The kinetics and magnesium requirements for the folding of antigenomic delta ribozymes

Using an oligonucleotide hybridization assay to gain insight into the folding of delta ribozymes, we demonstrate a correlation between their folding and catalytic behavior. Together with recent structural information on the crystal structure of self-cleaved genomic delta ribozyme, in which the L3 loop interacts with J1/4 to form the newly proposed stem P1.1, we conclude that it is likely that the P1.1 stem forms only in the presence of Mg(2+). This stem can be detected in both the self-cleaved and trans-acting delta ribozymes. When the trans-acting version of antigenomic delta ribozyme was studied, it is demonstrated that its L3 loop requires magnesium and, apparently, formation of the P1 stem for the subsequently formation of the P1.1 stem. Most importantly, the kinetics were monitored, and provide a significant addition to our understanding of ribozyme tertiary structure formation prior to the chemical cleavage step. Using previous kinetic data and our new findings, we discuss the rate-limiting characteristics of delta ribozyme folding.