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Free energy calculations of DNA translocation through protein nanopores and nanopore design for DNA sequencing

Free energy calculations of DNA translocation through protein nanopores and nanopore design for DNA sequencing
Free energy calculations of DNA translocation through protein nanopores and nanopore design for DNA sequencing
DNA sequencing has vastly opened up the world of molecular biology, leading to new areas of interest, especially in medical research. Unfortunately the methods of DNA sequencing have only ever seen gradual improvements, as Sanger sequencing is still very much the norm despite its high cost and slow speed. Nanopores present an exciting opportunity for DNA sequencing, however, despite the concept being presented in 1996 several problems have prevented the creation of a publicly available sequencing device. The two main focuses of research into nanopores so far have been improving the resolution between bases and the slowing down of DNA translocation through the pore so modern ammeters can read the sequence accurately. The simulation work presented in this thesis largely focuses on the energetics associated with DNA translocation. This is performed in several parts; an investigation into the probability of pore entry, study into the free energy of translocation for two proteins in addition to solvent contribution to this free energy, finally a theoretical project was undertaken to investigate bottom up nanopore design.
Manara, Richard
33709a59-e423-40dc-a1b8-0880df386cb4
Manara, Richard
33709a59-e423-40dc-a1b8-0880df386cb4
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394

(2015) Free energy calculations of DNA translocation through protein nanopores and nanopore design for DNA sequencing. University of Southampton, Chemistry, Doctoral Thesis, 288pp.

Record type: Thesis (Doctoral)

Abstract

DNA sequencing has vastly opened up the world of molecular biology, leading to new areas of interest, especially in medical research. Unfortunately the methods of DNA sequencing have only ever seen gradual improvements, as Sanger sequencing is still very much the norm despite its high cost and slow speed. Nanopores present an exciting opportunity for DNA sequencing, however, despite the concept being presented in 1996 several problems have prevented the creation of a publicly available sequencing device. The two main focuses of research into nanopores so far have been improving the resolution between bases and the slowing down of DNA translocation through the pore so modern ammeters can read the sequence accurately. The simulation work presented in this thesis largely focuses on the energetics associated with DNA translocation. This is performed in several parts; an investigation into the probability of pore entry, study into the free energy of translocation for two proteins in addition to solvent contribution to this free energy, finally a theoretical project was undertaken to investigate bottom up nanopore design.

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More information

Published date: 19 February 2015
Organisations: University of Southampton, Chemistry

Identifiers

Local EPrints ID: 374791
URI: http://eprints.soton.ac.uk/id/eprint/374791
PURE UUID: f725b80e-2a15-48c8-b1a5-cc689ff0c72f
ORCID for Syma Khalid: ORCID iD orcid.org/0000-0002-3694-5044

Catalogue record

Date deposited: 11 May 2015 10:30
Last modified: 14 Jul 2018 00:32

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