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Issue 3, 2021

Translocation of flexible and tensioned ssDNA through in silico designed hydrophobic nanopores with two constrictions

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Abstract

Protein-inspired nanopores with hydrophobic constriction regions have previously been shown to offer some promise for DNA sequencing. Here we explore a series of pores with two hydrophobic constrictions. The impact of nanopore radius, the nature of residues that define the constriction region and the flexibility of the ssDNA is explored. Our results show that aromatic residues slow down DNA translocation, and in the case of short DNA strands, they cause deviations from a linear DNA conformation. When DNA is under tension, translocation is once again slower when aromatic residues are present in the constriction. However, the lack of flexibility in the DNA backbone provides a narrower window of opportunity for the DNA bases to be retained inside the pore via interaction with the aromatic residues, compared to more flexible strands. Consequently, there is more variability in translocation rates for strands under tension. DNA entry into the pores is correlated to pore width, but no such correlation between width and translocation rate is observed.

Graphical abstract: Translocation of flexible and tensioned ssDNA through in silico designed hydrophobic nanopores with two constrictions

Supplementary files

Article information


Submitted
29 Jun 2020
Accepted
20 Dec 2020
First published
06 Jan 2021

Nanoscale, 2021,13, 1673-1679
Article type
Paper

Translocation of flexible and tensioned ssDNA through in silico designed hydrophobic nanopores with two constrictions

P. Rattu, B. Belzunces, T. Haynes, C. Skylaris and S. Khalid, Nanoscale, 2021, 13, 1673 DOI: 10.1039/D0NR04890A

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