A COMPARISON OF THERMODYNAMIC FOLDINGS WITH COMPARATIVELY DERIVED STRUCTURES OF 16S AND 16S-LIKE RIBOSOMAL-RNAS

To increase our understanding of the dynamics and complexities of the RNA folding process, and therewith to improve our ability to predict R NA secondary structure by computational means, we have examined the fo ldings of a large number of phylogenetically and structurally diverse 16S and 16S-like rRNAs and compared these results with their comparati vely derived secondary structures. Our initial goals are to establish the range of prediction success for this class of rRNAs, and to begin comparing and contrasting the foldings of these RNAs. We focus here on structural features that are predicted with confidence as well as tho se that are poorly predicted. Whereas the large set of Archaeal and (e u)Bacterial 16S rRNAs ail fold well (69% and 55% respectively), some a s high as 80%, many Eucarya and mitochondrial 16S rRNAs are poorly pre dicted (similar to 30%), with a few of these predicted as low as 10-20 %. In general, base pairs interacting over a short distance and, in pa rticular, those closing hairpin loops, are predicted significantly bet ter than long-range base pairs and those closing multistem loops and b ulges. The prediction success of hairpin loops varies, however, with t heir size and context. Analysis of some of the RNAs that do not fold w ell suggests that the composition of some hairpin loops (e.g., tetralo ops) and the higher frequency of noncanonical pairs in their comparati vely derived structures might contribute to these lower success rates. Eucarya and mitochondrial rRNAs reveal further novel tetraloop motifs , URRG/A and CRRG, that interchange with known stable tetraloop in the procaryotes.