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RNA. 2007 Jul;13(7):939-51. Epub 2007 May 16.

Predicting helical coaxial stacking in RNA multibranch loops.

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1
Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA.

Abstract

The hypothesis that RNA coaxial stacking can be predicted by free energy minimization using nearest-neighbor parameters is tested. The results show 58.2% positive predictive value (PPV) and 65.7% sensitivity for accuracy of the lowest free energy configuration compared with crystal structures. The probability of each stacking configuration can be predicted using a partition function calculation. Based on the dependence of accuracy on the calculated probability of the stacks, a probability threshold of 0.7 was chosen for predicting coaxial stacks. When scoring these likely stacks, the PPV was 66.7% at a sensitivity of 51.9%. It is observed that the coaxial stacks of helices that are not separated by unpaired nucleotides can be predicted with a significantly higher accuracy (74.0% PPV, 66.1% sensitivity) than the coaxial stacks mediated by noncanonical base pairs (55.9% PPV, 36.5% sensitivity). It is also shown that the prediction accuracy does not show any obvious trend with multibranch loop complexity as measured by three different parameters.

PMID:
17507661
PMCID:
PMC1894924
DOI:
10.1261/rna.305307
[Indexed for MEDLINE]
Free PMC Article
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