Characterizing the loop-loop mutant of the guanine riboswitch

One method for the control of gene expression is the specific binding of small metabolite molecules to riboswitch RNA elements. Riboswitches are located in the 5' untranslated regions of messenger RNA and consist of an aptamer domain responsible for ligand binding and an expression platform. The guanine riboswitch binds guanine and hypoxanthine with high specificity. The aptamer domain consists of a three-helix junction which is stabilized by long-range base pair interactions between two loops. Previously, using NMR-spectroscopy, we have found that the long range interactions are already present in the free RNA and that magnesium-ions are not required for ligand binding and structure formation but stabilize the existing structure. Mutating one of the essential long range base pair in the loop-loop region we found, that the long range interactions are disrupted in the free form and that ligand binding and structure formation depend on the presence of magnesium. Here, we present the X-ray structure of this loop-loop mutant and discuss the influence of the loop-loop interactions on the threedimensional structure.