BIOL Suzanne Walker  Tuesday, March 23, 2010 

103 - Effect of coaxial stacking of helices on RNA secondary structure prediction

Russell C Goodman1,, Zhenjiang Xu1, David H Mathews1,2. (1) Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14627, United States, (2) Department of Biostatistics and Computational Biology, University of Rochester, Rochester, New York 14627, United States

Multibranchloops are nearly ubiquitous among ncRNA. They have three known stabilizing structural features: dangling ends, mismatches, and coaxial stacking. Almost universally, dynamic programming algorithms for RNA secondary structure prediction incorporate mismatches and dangling ends into their predictions; however, our program, RNAstructure, incorporates coaxial stacking into RNA secondary structure prediction. Our analysis of incorporating coaxial stacking into RNA secondary structure prediction algorithms indicated a statistically significant increase in RNA secondary structure prediction accuracy. Preliminary analysis of the folding landscape of RNAs with coaxial stacking and without coaxial stacking revealed that when coaxial stacking is used in secondary structure prediction algorithms, the probability of folding to the lowest energy structure may be increased, and algorithms run without coaxial stacking, on average, produce twice as many structures with the same folding free energy change. These findings suggest that coaxial stacking of helices plays a significant role in improving the accuracy and fidelity of secondary structure prediction.

Tuesday, March 23, 2010 05:00 PM
Chemical Biology and Biomolecules (05:00 PM - 06:00 PM)
Location: The Moscone Center
Room: Hall D


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