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Albany 2015:Book of Abstracts

Albany 2015
Conversation 19
June 9-13 2015
©Adenine Press (2012)

Exact probability calculation of RNA loop formation identifies folding motifs in secondary structures

RNA secondary structure prediction is widely used to analyze RNA sequences. In an RNA partition function calculation, free energy nearest neighbor parameters are used in a dynamic programming algorithm to estimate statistical properties of the secondary structure ensemble. Previously, partition functions have largely been used to estimate the probability that a given pair of nucleotides form a base pair, the stacking probability of two pairs, or the accessibility to binding of continuous nucleotides. Here it is demonstrated that an RNA partition function can also be used to calculate the probability of hairpin loops, internal loops, bulge loops, and multibranch loops at a given position. This calculation can also be used to predict the probability of base pair stacking interactions and helices. Benchmarking on a large set of RNA sequences with known secondary structures indicated that loops and helices that were calculated to be more probable were more likely to be present in the known structure. An energy model which explicitly includes coaxial stacking parameters is shown to improve the predicted probabilities of multibranch loops. This method could be useful to further assess confidence in predicted secondary structures. It could also be used to search for secondary structures of interest, such as loops that are expected to bind to a drug.

Michael F. Sloma
David H. Mathews

Department of Biochemistry and Biophysics and Center for RNA Biology
University of Rochester Medical Center
Rochester, NY 14642, USA

Phone: (585) 275-1748
michael_sloma@urmc.rochester.edu