Sequence-Dependent Folding and Unfolding of Ligand-Bound Purine Riboswitches

Riboswitch regulation of gene expression requires ligand-mediated RNA folding. From the fluorescence lifetime distribution of bound 2-aminopurine ligand, we resolve three RNA conformers (C-o, C-i, C-c) of the liganded G- and A-sensing riboswitches from Bacillus subtilis. The ligand binding affinities, and sensitivity to Mg2+, together with results from mutagenesis, suggest that C-o and C-i are partially unfolded species compromised in key loop-loop interactions present in the fully folded C-c. These data verify that the ligand-bound riboswitches may dynamically fold and unfold in solution, and reveal differences in the distribution of folded states between two structurally homologous purine riboswitches: Ligand-mediated folding of the G-sensing riboswitch is more effective, less dependent on Mg2+, and less debilitated by mutation, than the A-sensing riboswitch, which remains more unfolded in its liganded state. We propose that these sequence-dependent RNA dynamics, which adjust the balance of ligand-mediated folding and unfolding, enable different degrees of kinetic discrimination in ligand binding, and fine-tuning of gene regulatory mechanisms. (C) 2009 Wiley Periodicals, Inc. Biopolymers 91: 953-965, 2009.