An alternative route for the folding of large RNAs: apparent two-state folding by a group II intron ribozyme.

摘要: Abstract Despite a growing literature on the folding of RNA, our understanding tertiary in large RNAs derives from studies small set molecular examples, with primary focus group I introns and RNase P RNA. To broaden scope RNA models to better understand II intron function, we have examined ribozyme (D135) that is derived self-splicing ai5γ yeast mitochondria. The D135 folds homogeneously cooperatively into compact, well-defined structure includes all regions critical for active-site organization substrate recognition. When was treated increasing concentrations Mg2+ then subjected hydroxyl radical footprinting, similar dependencies were seen internalization molecule, suggesting highly cooperative behavior. In this work, show global compaction molecule same magnesium dependence as local previously observed. Furthermore, urea denaturation indicate unfolding governed by thermodynamic parameters those forward folding. fact, unfolded state its native, active structure, thereby demonstrating functional reversibility Taken together, data are consistent two-state ribozyme, which surprising given size multi-domain findings establish accumulation stable intermediates prior formation native not universal feature there an alternative paradigm landscape relatively smooth, lacking rugged features obstruct state.