RNA molecules with structure dependent functions are uniquely folded

S.-Y. Le
2002 Nucleic Acids Research  
Cis-acting elements in post-transcriptional regulation of gene expression are often correlated with distinct local RNA secondary structure. These structures are expected to be signi®cantly more ordered than those anticipated at random because of evolutionary constraints and intrinsic structural properties. In this study, we introduce a computing method to calculate two quantitative measures, NRd and Stscr, for estimating the uniqueness of an RNA secondary structure. NRd is a normalized score
more » ... ed on evaluating how different a natural RNA structure is from those predicted for its randomly shuf¯ed variants. The lower the score NRd the more well ordered is the natural RNA structure. The statistical signi®cance of NRd compared with that computed from structural comparisons among large numbers of randomly permuted sequences is represented by a standardized score, Stscr. We tested the method on the trans-activation response element and Rev response element of HIV-1 mRNA, internal ribosome entry sequence of hepatitis C virus, Tetrahymena thermophila rRNA intron, 100 tRNAs and 14 RNase P RNAs. Our data indicate that functional RNA structures have high Stscr, while other structures have low Stscr. We conclude that RNA functional molecules and/or cis-acting elements with structure dependent functions possess well ordered conformations and they are uniquely folded as measured by this technique.
doi:10.1093/nar/gkf473 pmid:12177299 pmcid:PMC134240 fatcat:ae3t4f6qnfaddepdh3qzccztvy