Water Mediates Recognition of DNA Sequence via Ionic Current Blockade in a Biological Nanopore

Swati Bhattacharya, Jejoong Yoo, Aleksei Aksimentiev

Research output: Contribution to journalArticlepeer-review


Electric field-driven translocation of DNA strands through biological nanopores has been shown to produce blockades of the nanopore ionic current that depend on the nucleotide composition of the strands. Coupling a biological nanopore MspA to a DNA processing enzyme has made DNA sequencing via measurement of ionic current blockades possible. Nevertheless, the physical mechanism enabling the DNA sequence readout has remained undetermined. Here, we report the results of all-atom molecular dynamics simulations that elucidated the physical mechanism of ionic current blockades in the biological nanopore MspA. We find that the amount of water displaced from the nanopore by the DNA strand determines the nanopore ionic current, whereas the steric and base-stacking properties of the DNA nucleotides determine the amount of water displaced. Unexpectedly, we find the effective force on DNA in MspA to undergo large fluctuations, which may produce insertion errors in the DNA sequence readout.

Original languageEnglish (US)
Pages (from-to)4644-4651
Number of pages8
JournalACS Nano
Issue number4
StatePublished - Apr 26 2016


  • blockade current
  • molecular dynamics
  • nanopore sequencing
  • nucleic acids
  • solvation

ASJC Scopus subject areas

  • Materials Science(all)
  • Engineering(all)
  • Physics and Astronomy(all)


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