AN ANALYSIS OF LARGE RIBOSOMAL-RNA SEQUENCES FOLDED BY A THERMODYNAMIC METHOD

Background: The secondary structure of RNA can be predicted by the the rmodynamics-based method of Zuker and Turner. The accuracy of the meth od's secondary structure predictions for rRNA can be assessed by using as reference the currently available rRNA secondary structure models that have been derived from comparative analysis of rRNA sequence alig nments. Results: We folded 72 23S rRNA sequences with the Zuker-Turner method and scored the resulting secondary structure predictions again st the comparative model. Empirically, trends in the score were observ ed as a function of the phylogenetic memberships of the sequences and as a function of the base pairs secondary structural contexts. Further , three parameters were found that (anti-)correlate with the score. Co nclusions: Three semiquantitative predictors of score were found: % of noncanonical base pairs, % of hairpin loops that were stable tetraloo ps, and sequence %G+C. The folding of rRNA is a tractable problem and thermodynamics-based folding algorithms, in particular, are useful in the study of this folding problem even for large RNA molecules (e.g. 1 6S and 23S rRNA). (C) Current Biology Ltd.