Abstract:

We report Zn2+-dependent deoxyribozymes that ligate RNA. The DNA enzymes were identified by in vitro selection and ligate RNA with k obs up to 0.5 min-1 at 1 mM Zn2+ and 23 °C, pH 7.9, which is substantially faster than our previously reported Mg 2+-dependent deoxyribozymes. Each new Zn2+-dependent deoxyribozyme mediates the reaction of a specific nucleophile on one RNA substrate with a 2′,3′-cyclic phosphate on a second RNA substrate. Some of the Zn2+-dependent deoxyribozymes create native 3′-5′ RNA linkages (with kobs up to 0.02 min -1), whereas all of our previous Mg2+-dependent deoxyribozymes that use a 2′,3′-cyclic phosphate create non-native 2′-5′ RNA linkages. On this basis, Zn2+-dependent deoxyribozymes have promise for synthesis of native 3′-5′-linked RNA using 2′,3′-cyclic phosphate RNA substrates, although these particular Zn2+-dependent deoxyribozymes are likely not useful for this practical application. Some of the new Zn2+-dependent deoxyribozymes instead create non-native 2′-5′ linkages, just like their Mg2+ counterparts. Unexpectedly, other Zn2+- dependent deoxyribozymes synthesize one of three unnatural linkages that are formed upon the reaction of an RNA nucleophile other than a 5′-hydroxyl group. Two of these unnatural linkages are the 3′-2′ and 2′-2′ linear junctions created when the 2′-hydroxyl of the 5′-terminal guanosine of one RNA substrate attacks the 2′,3′-cyclic phosphate of the second RNA substrate. The third unnatural linkage is a branched RNA that results from attack of a specific internal 2′-hydroxyl of one RNA substrate at the 2′,3′-cyclic phosphate. When compared with the consistent creation of 2′-5′ linkages by Mg2+-dependent ligation, formation of this variety of RNA ligation products by Zn2+-dependent deoxyribozymes highlights the versatility of transition metals such as Zn2+ for mediating nucleic acid catalysis.