Improved parameters for prediction of RNA structure

Abstract

Thermodynamic studies of oligoribonucleotides are providing parameters and insights for the fundamental interactions that determine RNA structure. These results can be used to predict the secondary structure of RNA from its sequence. Comparisons of predicted structures with those deduced from phylogenetic data indicate a modest success rate that is improving as more parameters are determined experimentally. Two major fundamental interactions in RNA are stacking and hydrogen bonding. Both contribute similar increments to free-energy changes for associations of oligoribonucleotides. Thus, parameters for stacking and hydrogen bonding will likely be important for predicting the three-dimensional structures of RNAs and for interpreting RNA-RNA associations. Both applications should be important for providing a full understanding of catalysis by RNA.