title: Mispaired P3 region in the hierarchical folding pathway of the Tetrahymena ribozyme.
abstract: BACKGROUND
  The Tetrahymena group I ribozyme folds into a complex three-dimensional structure for performing catalytic reactions. The catalysis depends on its catalytic core consisting of two helical domains, P4-P6 and P3-P7, connected by single stranded regions. In the folding process, most of this ribozyme folds in a hierarchical manner in which a kinetically stable intermediate determines the overall folding rate.
  
  
  RESULTS
  Although the nature of this intermediate has not yet been elucidated, a mispaired P3 stem (alt-P3) appears a likely candidate. To examine the effects of the alt-P3 structure on the kinetic and thermodynamic properties of the active structure of the ribozyme or its P3-P7 domain formation, we prepared and analysed variant ribozymes in which relative stabilities of the original P3 and alt-P3 structure were altered systematically.
  
  
  CONCLUSIONS
  The results indicate that the alt-P3 structure is not the major rate-limiting factor in the folding process.
authors.affiliation: Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan.
authors.forename: Yasushi
authors.initials: Y
authors.lastname: Ohki
authors.forename: Yoshiya
authors.initials: Y
authors.lastname: Ikawa
authors.forename: Hideaki
authors.initials: H
authors.lastname: Shiraishi
authors.forename: Tan
authors.initials: T
authors.lastname: Inoue
mesh_terms: D000818:Animals; D001483:Base Sequence; D007700:Kinetics; D008274:Magnesium / Q000378:metabolism; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D015345:Oligonucleotide Probes; D017510:Protein Folding; D016337:RNA, Catalytic / Q000737:chemistry / Q000378:metabolism*; D013768:Tetrahymena / Q000201:enzymology*
chemical_list: D015345:Oligonucleotide Probes; D016337:RNA, Catalytic; D008274:Magnesium