Specific Structural Elements of the T-Box Riboswitch Drive the Two-Step Binding of the tRNA Ligand

Abstract

bound form of the dye is enhanced 1100-fold. The crystal structure of the RNA-dye complex revealed a three-tiered G-quadruplex RNA structure, with the dye binding to one face of the G-quadruplex. Moreover, the folding of the aptamer is strongly coupled to the binding of the dye, thus making the dye fluorescence a direct reporter of the folding state of the G-quadruplex RNA. Previous studies by our lab of a DNA G-quadruplex, revealed that it changes conformation and eventually unfolds under high pressure. We find that pressure modifies the folding of RNA Mango-dye complex as well, and appears to significantly slow the folding reaction. In addition, it is known that potassium ions play a crucial role in stabilizing G-quadruplexes. High pressure fluorescence experiments on RNA Mango at different salt concentrations will be presented as well. These results help to better understand the folding mechanism of RNA G-quadruplexes.