Improved statistical methods reveal direct interactions between 16S and 23S rRNA

Recent biochemical studies have indicated a number of regions in both the 1 6S and 23S rRNA that are exposed on the ribosomal subunit surface. In order to predict potential interactions between these regions we applied novel p hylogenetically-based statistical methods to detect correlated nucleotide c hanges occurring between the rRNA molecules. With these methods we discover ed a number of highly significant correlated changes between different sets of nucleotides in the two ribosomal subunits, The predictions with the hig hest correlation values belong to regions of the rRNA subunits that are in close proximity according to recent crystal structures of the entire riboso me, We also applied a new statistical method of detecting base triple inter actions within these same rRNA subunit regions. This base triple statistic predicted a number of new base triples not detected by pair-wise interactio n statistics within the rRNA molecules. Our results suggest that these stat istical methods may enhance the ability to detect novel structural elements both within and between RNA molecules.