Strategies for phosphodiester complexation and cleavage

Abstract

Abstract Staphylococcal nuclease catalyses the hydrolysis of DNA phosphate linkages with a rate enhancement of the order of 1016. The active site possesses two guanidinium groups and a Ca2+, all of which are proposed to stabilize the formation of the phosphorane intermediate formed along the hydrolysis reaction pathway. In an attempt to achieve a fraction of the natural rate enhancement in aqueous media, several receptors possessing guanidinium groups preorganized and complementary to a phosphodiester have been synthesized. The guanidinium receptor designs were based upon analysis of multiple polyazaclefts used to study the binding of phosphodiesters in nonaqueous media. The spatial relationships of the hydrogen bonding groups with respect to each other are found to be crucial to the strength of binding, with spacers that hold the hydrogen bonding groups at a slightly greater distance than isophthaloyl spacers being optimum. The bis-guanidinium receptors do enhance the cleavage of RNA at low equivalents of the receptors to RNA phosphates. A quantitative assay to measure rates of RNA hydrolysis at 37 °C is briefly discussed.