An obligate intermediate along the slow folding pathway of a group II intron ribozyme
Open Access
- 1 January 2005
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 33 (21), 6674-6687
- https://doi.org/10.1093/nar/gki973
Abstract
Most RNA molecules collapse rapidly and reach the native state through a pathway that contains numerous traps and unproductive intermediates. The D135 group II intron ribozyme is unusual in that it can fold slowly and directly to the native state, despite its large size and structural complexity. Here we use hydroxyl radical footprinting and native gel analysis to monitor the timescale of tertiary structure collapse and to detect the presence of obligate intermediates along the folding pathway of D135. We find that structural collapse and native folding of Domain 1 precede assembly of the entire ribozyme, indicating that D1 contains an on-pathway intermediate to folding of the D135 ribozyme. Subsequent docking of Domains 3 and 5, for which D1 provides a preorganized scaffold, appears to be very fast and independent of one another. In contrast to other RNAs, the D135 ribozyme undergoes slow tertiary collapse to a compacted state, with a rate constant that is also limited by the formation D1. These findings provide a new paradigm for RNA folding and they underscore the diversity of RNA biophysical behaviors.Keywords
This publication has 64 references indexed in Scilit:
- Principles of RNA Compaction: Insights from the Equilibrium Folding Pathway of the P4-P6 RNA Domain in Monovalent CationsJournal of Molecular Biology, 2004
- Monovalent Ion-mediated Folding of the Tetrahymena thermophila RibozymeJournal of Molecular Biology, 2004
- Architecture and folding mechanism of the Azoarcus Group I Pre-tRNAJournal of Molecular Biology, 2004
- An Alternative Route for the Folding of Large RNAs: Apparent Two-state Folding by a Group II Intron RibozymeJournal of Molecular Biology, 2003
- The Fastest Global Events in RNA Folding: Electrostatic Relaxation and Tertiary Collapse of the Tetrahymena RibozymeJournal of Molecular Biology, 2003
- Protein-dependent transition states for ribonucleoprotein assemblyJournal of Molecular Biology, 2001
- Antagonistic substrate binding by a group II intron ribozymeJournal of Molecular Biology, 1999
- Folding intermediates of a self-splicing RNA: mispairing of the catalytic coreJournal of Molecular Biology, 1998
- [6] Efficient site-directed mutagenesis using uracil-containing DNAMethods in Enzymology, 1991
- Comparative and functional anatomy of group II catalytic introns — a reviewGene, 1989