Abstract
Background: Hepatitis delta virus (HDV) ribozymes cleave RNA in the presence of divalent metal ions. We have previously elucidated the solution conformation of a minimized trans‐acting HDV ribozyme and obtained evidence by NMR study that an Mg^2+^ ion binds to a site close to the cleavage site.
Results: We examined two ribozyme systems: a pre‐cleavage complex with a non‐cleavable substrate analogue (mS8) and a post‐cleavage complex with a 3′ cleavage product (P7). Upon titration with MgCl~2~, the complex with P7 showed a profound spectral change, while that with mS8 showed broadening of the signals. Analysis of the NOESY spectra of the P7 complex at high Mg^2+^ concentration revealed that a G:U pair is formed within the L3 loop, and the P1 and P4 stems are stabilized with respect to those of the pre‐cleavage complex.
Conclusion: The present analysis indicates that the cleavage reaction of the HDV ribozyme produces a big conformational change. Furthermore, presence of the 5′‐terminal cytidine residue prevents this conformational change and its absence stabilizes the product–ribozyme complex in the presence of Mg^2+^. The structure of the Mg^2+^‐bound P7 complex is similar to the crystal structure found for a product–ribozyme complex but is different from the pre‐cleavage structure.