A densely modified M2+-independent DNAzyme that cleaves RNA efficiently with multiple catalytic turnover

Sequence-specific cleavage of RNA targets in the absence of a divalent metal cation (M2+) has been a long-standing goal in bioorganic chemistry. Herein, we report the in vitro selection of novel RNA cleaving DNAzymes that are selected using 8-histaminyl-deoxyadenosine (dA(im)TP), 5-guanidinoallyl-deoxyuridine (dU(ga)TP), and 5-aminoallyl-deoxycytidine (dC(aa)TP) along with dGTP. These modified dNTPs provide key functionalities reminiscent of the active sites of ribonucleases, notably RNase A. Of several such M2+-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 Mg2+ was present, attaining values of k(cat) of 1.06 min(-1) and a K-M of 1.37 mM corresponding to a catalytic efficiency of similar to 10(6) M-1 min(-1). Therefore, Dz7-38-32 represents a promising candidate towards the development of therapeutically efficient DNAzymes.