title: Mg(2+) shifts ligand-mediated folding of a riboswitch from induced-fit to conformational selection.
abstract: Bacterial riboswitches couple small-molecule ligand binding to RNA conformational changes that widely regulate gene expression, rendering them potential targets for antibiotic intervention. Despite structural insights, the ligand-mediated folding mechanisms of riboswitches are still poorly understood. Using single-molecule fluorescence resonance energy transfer (smFRET), we have investigated the folding mechanism of an H-type pseudoknotted preQ1 riboswitch in dependence of Mg(2+) and three ligands of distinct affinities. We show that, in the absence of Mg(2+), both weakly and strongly bound ligands promote pseudoknot docking through an induced-fit mechanism. By contrast, addition of as low as 10 μM Mg(2+) generally shifts docking toward conformational selection by stabilizing a folded-like conformation prior to ligand binding. Supporting evidence from transition-state analysis further highlights the particular importance of stacking interactions during induced-fit and of specific hydrogen bonds during conformational selection. Our mechanistic dissection provides unprecedented insights into the intricate synergy between ligand- and Mg(2+)-mediated RNA folding.
authors.affiliation: Biophysics, ‡Single Molecule Analysis Group, Department of Chemistry, University of Michigan , 930 N. University, Ann Arbor, Michigan 48109, United States.
authors.forename: Krishna C
authors.initials: KC
authors.lastname: Suddala
authors.affiliation: Biophysics, ‡Single Molecule Analysis Group, Department of Chemistry, University of Michigan , 930 N. University, Ann Arbor, Michigan 48109, United States.
authors.forename: Jiarui
authors.initials: J
authors.lastname: Wang
authors.affiliation: Biophysics, ‡Single Molecule Analysis Group, Department of Chemistry, University of Michigan , 930 N. University, Ann Arbor, Michigan 48109, United States.
authors.forename: Qian
authors.initials: Q
authors.lastname: Hou
authors.affiliation: Biophysics, ‡Single Molecule Analysis Group, Department of Chemistry, University of Michigan , 930 N. University, Ann Arbor, Michigan 48109, United States.
authors.forename: Nils G
authors.initials: NG
authors.lastname: Walter
mesh_terms: D031541:Fluorescence Resonance Energy Transfer; D006860:Hydrogen Bonding; D008024:Ligands; D008274:Magnesium / Q000737:chemistry / Q000494:pharmacology*; D009690:Nucleic Acid Conformation / Q000187:drug effects*; D059370:RNA Folding / Q000187:drug effects*; D012329:RNA, Bacterial / Q000737:chemistry*; D058928:Riboswitch
chemical_list: D008024:Ligands; D012329:RNA, Bacterial; D058928:Riboswitch; D008274:Magnesium