Minimization of genomic human hepatitis delta virus ribozyme

In order to determine the minimum structure of the human hepatitis delta virus (HDV) ribozyme, several variants were constructed by replacing stem IV with UU, CG, A, C, G or U (MTS-N). Cleavage assays of these cis- and trans-acting shortened HDV ribozymes (cis- and trans-MTS-N) showed that almost all had cleavage activity except MTS-CG and MTS-G. Trans-MTS-CG/G seem to have different stable secondary structures from others by RNA folding program. Among them, both cis- and trans-MTS-U showed the most efficient activity. As a result of point mutations of trans-MTS-U in single-stranded regions, there are more strict base requirements at that position than that of cis-acting HDV ribozyme (HDV88). Therefore, stem IV plays a role to support an active conformation, and it is not directly involved in the catalytic core of the HDV ribozyme. Both cis- and trans-acting MTS-U are, to our knowledge, the smallest HDV ribozyme thus reported.