021/nn3019943},
	author = {Bhattacharya, Swati and Derrington, Ian M and Pavlenok, Mikhail and Niederweis, Michael and Gundlach, Jens H and Aleksei Aksimentiev}
}
