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Issue 30, 2018
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Simulation-guided engineering of an enzyme-powered three dimensional DNA nanomachine for discriminating single nucleotide variants

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Abstract

Single nucleotide variants (SNVs) are important both clinically and biologically because of their profound biological consequences. Herein, we engineered a nicking endonuclease-powered three dimensional (3D) DNA nanomachine for discriminating SNVs with high sensitivity and specificity. Particularly, we performed a simulation-guided tuning of sequence designs to achieve the optimal trade-off between device efficiency and specificity. We also introduced an auxiliary probe, a molecular fuel capable of tuning the device in solution via noncovalent catalysis. Collectively, our device produced discrimination factors comparable with commonly used molecular probes but improved the assay sensitivity by ∼100 times. Our results also demonstrate that rationally designed DNA probes through computer simulation can be used to quantitatively improve the design and operation of complexed molecular devices and sensors.

Graphical abstract: Simulation-guided engineering of an enzyme-powered three dimensional DNA nanomachine for discriminating single nucleotide variants

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Publication details

The article was received on 23 Jun 2018, accepted on 30 Jun 2018 and first published on 02 Jul 2018


Article type: Edge Article
DOI: 10.1039/C8SC02761G
Citation: Chem. Sci., 2018,9, 6434-6439
  • Open access: Creative Commons BY-NC license
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    Simulation-guided engineering of an enzyme-powered three dimensional DNA nanomachine for discriminating single nucleotide variants

    Y. Li, G. A. Wang, S. D. Mason, X. Yang, Z. Yu, Y. Tang and F. Li, Chem. Sci., 2018, 9, 6434
    DOI: 10.1039/C8SC02761G

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