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Issue 7, 2019
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Exploration of solid-state nanopores in characterizing reaction mixtures generated from a catalytic DNA assembly circuit

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Abstract

Recent advances have proven that using solid-state nanopores is a promising single molecular technique to enrich the DNA assembly signaling library. Other than using them for distinguishing structures, here we innovatively adapt solid-state nanopores for use in analyzing assembly mixtures, which is usually a tougher task for either traditional characterization techniques or nanopores themselves. A trigger induced DNA step polymerization (SP-CHA), producing three-way-DNA concatemers, is designed as a model. Through counting and integrating the translocation-induced current block when each concatemer passes through a glass conical glass nanopore, we propose an electrophoresis-gel like, but homogeneous, quantitative method that can comprehensively profile the “base-pair distribution” of SP-CHA concatemer mixtures. Due to the higher sensitivity, a number of super long concatemers that were previously difficult to detect via gel electrophoresis are also revealed. These ultra-concatemers, longer than 2 kbp, could provide a much enhanced signal-to-noise ratio for nanopores and are thus believed to be more accurate indicators for the existence of a trigger, which may be of benefit for further applications, such as molecular machines or biosensors.

Graphical abstract: Exploration of solid-state nanopores in characterizing reaction mixtures generated from a catalytic DNA assembly circuit

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Publication details

The article was received on 01 Nov 2018, accepted on 12 Dec 2018 and first published on 13 Dec 2018


Article type: Edge Article
DOI: 10.1039/C8SC04875D
Citation: Chem. Sci., 2019,10, 1953-1961
  • Open access: Creative Commons BY license
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    Exploration of solid-state nanopores in characterizing reaction mixtures generated from a catalytic DNA assembly circuit

    Z. Zhu, R. Wu and B. Li, Chem. Sci., 2019, 10, 1953
    DOI: 10.1039/C8SC04875D

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