Abstract

A novel chemo-genetic approach for the analysis of general acid-base catalysis by nucleobases in ribozymes is reviewed. This involves substitution of a C-nucleoside with imidazole in place of a natural nucleobase. The Varkud satellite ribozyme in which the nucleobase at the critical 756 position has been replaced by imidazole is active in both cleavage and ligation reactions. Similarly, a modified hairpin ribozyme with the nucleobase at position 8 substituted by imidazole is active in cleavage and ligation reactions. Although the rates are lower than those of the natural ribozymes, they are significantly greater than other variants at these positions. The dependence of the hairpin ribozyme reaction rates on pH has been studied. Both cleavage and ligation reactions display a bell-shaped pH dependence, consistent with general acid-base catalysis involving the nucleotide at position 8.