DNA-Based Multiconstituent Dynamic Networks: Hierarchical Adaptive Control over the Composition and Cooperative Catalytic Functions of the Systems

The information encoded in the base sequences of nucleic acids is used to construct 3 × 2 or 3 × 3 constitutional dynamic networks (CDNs) composed of six or nine constituents, respectively. In the presence of appropriate triggers, the adaptive and hierarchical reconfiguration of the CDNs is demonstrated. The reconfiguration of the CDNs, which involves the triggered stabilization and upregulation of a specific constituent is accompanied by the upregulation of the constituents that do not share component connectivities with the trigger-stabilized constituent, and by the concomitant downregulation of the constituents sharing component connectivities with the trigger-stabilized constituent. Using a set of different triggers, a series of reconfigured networks-in-networks are demonstrated. The operation and reconfiguration of the CDNs are based on the following motives: (i) Each of the constituents in the 3 × 2 or 3 × 3 CDNs is composed of a supramolecular structure consisting of two duplex-bridged double-loop quasi-circle units. The hybridization of a single-stranded trigger with the double-loop domain stabilizes the respective constituent, and this results in the reconfiguration of the CDNs. (ii) To each of the constituents is conjugated a Mg2+-ion-dependent DNAzyme that cleaves a sequence-specific fluorophore/quencher substrate. The time-dependent fluorescence changes upon the cleavage of the different substrates by the reporter DNAzymes, and the use of appropriate calibration curves, provide means to quantitatively evaluate the contents of all constituents in the different CDNs. The triggered transitions of the parent 3 × 2 or 3 × 3 CDNs into three different CDNs using three different triggers, respectively, are exemplified. In addition, the transitions of the parent 3 × 2 or 3 × 3 CDNs using sequential triggers are demonstrated. Adaptive equilibrated reconfiguration of the CDNs subjected to triggers is demonstrated, and hierarchical adaptive dynamic transitions of the CDNs, subjected to two sequential triggering signals are highlighted. In addition, emerging catalytic functions driven by the adaptive and hierarchical transitions across different equilibrated states of the 3 × 3 CDNs are demonstrated.