FIG. 1.

Stages of DNAzyme-mediated RNA cleavage. For simplicity, conformationally similar stages have been elided together (see Borggräfe et al. [23] for detailed binding kinetics). The unassociated DNAzyme (state A) binds to the target RNA (state B₀). Monovalent metal ions bind, stabilizing the DNAzyme/RNA complex (state B₁). Cofactor (M²⁺) (e.g. Mg²⁺, Ca²⁺, Na⁺, etc.) binding causes conformational activation of the DNAzyme (state B₂). Once M²⁺ equilibrium is reached the substrate is cleaved (state C₀). M²⁺ is released and the DNAzyme unwinds and dissociates from the cleaved RNA (state C₁/C₂). This process may repeat over multiple cycles. Adapted from Ref. Chakravarthy et al. [1].