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

Chemical Science
Ki Tae Kim, Nicolas Winssinger

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.

References

Aug 10, 2000·Analytical Biochemistry·S AyyadevaraR J Shmookler Reis
May 3, 2003·Carcinogenesis·Mirian BrinkPiet A van den Brandt
Jan 30, 2004·Journal of the American Chemical Society·Shinsuke SandoEric T Kool
May 28, 2004·Nature·William E Evans, Mary V Relling
May 25, 2005·BMC Bioinformatics·Bernhard HauboldThomas Wiehe
Aug 3, 2006·Journal of the American Chemical Society·Anca Dragulescu-AndrasiDanith H Ly
Sep 14, 2006·Chemical Reviews·Adam P Silverman, Eric T Kool
Sep 14, 2006·Cancer Biology & Therapy·Sarah EdkinsP Andrew Futreal
Mar 30, 2007·Annual Review of Biomedical Engineering·Sobin Kim, Ashish Misra
Jan 26, 2008·Chemical Communications : Chem Comm·Zbigniew L Pianowski, Nicolas Winssinger
Jul 17, 2008·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Alfonso Quintás-Cardama, Jorge Cortes
Sep 2, 2008·Nature·John NovembreCarlos D Bustamante
Apr 22, 2009·Journal of the American Chemical Society·Zbigniew PianowskiNicolas Winssinger
Nov 6, 2009·Journal of the American Chemical Society·Raphael M Franzini, Eric T Kool
Jun 30, 2010·Chemical Reviews·Dmitry M Kolpashchikov
Oct 12, 2010·Chemical Communications : Chem Comm·Daniel J Kleinbaum, Eric T Kool
Oct 19, 2012·Organic & Biomolecular Chemistry·Claudia PercivalleSylvain Ladame
May 2, 2013·Chemistry : a European Journal·Kalyan K Sadhu, Nicolas Winssinger
Mar 22, 2014·Cancer Cell·Andrew G StephenFrank McCormick
May 8, 2015·Accounts of Chemical Research·Sofia Barluenga, Nicolas Winssinger
Jun 24, 2015·Nature Chemistry·Juexiao Sherry Wang, David Yu Zhang
Oct 4, 2015·Nature·UNKNOWN 1000 Genomes Project ConsortiumGonçalo R Abecasis
Jan 7, 2016·Chemical Communications : Chem Comm·N KolevzonE Yavin
Mar 25, 2016·Journal of the American Chemical Society·Sherry Xi Chen, Georg Seelig
Sep 30, 2016·Journal of the American Chemical Society·Maria StancescuDmitry M Kolpashchikov
Jan 19, 2017·Journal of the American Chemical Society·Dalu ChangNicolas Winssinger
Feb 6, 2017·Molecular Therapy : the Journal of the American Society of Gene Therapy·Sung Jin KimSeong-Wook Lee
Mar 28, 2017·Journal of the American Chemical Society·Willem A Velema, Eric T Kool
May 4, 2017·Journal of the American Chemical Society·Judy M OblioscaHsin-Chih Yeh
May 10, 2017·ChemMedChem·Margherita Di Pisa, Oliver Seitz
May 10, 2017·Proceedings of the National Academy of Sciences of the United States of America·Mario AcunzoCarlo M Croce
Oct 4, 2017·Chemical Science·J SaarbachN Winssinger
Jan 5, 2018·Oncotarget·Na DengYuan Yuan

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Citations

Jul 2, 2021·Chemical Science·Ki Tae KimNicolas Winssinger
Jan 27, 2021·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Bonwoo KooKi Tae Kim
Feb 11, 2021·Journal of the American Chemical Society·Emma E WatsonNicolas Winssinger

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Methods Mentioned

BETA
PCR
biosensors
biopsies
Fluorescence
genotyping
biopsy

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