title: Folding of the hairpin ribozyme in its natural conformation achieves close physical proximity of the loops.
abstract: The hairpin ribozyme is a self-cleaving motif found in the negatives strand of the satellite RNA of some plant viruses. In its natural context, the ribozyme comprises four helices, two of which contain conserved formally unpaired loops, that are adjacent arms of a four-way RNA junction. We show that the arms that would carry these loops are brought close together in the global conformation of the isolated junction. Using fluorescence resonance energy transfer, we demonstrate a two-magnesium ion-dependent conformational transition of the complete ribozyme that brings the loopbearing arms into close physical proximity. The ribozyme is active as a four-way junction, and the rate of cleavage may be modulated by the conformation of the four-way junction.
authors.affiliation: Department of Biochemistry, University of Dundee, United Kingdom.
authors.forename: A I
authors.initials: AI
authors.lastname: Murchie
authors.forename: J B
authors.initials: JB
authors.lastname: Thomson
authors.forename: F
authors.initials: F
authors.lastname: Walter
authors.forename: D M
authors.initials: DM
authors.lastname: Lilley
mesh_terms: D001483:Base Sequence; D004789:Enzyme Activation / Q000502:physiology; D005454:Fluorescence Polarization; D008274:Magnesium / Q000378:metabolism; D008969:Molecular Sequence Data; D017860:Nepovirus / Q000201:enzymology / Q000235:genetics; D009690:Nucleic Acid Conformation; D016337:RNA, Catalytic / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D019244:RNA, Satellite / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
chemical_list: D016337:RNA, Catalytic; D019244:RNA, Satellite; D012367:RNA, Viral; D008274:Magnesium