title: Ionic interactions and the global conformations of the hammerhead ribozyme.
abstract: Here we investigate the global conformation of the hammerhead ribozyme. Electrophoretic studies demonstrate that the structure is folded in response to the concentration and type of ions present. Folding based on colinear alignment of arms II and III is suggested, with a variable angle subtended by the remaining helix I. In the probable active conformation, a small angle is subtended between helices I and II. Using uranyl photocleavage, an ion binding site has been detected in the long single-stranded region. The folded conformation could generate a preactivation of the scissile bond to permit in-line attack of the 2'-hydroxyl group, with a bound metal ion playing an integral role in the chemistry.
authors.affiliation: Department of Biochemistry, The University, Dundee, UK.
authors.forename: G S
authors.initials: GS
authors.lastname: Bassi
authors.forename: N E
authors.initials: NE
authors.lastname: Møllegaard
authors.forename: A I
authors.initials: AI
authors.lastname: Murchie
authors.forename: E
authors.initials: E
authors.lastname: von Kitzing
authors.forename: D M
authors.initials: DM
authors.lastname: Lilley
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D002118:Calcium / Q000378:metabolism; D016384:Consensus Sequence; D004247:DNA / Q000378:metabolism; D004591:Electrophoresis, Polyacrylamide Gel; D008274:Magnesium / Q000378:metabolism*; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D009690:Nucleic Acid Conformation; D010782:Photolysis; D016337:RNA, Catalytic / Q000138:chemical synthesis / Q000737:chemistry*; D012367:RNA, Viral / Q000138:chemical synthesis / Q000737:chemistry*; D012964:Sodium / Q000378:metabolism*; D013096:Spermine / Q000378:metabolism; D014502:Uranyl Nitrate / Q000528:radiation effects; D014772:Viroids / Q000737:chemistry
chemical_list: D016337:RNA, Catalytic; D012367:RNA, Viral; D014502:Uranyl Nitrate; D013096:Spermine; D004247:DNA; D012964:Sodium; D008274:Magnesium; D002118:Calcium