The secondary structure of RNA can be predicted by the thermodynamics-based method
of Zuker and Turner. The accuracy of the method'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 alignments.
We folded 72 23S rRNA sequences with the Zuker-Turner method and scored the
resulting secondary structure predictions against the comparative model.
Empirically, trends in the score were observed 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.
Three semiquantitative predictors of score were found: % of noncanonical base
pairs, % of hairpin loops that were stable tetraloops, 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. 16S and 23S rRNA).
Fields DS and Gutell RR. (1996). An analysis of large rRNA sequences
folded by a thermodynamic method. Fold Des. 1(6):419-30.