Topologically switchable and gated transcription machinery.

Topological barriers control in nature the transcription machinery, thereby perturbing gene expression. Here we introduce synthetically designed DNA templates that include built-in topological barriers for switchable, triggered-controlled transcription of RNA aptamers. This is exemplified with the design of transcription templates that include reversible and switchable topological barriers consisting of a Sr-ion-stabilized G-quadruplex and its separation by kryptofix [2.

Biocatalytic cascades and intercommunicated biocatalytic cascades in microcapsule systems.

Biomolecule-loaded nucleic acid-functionalized carboxymethyl cellulose hydrogel-stabilized microcapsules (diameter 2 μm) are introduced as cell-like containments. The microcapsules are loaded with two DNA tetrahedra, T and T, functionalized with guanosine-rich G-quadruplex subunits, and/or with native enzymes (glucose oxidase, GOx, and/or β-galactosidase, β-gal). In the presence of K-ions and hemin, the T/T tetrahedra constituents, loaded in the microcapsules, assemble into a hemin/G-quadruplex bridged tetrahedra dimer DNAzyme catalyzing the oxidation of Amplex Red to Resorufin by generating HO.

Aptamer-modified DNA tetrahedra-gated metal-organic framework nanoparticle carriers for enhanced chemotherapy or photodynamic therapy.

UiO-66 metal-organic framework nanoparticles (NMOFs) gated by aptamer-functionalized DNA tetrahedra provide superior biomarker-responsive hybrid nano-carriers for biomedical applications. Hybrid nano-carriers consisting of ATP-aptamer or VEGF-aptamer functionalized tetrahedra-gated NMOFs are loaded with the chemotherapeutic drug, doxorubicin (DOX). In the presence of ATP or VEGF, both abundant in cancer cells, the tetrahedra-gated NMOFs are unlocked to release the drug.

DNAzyme- and light-induced dissipative and gated DNA networks.

Nucleic acid-based dissipative, out-of-equilibrium systems are introduced as functional assemblies emulating transient dissipative biological transformations. One system involves a Pb-ion-dependent DNAzyme fuel strand-driven network leading to the transient cleavage of the fuel strand to "waste" products. Applying the Pb-ion-dependent DNAzyme to two competitive fuel strand-driven systems yields two parallel operating networks.

DNA-based constitutional dynamic networks as functional modules for logic gates and computing circuit operations.

A nucleic acid-based constitutional dynamic network (CDN) is introduced as a single computational module that, in the presence of different sets of inputs, operates a variety of logic gates including a half adder, 2 : 1 multiplexer and 1 : 2 demultiplexer, a ternary multiplication matrix and a cascaded logic circuit. The CDN-based computational module leads to four logically equivalent outputs for each of the logic operations. Beyond the significance of the four logically equivalent outputs in establishing reliable and robust readout signals of the computational module, each of the outputs may be fanned out, in the presence of different inputs, to a set of different logic circuits.

Programmed catalysis within stimuli-responsive mechanically unlocked nanocavities in DNA origami tiles.

The assembly of reversible stimuli-responsive locked DNA origami tiles being unlocked, in the presence of appropriate triggers, to form nanocavities in the origami rafts, is introduced. In the presence of ATP, K-ion-stabilized G-quadruplexes or pH-responsive T-A·T triggers and appropriately engineered "helper units", the origami rafts are unlocked to form nanocavities. By the application of appropriate counter-triggers, the nanocavities are relocked, thus establishing the switchable and reversible "mechanical" opening and closure mechanism of the nanocavities.

Multiplexed and amplified chemiluminescence resonance energy transfer (CRET) detection of genes and microRNAs using dye-loaded hemin/G-quadruplex-modified UiO-66 metal-organic framework nanoparticles.

Dye-loaded UiO-66 metal-organic framework nanoparticles (NMOFs) modified with catalytic hemin/G-quadruplex DNAzyme labels act as functional hybrid modules for the chemiluminescence resonance energy transfer (CRET) analysis of miRNAs (miRNA-155 or miRNA-21) or genes (p53 or BRCA1). The dye-loaded NMOFs (dye = fluorescein (Fl) or rhodamine 6G (Rh 6G)) are modified with hairpin probes that are engineered to include in their loop domains recognition sequences for the miRNAs or genes, and in their stem regions caged G-quadruplex domains. In the presence of the analytes miRNAs or genes, the hairpin structures are opened, leading, in the presence of hemin, to the self-assembly of hemin/G-quadruplex DNAzyme labels linked to the dye-loaded NMOFs.

Biocatalytic reversible control of the stiffness of DNA-modified responsive hydrogels: applications in shape-memory, self-healing and autonomous controlled release of insulin.

The enzymes glucose oxidase (GOx), acetylcholine esterase (AchE) and urease that drive biocatalytic transformations to alter pH, are integrated into pH-responsive DNA-based hydrogels. A two-enzyme-loaded hydrogel composed of GOx/urease or AchE/urease and a three-enzyme-loaded hydrogel composed of GOx/AchE/urease are presented. The biocatalytic transformations within the hydrogels lead to the dictated reconfiguration of nucleic acid bridges and the switchable control over the stiffness of the respective hydrogels.