Characterization of G-Quadruplex/Hairpin Transitions of RNAs by19F NMR Spectroscopy.
2'-O-[(4-Trifluoromethyl-triazol-1-yl)methyl] reporter groups have been incorporated into guanosine-rich RNA models (including a known bistable Qd/Hp RNA and two G-rich regions of mRNA of human prion protein, PrP) and applied for the19F NMR spectroscopic characterization of plausible G-quadruplex/hairpin (Qd/Hp) transitions in these RNA structures. For the synthesis of the CF3-labeled RNAs, phosphoramidite building blocks of 2'-O-[(4-CF3-triazol-1-yl)methyl] nucleosides (cytidine, adenosine, and guanosine) were prepared and used as an integral part of the standard solid-phase RNA synthesis. The obtained19F NMR spectra supported the usual characterization data (obtained by UV- and CD-melting profiles and by1H NMR spectra of the imino regions) and additionally gave more detailed information on the Qd/Hp transitions. The molar fractions of the secondary structural species (Qd, Hp) upon thermal denaturation and under varying ionic conditions could be determined from the intensities and shifts of the19F NMR signals. For a well-behaved Qd/Hp transition, thermodynamic parameters could be extracted.
Department of Chemistry, University of Turku, Turku, 20014, Finland. ltgran@utu.fi.
Lotta
L
Granqvist
Department of Chemistry, University of Turku, Turku, 20014, Finland. pamavi@utu.fi.
Pasi
P
Virta
D066235:Fluorine-19 Magnetic Resonance Imaging / Q000379:methods*; D054856:G-Quadruplexes; D006801:Humans; D009690:Nucleic Acid Conformation; D009705:Nucleosides / Q000737:chemistry*; D009943:Organophosphorus Compounds / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*; D060327:Solid-Phase Synthesis Techniques; D013816:Thermodynamics
D009705:Nucleosides; D009943:Organophosphorus Compounds; C434331:phosphoramidite; D012313:RNA
19F NMR spectroscopy; G-quadruplex RNAs; RNA structures; bistable RNAs; fluorinated ligands