Hammerhead ribozyme

The Hammerhead ribozyme is a small ribozyme (RNA motif) consisting of three helices that cross in a conserved core. When folded correctly, the Hammerhead ribozyme stimulates an almost complete cleavage of the phosphodiester chain at a specific internal site, resulting in 2',3'-cyclic and 5'-hydroxy termini. The cleavage rate is approximately 1 min(-1) at 25 degrees C, pH 7.5 and increases proportionally with the hydroxide ion concentration between pH 5 and pH 9.

The well-studied minimal Hammerhead motif is inactive under physiological conditions and requires high Mg(2+) concentrations for efficient cleavage.

In contrast, natural Hammerhead ribozymes are active under physiological conditions and contain motifs outside the catalytic core that reduce the need for Mg(2+).

For example, compared to the minimal Hammerhead motif, the natural Schistosoma ribozyme requires 100 times less Mg(2+) to achieve a cleavage rate of 1 min(-1). The improved catalysis results from tertiary interactions between the loops in strains I and II and probably results from the increase in the population of the active conformation. Under optimal pH and Mg(2+) conditions, this ribozyme cleaves at a rate of over 870 min(-1) at 25 degrees C, further emphasizing the impressive catalytic power of this ribozyme.

1. Blount KF et al (2002) The hammerhead ribozyme. Biochem Soc Trans 30:1119-1122.
2. Canny MD et al. (2004) Fast cleavage kinetics of a natural hammerhead ribozyme. J Am Chem Soc 126:10848-10849.