The P4-P6 domain directs higher order folding of the Tetrahymena ribozyme core

Biochemistry. 1997 Mar 18;36(11):3159-69. doi: 10.1021/bi962428+.


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Animals
  • Base Sequence
  • Edetic Acid
  • Ferrous Compounds
  • Genes, Protozoan
  • Introns
  • Models, Structural
  • Molecular Sequence Data
  • Nucleic Acid Conformation*
  • Plasmids
  • Polymerase Chain Reaction
  • RNA, Catalytic / chemistry*
  • RNA, Catalytic / isolation & purification
  • RNA, Catalytic / metabolism
  • RNA, Protozoan / chemistry
  • RNA, Protozoan / isolation & purification
  • RNA, Protozoan / metabolism
  • Solvents
  • Sulfuric Acid Esters
  • Templates, Genetic
  • Tetrahymena / genetics*


  • Ferrous Compounds
  • RNA, Catalytic
  • RNA, Protozoan
  • Solvents
  • Sulfuric Acid Esters
  • Fe(II)-EDTA
  • Edetic Acid
  • dimethyl sulfate