Group II intron ribozymes that cleave DNA and RNA linkages with similar efficiency, and lack contacts with substrate 2′-hydroxyl groups

Abstract

Background: Group II introns are self-splicing RNAs that have mechanistic similarity to the spliceosome complex involved in messenger RNA splicing in eukaryotes. These autocatalytic molecules can be recon-figured into highly specific, multiple-turnover ribozyines that cleave oligonucleorides in trans. We set out to use a simplified system of this kind to study the mechanisin of cleavage. Results: Unlike other catalytic RNA molecules, the group II ribozymes cleave DNA linkages almost as readily as RNA linkages. One ribozyme variant cleaves DNA linkages with an efficiency comparable to that of restriction endonuclease EcoRI. Single deoxynucleotide substitutions in the substrate showed that the ribozymes bind substrate without engaging 2′-hydroxyl groups. Conclusions: The ribose 2′-hydroxyl group at the cleavage site has little role in transition-state stabilization by group II ribozymes. Substrate 2′-hydroxyl groups are not involved in substrate binding, suggesting that only base-pairing is required for substrate recognition.