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Enhanced SNP-sensing using DNA-templated reactions through confined hybridization of minimal substrates (CHOMS)

Abstract

DNA or RNA templated reactions are attractive for nucleic acid sensing and imaging. As for any hybridization-based sensing, there is a tradeoff between sensitivity (detection threshold) and resolution (single nucleotide discrimination). Longer probes afford better sensitivity however compromise single nucleotide resolution due to the small thermodynamic penalty of a single mismatch. Herein we report a design that overcomes this tradeoff. The reaction is leveraged on the hybridization of a minimal substrate (covering 4 nucleotide) that is confined by two guide DNAs functionalized respectively with a ruthenium photocatalyst. The use of a catalytic reaction is essential to bypass exchange of guide DNA while achieve signal amplification through substrate turnover. The guide DNAs restrain the reaction to a unique site and enhance hybridization of short substrates by providing two π-stacking interactions. The reaction was show to enable detection of SNP and SNV down to 50 pM with a discrimination factor ranging from 24-309 (median 82, 27 examples from 3 oncogenes). The clinical diagnostic potential of the technology was demonstrated with the analysis of RAS amplicon obtained directly from cell culture.

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Supplementary files

Article information


Submitted
07 Feb 2020
Accepted
24 Mar 2020
First published
24 Mar 2020

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

Chem. Sci., 2020, Accepted Manuscript
Article type
Edge Article

Enhanced SNP-sensing using DNA-templated reactions through confined hybridization of minimal substrates (CHOMS)

K. T. Kim and N. Winssinger, Chem. Sci., 2020, Accepted Manuscript , DOI: 10.1039/D0SC00741B

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