Mispaired P3 region in the hierarchical folding pathway of the Tetrahymena ribozyme.
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.
Ohki
Yasushi
Y
Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan.
Ikawa
Yoshiya
Y
Shiraishi
Hideaki
H
Inoue
Tan
T
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*
D015345:Oligonucleotide Probes; D016337:RNA, Catalytic; D008274:Magnesium