Hammerhead ribozyme: a three dimensional model based on photo-crosslinking data.

The hammerhead ribozyme is a small catalytic RNA motif made up of 3 base-paired stems connected by conserved sequences which are essential for catalysis. We have modelled its 3 dimensional structure, taking advantage of proximity data between several substrate and ribozyme residues determined by photo-crosslinking experiments. It is characterized by an Y shape of the 3 stems stabilized in the central core by a network of hydrogen bonds involving in particular 2 non Watson-Crick G:A base-pairs. The 5' conserved sequence CUGA makes a sharp turn, the G residue exchanging hydrogen bonds with a conserved base-pair of stem III. The substrate is stretched at the cleavage site. Overall this structure is consistent with that deduced from X-ray crystallography but differences are observed at the level of the CUGA turn.