The ribose 2′-hydroxyl group confers upon RNA
many unique molecular properties. To better appreciate
its contribution to structure and stability and to monitor
how substitutions of the 2′ hydroxyl can alter an
RNA molecule, each loop pyrimidine ribonucleotide in the
UUCG tetraloop was substituted with a nucleotide containing
either a fluorine (2′-F), hydrogen (2′-H),
amino (2′-NH2), or methoxy (2′-OCH3)
group, in the context of both the C:G and G:C loop-closing
base pair. The thermodynamic parameters of these tetraloop
variants have been determined and NMR experiments used
to monitor the structural changes resulting from the substitutions.
The modified riboses are better tolerated in the G[UUCG]C
tetraloop, which may be due to its increased loop flexibility
relative to the C[UUCG]G loop. Even for these
simple substitutions, the free-energy change reflects a
complex interplay of hydrogen bonding, solvation effects,
and intrinsic pucker preferences of the nucleotides.