Predicting helical coaxial stacking in RNA multibranch loops

RNA. 2007 Jul;13(7):939-51. doi: 10.1261/rna.305307. Epub 2007 May 16.


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.

Publication types

  • Evaluation Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods*
  • Crystallography, X-Ray
  • Models, Biological
  • Models, Molecular
  • Nucleic Acid Conformation*
  • RNA / chemistry*
  • RNA, Ribosomal / chemistry
  • Sensitivity and Specificity
  • Sequence Analysis, RNA / methods*


  • RNA, Ribosomal
  • RNA