FIGURE 3.

The sequence and structure of the VS ribozyme. (A) The VS ribozyme secondary structure. This consists of seven helical segments labeled I through VII that are associated through three three-way junctions. Cleavage occurs within the internal loop of helix I ([arrow] the position of cleavage and ligation) and requires the A730 loop within helix VI. The key nucleotides A756 and G638 are highlighted. (B) A model of the complete VS ribozyme derived from analysis of SAXS data (Lipfert et al. 2008). This is also in agreement with earlier studies based on analysis of the conformations of the individual component helical junctions (Lafontaine et al. 2002a). (Yellow) The A730 loop; (magenta sphere) the scissile phosphate.