An Investigation into ssDNA translocation through protein nanopores

Abstract

DNA sequencing is of great significance to molecular biology with myriad applications in fields such as medical research, and yet for the majority of its history the only commercially available method has been Sanger sequencing, which is still a costly and slow process despite recent improvements. Protein nanopores present an exciting direction for DNA sequencing, with the first commercial devices becoming available in 2015. Current research into sequencing with protein nanopores is mainly focussed on slowing down DNA translocation through the pore and improving the read resolution between bases. This work focusses on investigating the suitability of protein nanopores incorporating a hydrophobic constriction region for DNA sequencing applications, with two directions of approach. An investigation into the conformational behaviour and translocation speed through the protein nanopores, and a subsequent investigation into the ability of the protein nanopores to discern between individual nucleotides during translocation. It is shown that ssDNA translocates through these pores in an extended linear conformation, without the formation of secondary structures that can reduce the accuracy of DNA sequencing. The ability of these pores to distinguish between different nucleotides during translocation remains unclear, however the easily modifiable nature of the hydrophobic constrictions leaves myriad possible routes to improve this aspect of ssDNA sequencing.

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

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