Unifying the Current Data on the Mechanism of Cleavage–Transesterification of RNA

The various mechanisms by which RNA is hydrolyzed are currently under intense investigation. The first step in the hydrolysis pathway is a cleavage–transesterification in which a 2′-OH group attacks a 3′,5′-phosphodiester linkage with departure of the 5′ group. The second step involves the opening of a 2′,3′-cyclic phosphodiester. Complications in these steps arise from multiple possible pathways involving specific acid and base as well as general acid and base catalysis. In addition, controversy exists concerning the protonation states of the phosphodiesters and any intermediate phosphoranes under various experimental conditions. A summary of mechanistic studies involving general and specific acid/base catalysis of RNA hydrolysis and the hydrolysis of RNA analogs is presented herein, along with the interpretations given by the original authors. Included are theoretical calculations, kinetic studies, pK_a determinations, isotope effects, Hammett and Brønsted correlations, and model studies. Recent analyses of the mechanism of RNase A are also briefly reviewed. Two limiting mechanisms for the cleavage–transesterification step that unify the data in the literature and differ only in the role of the phosphorane and its protonation state are given at the outset. An analysis of the literature studies supporting these mechanisms is then provided.