In Vitro Selection of High Temperature Zn2+-Dependent DNAzymes

In vitro selection of Zn²⁺-dependent RNA-cleaving DNAzymes with activity at 90°C has yielded a diverse spool of selected sequences. The RNA cleavage efficiency was found in all cases to be specific for Zn²⁺ over Pb²⁺, Ca²⁺, Cd²⁺, Co²⁺, Hg²⁺, and Mg²⁺. The Zn²⁺-dependent activity assay of the most active sequence showed that the DNAzyme possesses an apparent Zn²⁺-binding dissociation constant of 234 μM and that its activity increases with increasing temperatures from 50–90°C. A fit of the Arrhenius plot data gave E_a = 15.3 kcal mol⁻¹. Surprisingly, the selected Zn²⁺-dependent DNAzymes showed only a modest (∼3-fold) activity enhancement over the background rate of cleavage of random sequences containing a single embedded ribonucleotide within an otherwise DNA oligonucleotide. The result is attributable to the ability of DNA to sustain cleavage activity at high temperature with minimal secondary structure when Zn²⁺ is present. Since this effect is highly specific for Zn²⁺, this metal ion may play a special role in molecular evolution of nucleic acids at high temperature.