In vitro evolution of an RNA-cleaving DNA enzyme into an RNA ligase switches the selectivity from 3′-5′ to 2′-5′

Deoxyribozymes that ligate RNA expand the scope of nucleic acid catalysis and allow preparation of site-specifically modified RNAs. Previously, deoxyribozymes that join a 5′-hydroxyl and a 2′,3′-cyclic phosphate were identified by in vitro selection from random DNA pools. Here, the alternative strategy of in vitro evolution was used to transform the 8-17 deoxyribozyme that cleaves RNA into a family of DNA enzymes that ligate RNA. The parent 8-17 DNA enzyme cleaves native 3′-5′ phosphodiester linkages but not 2′-5′ bonds. Surprisingly, the new deoxyribozymes evolved from 8-17 create only 2′-5′ linkages. Thus, reversing the direction of the DNA-mediated process from ligation to cleavage also switches the selectivity in forming the new phosphodiester bond. The same change in selectivity was observed upon evolution of the 10-23 RNA-cleaving deoxyribozyme into an RNA ligase. The DNA enzymes previously isolated from random pools also create 2′-5′ linkages. Therefore, deoxyribozyme-mediated formation of a non-native 2′-5′ phosphodiester linkage from a 5′-hydroxyl and a 2′,3′-cyclic phosphate is strongly favored in many different contexts.