Issue 7, 2019

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

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

Supplementary files

Article information

Article type
Edge Article
Submitted
01 Nov 2018
Accepted
12 Dec 2018
First published
13 Dec 2018
This article is Open Access

All publication charges for this article have been paid for by the Royal Society of Chemistry
Creative Commons BY license

Chem. Sci., 2019,10, 1953-1961

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

This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. You can use material from this article in other publications without requesting further permissions from the RSC, provided that the correct acknowledgement is given.

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