Abstract
Riboswitches are regulatory elements present in bacterial messenger RNA acting as sensors of small molecules and consequently playing a vital role in bacterial gene regulation. The SAM-II riboswitch is a class of riboswitches that recognizes S-adenosyl methionine. It has been previously shown that the presence of Mg(2+) ions stabilizes the preexisting minor state of the riboswitch, which is structurally characterized having a nucleated pseudoknot, leading to the increase of its probability. In this study, an analytical equilibrium model is developed to describe the impact of Mg(2+) ion concentration on the folding of the SAM-II riboswitch, thus linking RNA folding and tertiary interactions energetics to ligand binding. The model enables quantitative predictions of equilibrium folding intermediates as a function of concentration of Mg(2+) ions.