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Transient dissipative dimerization and transient gated dimerization of DNA tetrahedra nanostructures are introduced as functional modules to emulate transient and gated protein-protein interactions and emergent protein-protein guided transient catalytic functions, operating in nature. Four tetrahedra are engineered to yield functional modules that, in the presence of pre-engineered auxiliary nucleic acids and the nicking enzyme Nt.BbvCI, lead to the fueled transient dimerization of two pairs of tetrahedra. The dynamic transient formation and depletion of DNA tetrahedra are followed by transient FRET signals generated by fluorophore-labeled tetrahedra. The integration of two inhibitors within the mixture of the four tetrahedra and two auxiliary modules, fueling the transient dimerization, results in selective inhibitor-guided gated transient dimerization of two different DNA tetrahedra dimers. Kinetic models for the dynamic transient dimerization and gated transient dimerization of the DNA tetrahedra are formulated and computationally simulated. The derived rate-constants allow the prediction and subsequent experimental validation of the performance of the systems under different auxiliary conditions. In addition, by appropriate modification of the four tetrahedra structures, the triggered gated emergence of selective transient catalytic functions driven by the two pairs of DNA tetrahedra dimers is demonstrated.

The sensing modules for analyzing miRNAs or the endonucleases consist of tetrahedra functionalized with three different fluorophore–quencher pairs in spatially quenched configurations and hairpin units acting as recognition elements for the analytes. Three different miRNAs (miRNA-21, miRNA-221, and miRNA-155) or three different endonucleases (Nt.BbvCI, EcoRI, and HindIII) uncage the respective hairpins, leading to the switched-on fluorescence of the respective fluorophores and to the multiplex detection of the respective analytes. In addition, a tetrahedron module for the multiplexed analysis of aptamer ligand complexes (ligands = ATP, thrombin, VEGF) is introduced. The module includes edges modified with three spatially separated fluorophore–quencher pairs that were stretched by the respective aptamer strands to yield a switched-on fluorescent state. Formation of the respective aptamer ligands reconfigures the edges into fluorophore-quenched caged-hairpin structures that enable the multiplexed analysis of the aptamer–ligand complexes. The facile permeation of the tetrahedra structures into cells is used for the imaging of MCF-7 and HepG2 cancer cells and their discrimination from normal epithelial MCF-10A breast cells.

Models for gene expression instability by noncanonical DNA-nanostructures are introduced. The systems consist of a promoter-template scaffold that acts as a polymerization/nicking machinery that models, in the presence of polymerase/Nt.BbvCI and dNTPs, the autonomous synthesis of displaced strands mimicking the native "genes". Incorporation of noncanonical DNA structures into the scaffolds consisting of Sr2+-ion-stabilized G-quadruplexes, T-A·T triplexes, or ATP-aptamer complexes results in the perturbation of the polymerization/nicking DNA machineries and the synthesis of displaced strands-"genes" exhibiting other structures. By the dissociation of the noncanonical blockage units, the regeneration of the synthesis of the original intact displaced strands-"genes" is demonstrated. The study introduces conceptual means to eliminate destructive gene expression instability pathways.

Two different drug micro-carriers consisting of doxorubicin-dextran (DOX-D)- and camptothecin-modified carboxymethyl cellulose (CPT-CMC)-loaded nucleic acid-stabilized microcapsules, MC-1 and MC-2, or two different nanocarriers consisting of nucleic-acid-locked doxorubicin (DOX)- and camptothecin (CPT)-loaded metal-organic framework nanoparticles, NMOF-1 and NMOF-2, are coupled to auxiliary constitutional dynamic networks, CDNs, for the triggered release of the drugs. CDN "S" composed of four constituents AA'', AB', BA', and BB', and two hairpin structures, H1 and H2, leads to the CDN "S"-guided unlocking of the MC-1/MC-2 carriers and the release of DOX-D and CPT-CMC or of the NMOF-1 and NMOF-2 carriers that release DOX and CPT, respectively. The unlocking processes are activated by the cleavage of H1 and H2 by BB' and BA', respectively, to yield fragmented strands that unlock the gating units of the microcapsules/NMOFs carriers. In the presence of miRNA-155 or miRNA-124, dictated orthogonal reconfiguration of CDN "S" into CDN "X" or "Y" proceeds. The miRNA-155 stimulates the reconfiguration of CDN "S" to CDN "X", where AA' and BB' are upregulated, and AB' and BA' are downregulated, leading to the enhanced release of DOX-D or DOX from the microcapsule/NMOFs carriers, and to the concomitant inhibition of the release of CPT-CMC or CPT from the respective carriers. Similarly, the miRNA-124-triggered reconfiguration of CDN "S" to CDN "Y" results in the BA'-guided cleavage of H2 and the preferred release of CPT-CMC or CPT from the respective carriers. The miRNA-triggered CDN-driven unlocking of the carriers stimulates the amplified and selective release of the drugs from the microcapsules/NMOFs carriers.

Nucleic acid-based constitutional dynamic networks (CDNs) attract growing interest as a means to mimic complex biological networks. The triggered stabilization of the CDNs allows the dictated guided reversible reconfiguration and re-equilibration of the CDNs to other CDN configurations, where some of the constituents are up-regulated, while other constituents are down-regulated. Although substantial progress in controlling the adaptive dynamic control of the compositions of networks by means of auxiliary triggers was demonstrated, the use of CDNs as active ensembles for controlling chemical functionalities is still a challenge. We report on the assembly of signal-triggered CDN systems that guide the switchable aggregation of Au nanoparticles (NPs), thereby controlling their plasmonic properties and their catalytic functions (Au NPs-catalyzed oxidation of l-DOPA to dopachrome). In addition, we demonstrate that the triggered and orthogonal up-regulation and down-regulation of the constituents of the CDNs leads to the dictated aggregation of different-sized CdSe/ZnS quantum dots (QDs), cross-linked by K+-ion-stabilized G-quadruplex units. The incorporation of hemin into the G-quadruplex cross-linking units yields horseradish peroxidase-mimicking DNAzyme units that catalyze the generation of chemiluminescence via the oxidation of luminol by H2O2. The resulting chemiluminescence stimulates the chemiluminescence resonance energy transfer (CRET) process to the QDs, resulting in the luminescence of the two-sized QDs. By the application of appropriate triggers, the CDN-dictated up-regulation and down-regulation of the different-sized QDs aggregates are demonstrated, and the control over the photophysical functions of the different-sized QDs, by means of the CDNs, is highlighted.

Graphene quantum dots (GQDs) and carbon dots (C-dots) have various alluring properties and potential applications, but they are often limited by unsatisfied optical performance such as low quantum yield, ambiguous fluorescence emission mechanism, and narrow emission wavelength. Herein, we report that bulk polymeric carbon nitride could be utilized as a layered precursor to prepare carbon nitride nanostructures such as nanorods, nanoleaves and quantum dots by chemical tailoring. As doped carbon materials, these carbon nitride nanostructures not only intrinsically emitted UV lights but also well inherited the explicit photoluminescence mechanism of the bulk pristine precursor, both of which were rarely reported for GQDs and C-dots. Especially, carbon nitride quantum dots (CNQDs) had a photoluminescence quantum yield (QY) up to 46%, among the highest QY for metal-free quantum dots so far. As examples, the CNQDs were utilized as a photoluminescence probe for rapid detection of Fe(3+) with a detection limit of 1 μM in 2 min and a photoconductor in an all-solid-state device. This work would open up an avenue for doped nanocarbon in developing photoelectrical devices and sensors.

Responsive assembly of 2D materials is of great interest for a range of applications. In this work, interfacial functionalized carbon nitride (CN) nanofibers were synthesized by hydrolyzing bulk CN in sodium hydroxide solution. The reversible assemble and disassemble behavior of the as-prepared CN nanofibers was investigated by using CO2 as a trigger to form a hydrogel network at first. Compared to the most widespread absorbent materials such as active carbon, graphene and previously reported supramolecular gel, the proposed CN hydrogel not only exhibited a competitive absorbing capacity (maximum absorbing capacity of methylene blue up to 402 mg/g) but also overcame the typical deficiencies such as poor selectivity and high energy-consuming regeneration. This work would provide a strategy to construct a 3D CN network and open an avenue for developing smart assembly for potential applications ranging from environment to selective extraction.