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Issue 11, 2018
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Aligner-mediated cleavage of nucleic acids and its application to isothermal exponential amplification

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Abstract

We herein describe a simple and versatile approach to use conventional nicking endonuclease (NEase) for programmable sequence-specific cleavage of DNA, termed aligner-mediated cleavage (AMC), and its application to DNA isothermal exponential amplification (AMC-based strand displacement amplification, AMC-SDA). AMC uses a hairpin-shaped DNA aligner (DA) that contains a recognition site in its stem and two side arms complementary to target DNA. Thus, it enables the loading of an NEase on DA's stem, localization to a specific locus through hybridization of the side arms with target DNA, and cleavage thereof. By using just one NEase, it is easy to make a break at any specific locus and tune the cleavage site to the single-nucleotide scale. This capability also endows the proposed AMC-SDA with excellent universality, since the cleavage of target DNA, followed by a polymerase-catalyzed extension along a particular primer as a key step for initiating SDA, no longer relies on any special sequence. Moreover, this manner of initiation facilitates the adoption of 3′-terminated primers, thus making AMC-SDA highly sensitive and highly specific, as well as simple primer design.

Graphical abstract: Aligner-mediated cleavage of nucleic acids and its application to isothermal exponential amplification

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Supplementary files

Article information


Submitted
04 Dec 2017
Accepted
21 Feb 2018
First published
28 Feb 2018

This article is Open Access
All publication charges for this article have been paid for by the Royal Society of Chemistry

Chem. Sci., 2018,9, 3050-3055
Article type
Edge Article

Aligner-mediated cleavage of nucleic acids and its application to isothermal exponential amplification

W. Wu, T. Zhang, D. Han, H. Fan, G. Zhu, X. Ding, C. Wu, M. You, L. Qiu, J. Li, L. Zhang, X. Lian, R. Hu, Y. Mu, J. Zhou and W. Tan, Chem. Sci., 2018, 9, 3050
DOI: 10.1039/C7SC05141G

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