Studies on RNA Cleavage: Catalyst Design and Mechanism

Suny At Buffalo, Amherst NY

Investigators

Abstract

This award in the Inorganic, Bioinorganic, and Organometallic Chemistry Program supports research by Janet R. Morrow and John P. Richard of the Chemistry Department, State University of New York at Buffalo. They will design catalysts to cleave RNA and DNA and attempt to determine the mechanism of these cleavage reactions. There are three main components to the project. First, new Zn(II) and Th(IV) dinuclear complexes will be prepared. These will have variable bridging ligands to control the geometry and separation of the metal ions. The investigators will also use various combinations of other metal ions in the compounds, including Cd, Cu, Ni, Pb, and In. Next, model RNA substrates will be used in reactivity studies to determine the site(s) at which different metal complexes provide transition state stabilization. Structure-reactivity effects on catalytic activity will be used to distinguish metal complexes that interact with the nucleophilic 2'-hydroxyl at the oxyphosphorane-like transition state from complexes that interact with the oxygen leaving group at this transition state. The mechanism of RNA cleavage will be examined to determine whether there is simultaneous activation of both the leaving group and incoming nucleophile, or if there is "double" Lewis acid activation by chelation of the nonbridging oxygens, with no interactions at the leaving group/nucleophile. Analytical and computational methods will be developed to examine relationships between metal-metal distance, geometry, and catalytic activity for cleavage of RNA. The third part of the study will focus on acid-base catalysis of the cleavage of the 3'-phosphodiester linkage at substrates that resemble RNA in order to distinguish acid-base catalysis that occurs at the leaving group/nucleophile from electrophilic catalysis at the nonbriding oxygens of the phosphate group. Cleavage agents for RNA may eventually have practical therapeutic applications, but at this point present substantial intellectual challenges. The mechanism of the reaction is not well understood and so the optimal design features of a cleavage agent are unknown. In this study, various dinuclear metal complexes will be used as cleavage agents and their mechanism of action determined. The role of acid-base mechanisms will also be considered. Graduate and undergraduate students will benefit from involvement in this interdisciplinary project that includes organic and inorganic synthesis and the determination of kinetic parameters. Students will participate in the Chemical Biology program at SUNY-Buffalo and be mentored by a team of investigators with a wide range of skills.