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

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.