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4′-C-[(4-trifluoromethyl-1 H -1,2,3-triazol-1-yl)methyl]thymidine as a sensitive F NMR sensor for the detection of oligonucleotide secondary structures

Journal of Organic Chemistry, ISSN: 1520-6904, Vol: 79, Issue: 8, Page: 3529-3536
2014
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4′-C-[(4-Trifluoromethyl-1H-1,2,3-triazol-1-yl)methyl]thymidine was synthesized and incorporated as a phosphoramidite into oligonucleotide sequences. Its applicability as a sensor for the F NMR spectroscopic detection of DNA and RNA secondary structures was demonstrated. On DNA, the F NMR measurements were focused on monitoring of duplex-triplex conversion, for which this fluorine-labeled 2′- deoxynucleoside proved to be a powerful sensor. This sensor seemingly favors DNA, but its behavior in the RNA environment also turned out to be informative. As a demonstration, invasion of a 2′-O-methyl oligoribonucleotide into an RNA hairpin model (HIV-1 TAR) was monitored by F NMR spectroscopy. According to the thermal denaturation studies by UV spectroscopy, the effect of the 4′-C-(4-trifluoromethyl-1H-1,2,3-triazol-1-yl)methyl moiety on the stability of these DNA and RNA models was marginal. © 2014 American Chemical Society.

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