A computational study on the ligand-induced stabilization of add riboswitch aptamer has been performed. Using accurate, atomistic molecular dynamics in combination with state-of-the-art techniques to analyze pulling simulations, we characterized the coupling between ligand binding and stabilization of the aptamer stem involved in the control of gene expression. The results indicate that the major role of the ligand is to favor the pre-organization of the riboswitch around the binding pocket. This is a first step towards the full characterization of ligand-dependent folding in adenine riboswitch.

This work has been accepted for publication on the RNA journal, and is available free of charge.  The preprint is available at arXiv:1309.5717.

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