NMR-assisted prediction of RNA secondary structure: identification of a probable pseudoknot in the coding region of an R2 retrotransposon.

ABSTRACT: As the rate of functional RNA sequence discovery escalates, high-throughput techniques for reliable structural determination are becoming crucial for revealing the essential features of these RNAs in a timely fashion. Computational predictions of RNA secondary structure quickly generate reasonable models but suffer from several approximations, including overly simplified models and incomplete knowledge of significant interactions. Similar problems limit the accuracy of predictions for other self-folding polymers, including DNA and peptide nucleic acid (PNA). The work presented here demonstrates that incorporating unassigned data from simple nuclear magnetic resonance (NMR) experiments into a dynamic folding algorithm greatly reduces the potential folding space of a given RNA and therefore

SUBMITTER: Hart JM 

PROVIDER: S-EPMC2646634 | biostudies-literature | 2008 Aug

REPOSITORIES: biostudies-literature