Mutational analysis of the antigenomic trans-acting delta ribozyme:: the alterations of the middle nucleotides located on the P1 stem

Our previous report on delta ribozyme cleavage using a trans-acting antigenomic delta ribozyme and a collection of short substrates showed that the middle nucleotides of the pi stem, the substrate binding site, are essential for the cleavage activity. Here we have further investigated the effect of alterations in the P1 stem on the kinetic and thermodynamic parameters of delta ribozyme cleavage using various ribozyme variants carrying single base mutations at putative positions reported. The kinetic and thermodynamic values obtained in mutational studies of the two middle nucleotides of the P1 stem suggest that the binding and active sites of the delta ribozyme are uniquely formed. Firstly the substrate and the ribozyme are engaged in the formation of a helix, known as the P1 stem, which may contain a weak hydrogen bond(s) or a bulge. Secondly, a tertiary interaction involving the base moieties in the middle of the P1 stem likely plays a role in defining the chemical environment. As a consequence, the active site might form simultaneously or subsequently to the binding site during later steps of the pathway.