Construction of new hairpin ribozymes with replaced domains.

We have constructed a new type of hairpin ribozyme by cleaving and reverse-joining one of the two catalytic domains to conserve an essential bending structure. The two domains of the new ribozymes were tethered by different lengths of cytidylate linkers. These ribozymes retained the cleavage activity and the cleavage activities depended on the linker lengths. Although these rejoined ribozymes showed weak turnover abilities, those with 18 cytidylates showed a larger kcat/K(m) value than the natural hairpin ribozymes. These modifications in the primary structure of the hairpin ribozyme confirm the bent conformation for the catalytic reaction of this ribozyme, and provide a new approach for the design of highly efficient ribozymes.