Computer Analysis of the Cleavage Reaction of Hammerhead Ribozyme

We have analyzed various in vitro cleavage reactions of hammerhead ribozyme by a computer program. Three energy changes: deltaE(s'), deltaE(r'), and deltaE, were calculated. deltaE(s') was the hypothetical energy requirement for the substrate to be activated from the most stable state to the relaxed state. deltaE(r') was the same energy requirement for the ribozyme. deltaE was the calculated free energy decrease by the formation of Rz-S complex from the relaxed ribozyme and the substrate. We found that high deltaE(s') or deltaE(r') reduced the cleavage efficiency of the reaction, and that the deltaE was related to both cleavage efficiency and the optimal temperature of the reaction. deltaE(s'), deltaE(r') can be calculated in advance according to the sequences of the ribozyme and the substrate. Our model, therefore, can be use in the designing of ribozymes.