title: Single-molecule analysis reveals multi-state folding of a guanine riboswitch.
abstract: Guanine-responsive riboswitches undergo ligand-dependent structural rearrangements to control gene expression by transcription termination. While the molecular basis for ligand recognition is well established, the associated structural rearrangements and the kinetics involved in the formation of the aptamer domain are less well understood. Using high-resolution optical tweezers, we followed the folding trajectories of a single molecule of the xpt-pbuX guanine aptamer from Bacillus subtilis. We report a rapid six-state conformational rearrangement, in which three of the states are guanine dependent, during the transition from the linear to the native receptor conformation. The folding completes in <1 s. The force-dependent equilibrium kinetics and the mutational data indicated that the flexible J2-J3 junction undergoes a ligand-dependent conformational switching, which triggers the formation of the long-range tertiary interactions and the P1 helix. In the absence of the right ligand, the junction failed to initiate the series of conformational rearrangements required for the riboswitch activities.
authors.affiliation: Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
authors.forename: Vishnu
authors.initials: V
authors.lastname: Chandra
authors.affiliation: Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
authors.forename: Zain
authors.initials: Z
authors.lastname: Hannan
authors.affiliation: Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
authors.forename: Huizhong
authors.initials: H
authors.lastname: Xu
authors.affiliation: Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.|Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.|Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
authors.forename: Maumita
authors.initials: M
authors.lastname: Mandal
mesh_terms: D001412:Bacillus subtilis / Q000235:genetics* / Q000378:metabolism; D006147:Guanine / Q000737:chemistry* / Q000378:metabolism; D008024:Ligands; D009690:Nucleic Acid Conformation; D058928:Riboswitch
chemical_list: D008024:Ligands; D058928:Riboswitch; D006147:Guanine