Effect of metal ions and sequence of deoxyribozymes on their RNA cleavage activity

Catalytic DNA is a promising class of nucleic acid enzyme for possible use as a therapeutic agent and is also interesting in comparison with catalytic RNAs. In this study, we investigated the effect of metal ions and sequence on an original deoxyribozyme, d(GCCTGGCAG(1)G(2)C(3)T(4)A(5)G(6)C(7)T(8)A(9)C(10)A(11)A(12)C(13)G(14)A(15)GTCCCT), which binds to an RNA substrate, r(AGGGACA down arrow UGCCAGGC), cleaving the RNA substrate at one site indicated by the arrow. The results show that the ability of metal ions to promote the RNA cleavage reaction by the original deoxyribozyme is Mn2+ > Mg2+ >Ca2+ much greater than Ba2+. This result is very similar to the previous tendency observed in the case of a hammerhead ribozyme. Thus, these results suggest that RNA cleavage by the deoxyribozyme dependence on metal ions for catalysis is similar to that with ribozymes. On the other hand, a nucleotide deletion from the active domain of the original deoxyribozyme results in a novel deoxyribozyme with high Ca2+-dependency, a situation which is not observed with the original deoxyribozyme or hammerhead ribozymes.