J. Pan et Sa. Woodson, FOLDING INTERMEDIATES OF A SELF-SPLICING RNA - MISPAIRING OF THE CATALYTIC CORE, Journal of Molecular Biology, 280(4), 1998, pp. 597-609
The Tetrahymena thermophila self-splicing RNA is trapped in an inactiv
e conformation during folding reactions at physiological temperatures.
The structure of this metastable intermediate was probed by chemical
modification interference and site-directed mutagenesis. Ln the inacti
ve structure, an incorrect base-pairing, which we call Alt P3, displac
es the P3 helix in the catalytic core of the intron. Mutations that st
abilize Alt P3 increase the fraction of pre-rRNA that becomes trapped
in the inactive structure, whereas mutations that destabilize Alt P3 r
educe accumulation of this conformer. At high concentrations of Mg2+,
the yield of correctly folded mutant pre-rRNAs is similar to wild-type
RNA. Under these conditions, the rate of folding for mutant RNAs is s
lower than for the wild-type, but is increased by addition of urea. Th
e results show that slow folding of the Tetrahymena pre-rRNA is a cons
equence of non-native secondary structure in the catalytic core of the
intron, which is linked to an alternative hairpin in the 5' exon. Thi
s illustrates how kinetically stable, long-range interactions shape RN
A folding pathways. (C) 1998 Academic Press.