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
Lotta Granqvist
Pasi Virta
10.1021/jo500326j.s001
https://acs.figshare.com/articles/journal_contribution/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/2304724
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.
2014-04-18 00:00:00
denaturation studies
RNA hairpin model
oligonucleotide sequences
19 F NMR measurements
HIV
RNA environment
19 F NMR spectroscopic detection
sensor
RNA models
DNA
19 F NMR spectroscopy
Sensitive 19 F NMR Sensor
TAR
UV spectroscopy