Energetics of RNA cleavage: implications for the mechanism of action of ribozymes

Abstract

A new class of ribozymes produce 2′, 3′-cyclk phosphate upon self-catalyzed cleavage of RNA molecules, similar to those observed during enzymatic (RNase-catalyzed) as well as non-enzymatic hydrolyses of RNAs. This product suggests that the reaction intermediate/transition state is a pentacoordinated oxyphosphorane. In order to elucidate the energetics of these RNA cleaving reactions, the reaction coordinate has been simulated and a pentacoordinated intermediate has been characterized via ab initio molecular orbital calculations utilizing the dianionk hydrolysis-intermediate of methyl ethylene phosphate as a model compound. The calculated reaction coordinate indicates that the transition state for the P−O(2′) bond cleavage is lower in energy than that for the P−O(5′) bond cleavage under uncatalyzed conditions. Thus, the dianionk pentacoordinated phosphorus intermediate tends to revert back to the starting RNA by cleaving the P−O(2′) bond rather than productively cleaving the P−O(5′) bond. In order for ribozymes to effectively cleave RNA molecules, it is therefore mandatory to stabilize the leaving 5′-oxygen, e.g. by means of a divalent magnesium ion.