Context dependence of hydrogen bond free energy revealed by substitutions in an RNA hairpin.

Prediction and modeling of RNA structure requires knowledge of the free energy contributions of various interactions. Many unusual hydrogen bonds were recently proposed in the structure of a GCAA hairpin determined from nuclear magnetic resonance. The contributions of these hydrogen bonds to the folding stability of the hairpin formed by rGGCGCAAGCC have now been investigated through the use of functional group substitutions. These and previous results suggest a strong context dependence for the free energy of hydrogen bond formation. The results also suggest that the phylogenetic preference for GNRA (where N = A, C, G, or U and R = A or G) tetraloops may have a functional rather than thermodynamic basis.