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Nanomaterials 2015, 5(1), 144-153;

The Nucleotide Capture Region of Alpha Hemolysin: Insights into Nanopore Design for DNA Sequencing from Molecular Dynamics Simulations

School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
Author to whom correspondence should be addressed.
Academic Editor: Stephen Ralph
Received: 26 November 2014 / Revised: 7 January 2015 / Accepted: 12 January 2015 / Published: 27 January 2015
(This article belongs to the Special Issue Frontiers in Nucleic Acid Nanotechnology)
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Nanopore technology for DNA sequencing is constantly being refined and improved. In strand sequencing a single strand of DNA is fed through a nanopore and subsequent fluctuations in the current are measured. A major hurdle is that the DNA is translocated through the pore at a rate that is too fast for the current measurement systems. An alternative approach is “exonuclease sequencing”, in which an exonuclease is attached to the nanopore that is able to process the strand, cleaving off one base at a time. The bases then flow through the nanopore and the current is measured. This method has the advantage of potentially solving the translocation rate problem, as the speed is controlled by the exonuclease. Here we consider the practical details of exonuclease attachment to the protein alpha hemolysin. We employ molecular dynamics simulations to determine the ideal (a) distance from alpha-hemolysin, and (b) the orientation of the monophosphate nucleotides upon release from the exonuclease such that they will enter the protein. Our results indicate an almost linear decrease in the probability of entry into the protein with increasing distance of nucleotide release. The nucleotide orientation is less significant for entry into the protein. View Full-Text
Keywords: alpha-hemolysin; exonuclease sequencing; molecular dynamics; nanopore sequencing alpha-hemolysin; exonuclease sequencing; molecular dynamics; nanopore sequencing

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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Manara, R.M.A.; Tomasio, S.; Khalid, S. The Nucleotide Capture Region of Alpha Hemolysin: Insights into Nanopore Design for DNA Sequencing from Molecular Dynamics Simulations. Nanomaterials 2015, 5, 144-153.

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