Folding intermediates of a self-splicing RNA: Mispairing of the catalytic core

Jie Pan, Sarah A. Woodson

Research output: Contribution to journalArticlepeer-review

163 Scopus citations


The Tetrahymena thermophila self-splicing RNA is trapped in an inactive conformation during folding reactions at physiological temperatures. The structure of this metastable intermediate was probed by chemical modification interference and site-directed mutagenesis. In the inactive structure, an incorrect base-pairing, which we call Alt P3, displaces the P3 helix in the catalytic core of the intron. Mutations that stabilize Alt P3 increase the fraction of pre-rRNA that becomes trapped in the inactive structure, whereas mutations that destabilize Alt P3 reduce 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 slower than for the wild-type, but is increased by addition of urea. The results show that slow folding of the Tetrahymena pre-rRNA is a consequence of non-native secondary structure in the catalytic core of the intron, which is linked to an alternative hairpin in the 5' exon. This illustrates how kinetically stable, long-range interactions shape RNA folding pathways.

Original languageEnglish (US)
Pages (from-to)597-609
Number of pages13
JournalJournal of molecular biology
Issue number4
StatePublished - Jul 24 1998
Externally publishedYes


  • Energy landscape
  • Group I intron
  • RNA folding
  • Ribozyme

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology


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