title: 4'-C-[(4-trifluoromethyl-1H-1,2,3-triazol-1-yl)methyl]thymidine as a sensitive (19)F NMR sensor for the detection of oligonucleotide secondary structures.
abstract: 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 (19)F NMR spectroscopic detection of DNA and RNA secondary structures was demonstrated. On DNA, the (19)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 (19)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.
authors.affiliation: Department of Chemistry, University of Turku , 20014 Turku, Finland.
authors.forename: Lotta
authors.initials: L
authors.lastname: Granqvist
authors.forename: Pasi
authors.initials: P
authors.lastname: Virta
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000032:analysis* / Q000737:chemistry*; D016325:HIV Long Terminal Repeat; D015497:HIV-1 / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D009841:Oligonucleotides / Q000032:analysis* / Q000737:chemistry*; D017433:Protein Structure, Secondary; D012313:RNA / Q000032:analysis* / Q000737:chemistry*; D013936:Thymidine / Q000031:analogs & derivatives* / Q000138:chemical synthesis / Q000737:chemistry; D014230:Triazoles / Q000138:chemical synthesis* / Q000737:chemistry*
chemical_list: C000592675:4'-C-((4-trifluoromethyl-1H-1,2,3-triazol-1-yl)methyl)thymidine; D009841:Oligonucleotides; D014230:Triazoles; D012313:RNA; D004247:DNA; D013936:Thymidine