Characterization of G-Quadruplex/Hairpin Transitions of RNAs by 19F 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 Grich regions of mRNA of human prion protein, PrP) and applied for the F-19 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 obtained F-19 NMR spectra supported the usual characterization data (obtained by UV-and CD-melting profiles and by H-1 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 the F-19 NMR signals. For a well-behaved Qd/Hp transition, thermodynamic parameters could be extracted.