Relative stability of helices determines the folding landscape of adenine riboswitch aptamers

Riboswitches, whose folding is controlled by binding of metabolites to the aptamer domain, regulate downstream gene expression. Folding properties of the aptamer strongly influence the conformation of the downstream expression platform, which controls transcription termination or translation initiation. We have characterized the energy landscape of the add riboswitch aptamer quantitatively by unfolding and refolding the molecule with mechanical force using the coarse-grained self-organized polymer model and Brownian dynamics simulation. Multiple folding states have been found during the folding process of the aptamer, both with and without adenine, consistent with single molecule studies of purine riboswitches. Adenine binding stabilizes the folded structure and significantly decreases the unfolding rate of the aptamer, the folding of which is in competition with the formation of the downstream stem-loop structure in the complete riboswitch. These results provide insights into the mechanism of gene regulation by the RNA switches.