In vitro selection and characterization of a highly efficient Zn(II)-dependent RNA-cleaving deoxyribozyme

Effects of metal ions and catalytic loop sequences on the complex formation of a deoxyribozyme and its RNA substrate

A deoxyribozyme is a catalytic DNA that catalyzes a site-specific RNA cleavage activity and requires various divalent cations. Earlier we have reported that by downsizing the catalytic loop of a deoxyribozyme from 15-mer to 11-mer it resulted in a short and novel Ca2+-dependent deoxyribozyme. In this paper, we investigate the complex formation of deoxyribozymes with their RNA substrates by using surface plasmon resonance (SPR) in order to determine quantitatively the effect of Ca2+ or Mg2+ on the recognition step between a deoxyribozyme and its RNA substrate. The results indicate that both the association and dissociation rate constants (k(a) and k(d)) for the deoxyribozyme-RNA complex depends on metal ions as well as the loop size of the deoxyribozyme. Metal ions with high RNA cleavage activity induced an increase in k(a) and a decrease in k(d). On the basis of the results, we propose that Ca2+ ions may play a role in the rearrangement of the 11-mer catalytic loop of the short Ca2+-dependent deoxyribozyme.

Preferential activation of the 8-17 deoxyribozyme by Ca(2+) ions. Evidence for the identity of 8-17 with the catalytic domain of the Mg5 deoxyribozyme

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 Mg(2+) (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 Ca(2+) as compared with Mg(2+). This preference for calcium ions critically depended on the nucleoside residues at two specific positions of the deoxyribozyme core. The Ca(2+) 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.