Poster abstracts
Poster number 136 submitted by Catharine Shipps
Determining the dominant secondary structures of a RNA molecule during contranscriptional folding dynamics by grouping similar dominant structures.
Catharine Shipps (Physics, The Ohio State University), Ralf Bundschuh (Physics, The Ohio State University)
Abstract:
Cotranscriptional folding dynamics of RNA molecules can have important functional consequences, e.g., in the case of riboswitches. Computational methods that predict these cotranscriptional folding dynamics generate a myriad of distinct intermediate RNA structures that are difficult to interpret thus requiring a method that summarizes the most prevalent of these structures to allow mechanistic insights into the essence of the folding process. There are already several computational tools in existence that can be used to determine dominant secondary structures during folding kinetics of shorter RNA molecules. However, during cotranscriptional folding the number of secondary structures accessible to a sequence grows exponentially with the length of the sequence and we found that the large number of secondary structures becomes prohibitively expensive when using these previous methods for molecules longer than 100bp or so. To help solve this computational efficiency problem as well as to make interpretation of the folding pathways more intuitive, we introduced and implemented the idea of further grouping similar dominant secondary structures. Our goal is to determine the ultimately dominant structures during cotranscriptional folding using this grouping method.
Keywords: RNA secondary structures, cotranscriptional folding , folding dynamics