Exploring RNA Intermediate Conformations with the Massively Parallel Genetic Algorithm

The bioinformatics revolution has led to an exponential increase in the availability of data on gene location, expression, and function for thousands of species. In the midst of this eruption of data, however, time and resources are often lacking for the analysis of information beyond that encoded by sequence alone. While proteins are the traditional candidates for detailed structural analysis, RNA secondary and tertiary structural studies remain crucial to the understanding of complex biological systems. The RNA structure-function relationship list is quite long. Structure and structural transitions are important in post-transcriptional regulation of gene expression, intermolecular interaction and dimerization, splice site recognition, and ribosomal frame-shifting to name a few contexts. The ribozymes constitute a class of RNA molecules whose sequence exists primarily to define their structural and enzyme-like properties. The RNA folding problem clearly is a significant venue for the use of computational approaches. As with most such