Abstract:

The 8–17 deoxyribozyme is a small RNA-cleaving DNA molecule of potential therapeutic interest. Here, the cleavage rates of 16 variants of the 8–17 deoxyribozyme were measured in the presence of different divalent metal ions. Despite the fact that 8–17 was originally selected in vitro for activity in the presence of Mg2+ (Santoro, S. W., and Joyce, G. F. (1997) Proc. Natl. Acad. Sci. U. S. A. 94, 4262–4266) nearly all the 8–17 variants exhibited substantially higher (up to 20-fold) reaction rates in Ca2+ as compared with Mg2+. This preference for calcium ions critically depended on the nucleoside residues at two specific positions of the deoxyribozyme core. The Ca2+ specificity of 8–17 is strongly reminiscent of the properties of Mg5, an RNA phosphodiester-cleaving deoxyribozyme previously isolated by Faulhammer and Famulok (Faulhammer, D., and Famulok, M. (1996) Angew. Chem. Int. Ed. Engl. 35, 2837–2841). Indeed, analysis of the Mg5 sequence revealed the presence of a complete 8–17 motif, coincident with the conserved region of Mg5. An 8–17 deoxyribozyme modeled after the Mg5 conserved region displayed catalytic features comparable with those reported for the full-length Mg5 deoxyribozyme.