The cleavage of phosphodiester bonds within small RNA bulges in the presence and absence of metal ion catalysts

This work studies the effect of RNA structure on the reactivity of RNA phos phodiester bonds. The aim of the study is to evaluate those structural para meters that affect reactivity to support the development of sequence-specif ic RNA cleaving agents. The cleavage of phosphodiester bonds within one- to five-nucleotide bulges has been studied in buffer solutions (pH 8.4), and in the presence of Zn2+ aqua ion (pH 6.4) or its 1,5,9-triazacyclododecane complex (pH 7.4). Molecular modelling has been applied to study the structu re of the substrates. The basis of the reactivity and the catalytic potenti al of metal ion-based cleaving agents are discussed.