The P4−P6 Domain Directs Higher Order Folding of the Tetrahymena Ribozyme Core

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Abstract
The active site of group I self-splicing introns occurs at the interface of two proposed structural domains. In the Tetrahymena intron, half of the catalytic core resides within the independently-folding P4−P6 domain while the other half belongs to a putative domain that includes helices P3, P7, P8, and P9 (P3−P9). To determine whether the P3−P9 region of the intron can also fold independently, we used Fe(II)-EDTA and dimethyl sulfate to probe the solvent accessibility of separate fragments of the Tetrahymena intron. These RNAs self-assemble into an active complex in trans, enabling analysis of their structural features both alone and within the complex. Our results show that while the P3−P9 region of the intron retains its secondary structure, most of the tertiary interactions within this region do not form stably in the absence of the P4−P6 domain. This indicates that the P4−P6 domain induces folding in the P3−P9 region, organizing the catalytic cleft between them. Thus the P4−P6 domain provides a scaffold for the folding of the Tetrahymena intron core.