Nucleobase catalysis in the hairpin ribozyme

Abstract

RNA catalysis is important in the processing and translation of RNA molecules, yet the mechanisms of catalysis are still unclear in most cases. We have studied the role of nucleobase catalysis in the hairpin ribozyme, where the scissile phosphate is juxtaposed between guanine and adenine bases. We show that a modified ribozyme in which guanine 8 has been substituted by an imidazole base is active in both cleavage and ligation, with ligation rates 10-fold faster than cleavage. The rates of both reactions exhibit bell-shaped dependence on pH, with pKa values of 5.7 ± 0.1 and 7.7 ± 0.1 for cleavage and 6.1 ± 0.3 and 6.9 ± 0.3 for ligation. The data provide good evidence for general acid–base catalysis by the nucleobases.