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

2014-04-18T00:00:00Z (GMT) by Lotta Granqvist Pasi Virta
4′-<i>C</i>-[(4-Trifluoromethyl-1<i>H</i>-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 <sup>19</sup>F NMR spectroscopic detection of DNA and RNA secondary structures was demonstrated. On DNA, the <sup>19</sup>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′-<i>O</i>-methyl oligoribonucleotide into an RNA hairpin model (HIV-1 TAR) was monitored by <sup>19</sup>F NMR spectroscopy. According to the thermal denaturation studies by UV spectroscopy, the effect of the 4′-<i>C</i>-(4-trifluoromethyl-1<i>H</i>-1,2,3-triazol-1-yl)­methyl moiety on the stability of these DNA and RNA models was marginal.