Abstract: Prof. Peter Clote and Kourosh Zarringhalam

Recent results on the thermodynamics and kinetics of RNA secondary structure

Prof. Peter Clote and Kourosh Zarringham  Physics & Astronomy Colloquium
2:30 p.m., December 2, 2011  Thompson Physical Laboratory 205

An RNA secondary structure is a type of planar graph, consisting of Watson-Crick
and wobble base pairs. From experimental data, it is known that the secondary structure forms quickly and acts as a scaffold for the formation of tertiary structure. While state-of-the-art protein secondary structure (alpha-helices, beta-sheets, etc.) is predicted by machine learning methods, RNA secondary structure can be predicted by dynamic programming using empirically determined free energies for stacked base pairs and various loops.

In this talk, we provide an overview of some thermodynamics-based algorithms developed by our lab. Topics will include how to compute the Boltzmann probability of all structural neighbors at a fixed base-pair distance from a target structure (conformational switches), the application of non-Boltzmannian sampling to approximate the partition function, analysis of kinetically trapped structures, and how to predict secondary structure by integrating chemical/enzymatic footprinting data.