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The conformation of the hammerhead ribozyme was studied by NMR. In the absence of magnesium ion, the U turn does not exist at the core region. Consequently, stem II extends to stem I. G5 in the core region forms a base pair with C17 at the cleavage site. On the mutation of G16.2C15.2 in stem III by C16.2G15.2, G5 and U4 at the core region interact with C16.2 and U16.1, respectively, where stem III becomes shorter, while stem I does longer. On the addition of magnesium ions, U4 turn occurs in wild type, but does not in the mutation.

NMR studies of the alternative conformation of hammerhead ribozyme in the solution