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

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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Identifiers

ORCID for Syma Khalid: orcid.org/0000-0002-3694-5044

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