Fast Cleavage Kinetics of a Natural Hammerhead Ribozyme

The hammerhead ribozyme is a small RNA motif that catalyzes the cleavage and ligation of RNA. The well-studied minimal hammerhead motif is inactive under physiological conditions and requires high Mg2+ concentrations for efficient cleavage. In contrast, natural hammerheads are active under physiological conditions and contain motifs outside the catalytic core that lower the requirement for Mg2+. Single-turnover kinetics were used here to characterize the Mg2+ and pH dependence for cleavage of a trans-cleaving construct of the Schistosoma mansoni natural hammerhead ribozyme. Compared to the minimal hammerhead motif, the natural Schistosoma ribozyme requires 100-fold less Mg2+ to achieve a cleavage rate of 1 min-1. The improved catalysis results from tertiary interactions between loops in stems I and II and likely arises from increasing the population of the active conformation. Under optimum pH and Mg2+ conditions this ribozyme cleaves at over 870 min-1 at 25 °C, further demonstrating the impressive cataly...