The fluorescent dyes methylene blue, MB+, and thionine, Th+, can be trapped in the pores of mesoporous silica, MP-SiO2, by means of functional nanostructures consisting of the Mg2+- or Zn2+-dependent DNAzyrne sequences. In the presence of Mg2+ or Zn2+ ions the respective DNAzymes are activated, leading to the specific cleavage of the respective caps, and the selective release of MB+ or Th+ The enlargement of the conserved loop domains of the Mg2+- or Zn2+-dependent DNAzyme sequences with foreign nucleotides prohibits the formation of active DNAzymes and eliminates the release of the respective dyes. This is due to the flexibility of the loops that lacks affinity for the association of the ions. The insertion of aptamer sequences (e.g., the adenosine-5'-triphosphate (ATP) aptamer) or ion-binding sequences (e.g., T-rich Hg2+ ion-binding domains) as foreign components to the loop regions allows the formation of active Mg2+- or Zn2+-dependent DNAzyme structures through the cooperative formation of aptamer-ATP complexes or T-Hg2+-bridges. These aptamer-substrate complexes or T-Hg2+-T bridges allosterically stabilize and activate the DNAzymes, thus allowing the selective release of the fluorescent substrates MB+ or Th+. The metal ion-driven DNAzyme release of substrates from the pores of MP-SiO2, and particularly the allosteric activation of the DNAzymes through cooperative aptamer-substrate complexes or metal-ion bridges, has important future nanomedical implications for targeted release of drugs. This is demonstrated with the triggered release of the anticancer drug, doxorubicin, by the Mg2+-DNAzyme-locked pores or by the aptamer-ATP complex-triggered activation of the Mg2+-dependent DNAzyme.