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Identification of four single-stranded DNA homopolymers with a solid-state nanopore in alkaline CsCl solution

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Abstract

DNA sequencing via solid-state nanopores is a promising technique with the potential to surpass the performance of conventional sequencers. However, the identification of all four nucleotide homopolymers with a typical SiN nanopore is yet to be clearly demonstrated because a guanine homopolymer rapidly forms a G-quadruplex in a typical KCl aqueous solution. To address this issue, we introduced an alkaline CsCl aqueous solution, which denatures the G-quadruplex into a single-stranded structure by disrupting the hydrogen-bonding network between the guanines and preventing the binding of the K+ ion to G-quartets. Using this alkaline CsCl solution, we provided a proof-of-principle that single-stranded DNA homopolymers of all four nucleotides could be statistically identified according to their blockade currents with the same single nanopore. We also confirmed that a triblock DNA copolymer of three nucleotides exhibited a trimodal Gaussian distribution whose peaks correspond to those of the DNA homopolymers. Our findings contribute to the development of practical DNA sequencing with a solid-state nanopore.

Graphical abstract: Identification of four single-stranded DNA homopolymers with a solid-state nanopore in alkaline CsCl solution

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Publication details

The article was received on 25 May 2018, accepted on 16 Oct 2018 and first published on 17 Oct 2018


Article type: Paper
DOI: 10.1039/C8NR04238A
Citation: Nanoscale, 2018, Advance Article
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    Identification of four single-stranded DNA homopolymers with a solid-state nanopore in alkaline CsCl solution

    Y. Goto, I. Yanagi, K. Matsui, T. Yokoi and K. Takeda, Nanoscale, 2018, Advance Article , DOI: 10.1039/C8NR04238A

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