title: Stability of hairpin ribozyme tertiary structure is governed by the interdomain junction.
abstract: The equilibrium distributions of hairpin ribozyme conformational isomers have been examined by time-resolved fluorescence resonance energy transfer. Ribozymes partition between active (docked) and inactive (extended) conformers, characterized by unique interdomain distance distributions, which define differences in folding free energy. The active tertiary structure is stabilized both by specific interactions between the catalytic and the substrate-binding domains and by the structure of the intervening helical junction. Under physiological conditions, the docking equilibrium of the natural four-way junction dramatically favors the active conformer, while those of a three-way and the two-way junction used in gene therapy applications favor the inactive conformer.
authors.affiliation: Markey Center for Molecular Genetics, Department of Microbiology and Molecular Genetics, The University of Vermont, Burlington 05405, USA.
authors.forename: N G
authors.initials: NG
authors.lastname: Walter
authors.forename: J M
authors.initials: JM
authors.lastname: Burke
authors.forename: D P
authors.initials: DP
authors.lastname: Millar
mesh_terms: D001665:Binding Sites / Q000187:drug effects; D002384:Catalysis / Q000187:drug effects; D020134:Catalytic Domain; D002412:Cations / Q000378:metabolism / Q000494:pharmacology; D015195:Drug Design; D004735:Energy Transfer; D004795:Enzyme Stability; D005453:Fluorescence; D015316:Genetic Therapy; D008274:Magnesium / Q000378:metabolism / Q000494:pharmacology; D009154:Mutation; D009690:Nucleic Acid Conformation / Q000187:drug effects; D016337:RNA, Catalytic / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism / Q000627:therapeutic use; D012964:Sodium / Q000378:metabolism / Q000494:pharmacology; D013237:Stereoisomerism; D013696:Temperature; D013816:Thermodynamics
chemical_list: D002412:Cations; D016337:RNA, Catalytic; D012964:Sodium; D008274:Magnesium