Thermodynamics of 2 '-ribose substitutions in UUCG tetraloops

The ribose 2'-hydroxyl group confers upon RNA many unique molecular propert ies. To better appreciate its contribution to structure and stability and t o monitor how substitutions of the 2' hydroxyl can alter an RNA molecule, e ach loop pyrimidine ribonucleotide in the UUCG tetraloop was substituted wi th 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 struc tural changes resulting from the substitutions. The modified riboses are be tter 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 subs titutions, the free-energy change reflects a complex interplay of hydrogen bonding, solvation effects, and intrinsic pucker preferences of the nucleot ides.