A densely modified M-independent DNAzyme that cleaves RNA efficiently with multiple catalytic turnover.

Sequence-specific cleavage of RNA targets in the absence of a divalent metal cation (M) has been a long-standing goal in bioorganic chemistry. Herein, we report the selection of novel RNA cleaving DNAzymes that are selected using 8-histaminyl-deoxyadenosine (dATP), 5-guanidinoallyl-deoxyuridine (dUTP), and 5-aminoallyl-deoxycytidine (dCTP) along with dGTP. These modified dNTPs provide key functionalities reminiscent of the active sites of ribonucleases, notably RNase A. Of several such M-free DNAymes, DNAzyme 7-38-32 cleaves a 19 nt all-RNA substrate with multiple-turnover, under simulated physiological conditions wherein only 0.5 mM Mg was present, attaining values of of 1.06 min and a of 1.37 μM corresponding to a catalytic efficiency of ∼10 M min. Therefore, Dz7-38-32 represents a promising candidate towards the development of therapeutically efficient DNAzymes.