FIGURE 2.

The sequence and structure of the hairpin ribozyme. (A) The hairpin ribozyme secondary structure. The natural ribozyme is built on a scaffold of a four-way helical junction, with the arms labeled A through D. The important nucleotides for ribozyme activity are all contained within the internal loops in helices A and B. The key nucleotides A38 and G8 are highlighted. (Arrow) The position of cleavage and ligation. (B) Crystal structure of the hairpin ribozyme in its four-way junction form (Rupert and Ferré-D'Amaré 2001). (C) Parallel-eye stereoscopic view of the active site of a transition state analog of the hairpin ribozyme in which the pentacoordinate phosphorane is substituted by a vanadium atom (Rupert et al. 2002).