Intercommunication of DNA-Based Constitutional Dynamic Networks

Abstract

Intercommunication between dynamic chemical networks plays a major role in cellular transformations. Inspired by nature, we introduce the intercommunication between two constitutional dynamic networks, CDNs, "S" and "T" composed, each, of four equilibrated supramolecular constituents AA', AB', BA', and BB', and of CC', CD', DC', and DD', respectively. Each of the constituents is conjugated to a Mg²⁺-ion-dependent DNAzyme unit that acts as a reporter element for the concentration of the respective constituent via the catalyzed cleavage of the fluorophore/quencher-functionalized substrate associated with the respective DNAzyme reporter. Also, constituents BB' (in CDN "S") and CC' (in CDN "T") include Mg²⁺-ion-dependent DNAzymes acting as activator units for generating triggering signals between the networks. Subjecting CDNs "S" and "T" to the catalytically cleavable hairpin trigger H_dd' or H_aa', respectively, yields input strands that intercommunicate the CDNs by affecting the time-dependent re-equilibration of the constituents of the counter CDN without affecting the dynamic equilibrium of the constituents of the CDN that generates the triggering strands. Treatment of CDNs "S" and "T" with hairpins H_dd' and H_aa' (or H_ba'), respectively, stimulates autonomous positive/positive or positive/negative feedback to the programmed time-dependent up-regulation or down-regulation of the equilibrated constituents in the two CDNs.