The University of Southampton
University of Southampton Institutional Repository

The nucleotide capture region of alpha hemolysin: insights into nanopore design for DNA sequencing from molecular dynamics simulations

The nucleotide capture region of alpha hemolysin: insights into nanopore design for DNA sequencing from molecular dynamics simulations
The nucleotide capture region of alpha hemolysin: insights into nanopore design for DNA sequencing from molecular dynamics simulations
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.
alpha-hemolysin, exonuclease sequencing, molecular dynamics, nanopore sequencing
2079-4991
144-153
Manara, Richard
33709a59-e423-40dc-a1b8-0880df386cb4
Tomasio, Susana
f6211d6f-c068-4007-8dfa-83a2da758d1a
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394
Manara, Richard
33709a59-e423-40dc-a1b8-0880df386cb4
Tomasio, Susana
f6211d6f-c068-4007-8dfa-83a2da758d1a
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394

Manara, Richard, Tomasio, Susana and Khalid, Syma (2015) The nucleotide capture region of alpha hemolysin: insights into nanopore design for DNA sequencing from molecular dynamics simulations. Nanomaterials, 5 (1), 144-153. (doi:10.3390/nano5010144).

Record type: Article

Abstract

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.

Full text not available from this repository.

More information

Accepted/In Press date: 12 January 2015
Published date: 27 January 2015
Keywords: alpha-hemolysin, exonuclease sequencing, molecular dynamics, nanopore sequencing
Organisations: Chemistry, Faculty of Natural and Environmental Sciences, Computational Systems Chemistry

Identifiers

Local EPrints ID: 374227
URI: http://eprints.soton.ac.uk/id/eprint/374227
ISSN: 2079-4991
PURE UUID: 96687f96-cdb3-454a-bcaf-502522169f2b
ORCID for Syma Khalid: ORCID iD orcid.org/0000-0002-3694-5044

Catalogue record

Date deposited: 10 Feb 2015 12:54
Last modified: 20 Jul 2019 00:51

Export record

Altmetrics

Download statistics

Downloads from ePrints over the past year. Other digital versions may also be available to download e.g. from the publisher's website.

View more statistics

Atom RSS 1.0 RSS 2.0

Contact ePrints Soton: eprints@soton.ac.uk

ePrints Soton supports OAI 2.0 with a base URL of http://eprints.soton.ac.uk/cgi/oai2

This repository has been built using EPrints software, developed at the University of Southampton, but available to everyone to use.

We use cookies to ensure that we give you the best experience on our website. If you continue without changing your settings, we will assume that you are happy to receive cookies on the University of Southampton website.

×