Figure 1

Minimal functional structure of hammerhead ribozyme. Three helical stems (H1, H2, H3) emanate from a junction on the ribozyme core [17, 18]. In nature, either helix H1 or H3 is terminated by a hairpin loop, which results in intra-molecular catalysis. Hammerhead ribozymes that catalyse the in-trans reaction, as depicted in the figure, can be made synthetically [19]. The core region has a specific sequence for all known active structures and is therefore termed ‘conserved’. Conserved bases are specified explicitly, with H representing any one of {A, C, U}. A dot (∙) stands for any base that will not cause hybridisation in this position; correspondingly two parentheses connected by a dash indicate an arbitrary pair of complementary bases. Hammerhead ribozyme cleaves the substrate strand that binds to form H1 and H3 as symbolically represented by the scissor and dashed lines.