NMR studies of the effect of GA-AG base pairs to the active conformation of hammerhead ribozyme.

The effect of the conserved bases (GA-AG base pairs) in the core region to active conformation of hammerhead ribozyme was studied by NMR. This ribozyme has two conformers in the solution. One is the same as the crystal structure, which has sheared GA-AG base pairs and Y-shape conformation, while the other has Watson-Crick GA-AG base pairs and the extend conformation between the stems I and II. On addition of magnesiun ions, the peaks around GA-AG base pairs and cleavage site in only Y-shape conformation, shift or became broadening, following to produce the peaks of product by the cleavage reaction.