The hammerhead ribozyme

Abstract

The hammerhead ribozyme is a small RNA motif consisting of three helices that intersect at a conserved core. When correctly folded, the hammerhead ribozyme stimulates nearly complete cleavage of the phosphodiester chain at a defined internal site to give 2',3'-cyclic and 5'-hydroxy termini. The cleavage rate is approx. 1 min(-1) at 25 degrees C, pH 7.5, and increases proportionally with hydroxide ion concentration between pH 5 and pH 9. As the rate of non-catalysed cleavage of RNA to form the same products is approx. 10(-6) min(-1) under similar conditions, an important goal is to understand how the folded structure of this small ribozyme increases the rate of alkaline cleavage 10(6)-fold at this specific site.