Inter-domain cross-linking and molecular modelling of the hairpin ribozyme

David J. Earnshaw, Benoît Masquida, Sabine Müller, Snorri Th Sigurdsson, Fritz Eckstein, Eric Westhof, Michael J. Gait*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

82 Citations (Scopus)


The hairpin ribozyme is a small catalytic RNA composed of two helical domains containing a small and a large internal loop and, thus, constitutes a valuable paradigm for the study of RNA structure and catalysis. We have carried out molecular modelling of the hairpin ribozyme to learn how the two domains (A and B) might fold and approach each other. To help distinguish alternative inter-domain orientations, we have chemically synthesized hairpin ribozymes containing 2'-2' disulphide linkages of known spacing (12 or 16 Å) between defined ribose residues in the internal loop regions of each domain. The abilities of cross-linked ribozymes to carry out RNA cleavage under single turnover conditions were compared to the corresponding disulphide-reduced, untethered ribozymes. Ribozymes were classed in three categories according to whether their cleavage rates were marginally, moderately, or strongly affected by cross-linking. This rank order of activity guided the docking of the two domains in the molecular modelling process. The proposed three-dimensional model of the hairpin ribozyme incorporates three different crystallographically determined structural motifs: in domain A, the 5'-GAR-3'-motif of the hammerhead ribozyme, in domain B, the J4/5 motif of group I ribozymes, and connecting the two domains, a 'ribose zipper', another group I ribozyme feature, formed between the hydroxyl groups of residues A10, G11 of domain A and C25, A24 of domain B. This latter feature might be key to the selection and precise orientation of the inter-domain docking necessary for the specific phosphodiester cleavage. The model provides an important basis for further studies of hairpin ribozyme structure and function.

Original languageEnglish
Pages (from-to)197-212
Number of pages16
JournalJournal of Molecular Biology
Issue number2
Publication statusPublished - 28 Nov 1997

Bibliographical note

Funding Information:
We thank Dr Wolfgang Pieken (Nexstar Pharmaceuticals Inc.) for provision of protected 2′-amino-2′-deoxynucleoside phosphoramidites, Richard Grenfell, Jan Fogg and Terry Smith for help in assembly of oligoribonucleotides, Mohinder Singh for help with polyacrylamide gel electrophoresis and Mark Farrow for advice. B.M. is supported by a Bourse-Docteur-Ingénieur Rhône-Poulenc Rorer/CNRS. Work in the laboratory of F.E. was supported by the Deutsche Forschungsgemeinschaft.

Other keywords

  • Hairpin ribozyme
  • Ribose zipper
  • RNA folding
  • RNA modelling
  • RNA-RNA cross-linking


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