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

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• 作者：Swati Bhattacharya ; Jejoong Yoo ; Aleksei Aksimentiev
• 刊名：ACS Nano
• 出版年：2016
• 出版时间：April 26, 2016
• 年：2016
• 卷：10
• 期：4
• 页码：4644-4651
• 全文大小：638K
• 年卷期：0
• ISSN：1936-086X

文摘

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.