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 °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 106-fold at this specific site.

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