Allosteric ligand–aptamer complexes orchestrate supramolecular or transient catalytic, transcription and fibrinogenesis processes

Abstract

Allosteric regulation, the modulation of biological macromolecular function through binding of molecules at distant sites distinct from the active site, is a fundamental principle in biology that governs enzyme activity, signaling, and gene expression. In this work, we present allosteric ligand/aptamer complexes, coupled to biocatalytic reaction modules composed of enzymes, DNAzymes, or transcription machineries, regulating the catalytic and transient functions of these frameworks. This principle is exemplified by the assembly of ligand/aptamer subunits supramolecular complexes that allosterically stabilize the Mg²⁺-dependent DNAzyme, allowing its ribonucleobase cleavage activity, promoting the formation of transcription templates that yield RNA products, and modulating the assembly of thrombin aptamer subunits that inhibit thrombin-induced coagulation. Specifically, melamine (Mel)/aptamer subunits complexes allosterically stabilize the assembly of Mg²⁺-dependent DNAzyme strands for substrate cleavage, the formation of thrombin aptamer subunits that inhibit the conversion of fibrinogen to fibrin, and the stabilization of a transcription template encoding the Malachite Green (MG) RNA aptamer. Furthermore, coupling an enzyme that depletes the ligand/aptamer complex, which allosterically stabilizes the biocatalytic reaction module, demonstrates the dissipative and transient operation of the catalytic system. This concept is illustrated by the adenosine (Ade)/aptamer subunits supramolecular complex, which stabilizes thrombin aptamer subunits to inhibit thrombin-induced fibrinogenesis, and promotes the formation of an active transcription template for RNA synthesis. In the presence of adenosine deaminase (ADA), Ade is transformed into inosine, which lacks affinity for the aptamer subunits, thereby degrading the Ade/aptamer assemblies and depleting the allosteric complexes. The temporal disassembly of these allosteric stabilizing complexes leads to the transient inhibition of thrombin-induced coagulation or to the transient operation of a transcription machinery.