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4′‑C‑[(4-Trifluoromethyl‑1H‑1,2,3-triazol-1-yl)methyl]thymidine as a Sensitive 19F NMR Sensor for the Detection of Oligonucleotide Secondary Structures

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journal contribution
posted on 18.04.2014, 00:00 by Lotta Granqvist, Pasi Virta
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 19F NMR spectroscopic detection of DNA and RNA secondary structures was demonstrated. On DNA, the 19F 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 19F 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.