Abstract
A sensitive uridine-derived sensor (viz., 2'-O-[(4-CF3-triazol-1-yl)methyl]uridine, 1) for (19)F NMR spectroscopic monitoring of RNA secondary structures is described. The applicability of 1 is demonstrated by monitoring the thermal denaturation of the following double and triple helical RNA models: (1) a miR 215 hairpin, (2) a poly U-A*U triple helix RNA (bearing two C-G*C(H+) interrupts), and (3) a polyadenylated nuclear-nuclear retention element complex. In these RNA models, the (19)F NMR shift of the 2'-O-(CF3-triazolylmethyl) group shows high sensitivity to secondary structural arrangements. Moreover, 1 favors the desired N-conformation, and its effect on both RNA duplex and triplex stabilities is marginal.
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