Improved Parameters for Prediction of RNA Secondary Structure and Insights into why RNA forms Double Helixes

Thermodynamic parameters for double helix formation have been measured for a large number of oligoribonucleotides. These data have been analyzed to provide free energy changes associated with base pairs, dangling ends, and base mismatches. The results suggest base stacking and base pairing are important determinants of RNA stability, but that hydrophobic bonding is not. The improved thermodynamic parameters are applied to predict secondary structures for the self splicing intervening sequence from the ribosomal RNA precursor of Tetrahymena thermophila.