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      Characterization of DNA duplex unzipping through a sub-2 nm solid-state nanopore

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          Abstract

          The unzipping and translocation of DNA duplexes through a sub-2 nm SiN x solid-state nanopore have been demonstrated by well-resolved three-level blockades.

          Abstract

          Herein, the unzipping and translocation of DNA duplexes through a sub-2 nm silicon nitride (SiN x) solid-state nanopore have been demonstrated by well-resolved three-level blockades. In order to examine our observations, we applied a simple model which is applicable to the unzipping and translocation processes of DNA duplexes through solid-state nanopores. The generation of these highly recognizable signatures is an important step towards the real applications of solid-state nanopores in complex samples.

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          The potential and challenges of nanopore sequencing.

          Daniel Branton, David W. Deamer, Andre Marziali … (2008)
          A nanopore-based device provides single-molecule detection and analytical capabilities that are achieved by electrophoretically driving molecules in solution through a nano-scale pore. The nanopore provides a highly confined space within which single nucleic acid polymers can be analyzed at high throughput by one of a variety of means, and the perfect processivity that can be enforced in a narrow pore ensures that the native order of the nucleobases in a polynucleotide is reflected in the sequence of signals that is detected. Kilobase length polymers (single-stranded genomic DNA or RNA) or small molecules (e.g., nucleosides) can be identified and characterized without amplification or labeling, a unique analytical capability that makes inexpensive, rapid DNA sequencing a possibility. Further research and development to overcome current challenges to nanopore identification of each successive nucleotide in a DNA strand offers the prospect of 'third generation' instruments that will sequence a diploid mammalian genome for approximately $1,000 in approximately 24 h.
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            Continuous base identification for single-molecule nanopore DNA sequencing.

            James Clarke, Hai-Chen Wu, Lakmal Jayasinghe … (2009)
            A single-molecule method for sequencing DNA that does not require fluorescent labelling could reduce costs and increase sequencing speeds. An exonuclease enzyme might be used to cleave individual nucleotide molecules from the DNA, and when coupled to an appropriate detection system, these nucleotides could be identified in the correct order. Here, we show that a protein nanopore with a covalently attached adapter molecule can continuously identify unlabelled nucleoside 5'-monophosphate molecules with accuracies averaging 99.8%. Methylated cytosine can also be distinguished from the four standard DNA bases: guanine, adenine, thymine and cytosine. The operating conditions are compatible with the exonuclease, and the kinetic data show that the nucleotides have a high probability of translocation through the nanopore and, therefore, of not being registered twice. This highly accurate tool is suitable for integration into a system for sequencing nucleic acids and for analysing epigenetic modifications.
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              Solid-state nanopores.

              Cees Dekker (2007)
              The passage of individual molecules through nanosized pores in membranes is central to many processes in biology. Previously, experiments have been restricted to naturally occurring nanopores, but advances in technology now allow artificial solid-state nanopores to be fabricated in insulating membranes. By monitoring ion currents and forces as molecules pass through a solid-state nanopore, it is possible to investigate a wide range of phenomena involving DNA, RNA and proteins. The solid-state nanopore proves to be a surprisingly versatile new single-molecule tool for biophysics and biotechnology.
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                Author and article information

                Journal
                Journal ID (publisher-id): CHCOFS
                Title: Chemical Communications
                Abbreviated Title: Chem. Commun.
                Publisher: Royal Society of Chemistry (RSC)
                ISSN (Print): 1359-7345
                ISSN (Electronic): 1364-548X
                Publication date Created: 2017
                Publication date (Electronic): 2017
                Volume: 53
                Issue: 25
                Pages: 3539-3542
                Affiliations
                [1 ]School of Chemistry & Molecular Engineering
                [2 ]East China University of Science and Technology
                [3 ]Shanghai
                [4 ]P. R. China
                [5 ]Department of Chemistry and Biochemistry
                [6 ]Mount Allison University
                [7 ]Sackville
                [8 ]Canada
                Article
                DOI: 10.1039/C7CC00060J
                SO-VID: 35fe301b-dbf0-4991-8b0b-0bcbed3ae7be
                Copyright © © 2017
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