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

Published inChemical Science, vol. 11, no. 16, p. 4150-4157
Publication date2020
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 but 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 nucleotides) which is confined by two guide DNAs functionalized respectively with a ruthenium photocatalyst. The use of a catalytic reaction is essential to bypass the exchange of guide DNAs while achieving signal amplification through substrate turnover. The guide DNAs restrain the reaction to a unique site and enhance the hybridization of short substrates by providing two π-stacking interactions. The reaction was shown to enable the detection of SNPs and SNVs down to 50 pM with a discrimination factor ranging from 24 to 309 (median 82, 27 examples from 3 oncogenes). The clinical diagnostic potential of the technology was demonstrated with the analysis of RAS amplicons obtained directly from cell culture.

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Citation (ISO format)
KIM, Kitae, WINSSINGER, Nicolas. Enhanced SNP-sensing using DNA-templated reactions through confined hybridization of minimal substrates (CHOMS). In: Chemical Science, 2020, vol. 11, n° 16, p. 4150–4157. doi: 10.1039/D0SC00741B
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ISSN of the journal2041-6520
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Creation05/04/2020 6:07:00 PM
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