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The photocatalytic degradation of p-chlorophenoxyacetic acid is studied in oxygenated aqueous suspensions of lanthanide oxide-doped titanium dioxide photocatalysts.

Photoinduced electron transfer was observed on supramolecular assemblies composed of bipyridinium salts and dialkoxy benzene-tethered ruthenium (II) trisbipyridine. Intramolecular pathways facilitated the transfer of electrons to the electron acceptors that were found in the supramolecular assemblies. Electron transfer also proceeded through a diffusional route associated with a free-uncomplexed compound.

The study compares conductivities of different conjugated and nonconjugated organic linked on both sides to small gold clusters with electrochemical results. The computation of the current uses a scattering approach and is based on an ab initio determination of the geometry and molecular levels of the gold-spacer-gold system at the Density Functional Theory level.

Bladder cancer (BC) has a high recurrence rate, necessitating frequent monitoring. We herein present an innovative method for detecting BC-related miR-183 and miR-155 microRNAs using pH-responsive triplex DNA nanoswitches (TDNs). This approach employs a stepwise surface plasmon resonance biosensing platform (TDNs-SPR assay) to detect these two miRNAs sequentially. The platform involves the assembly of two triplex pH-responsive probes, switch A (SA) and switch B (SB), on an SPR sensing interface by anchoring the probes to the surface through SA/miR-183 and SB/miR-155 binding to the S9.6 antibody-modified surface. The probes are functionalized with streptavidin-Au nanoparticles/biotinylated strands, which act as reporter units for the presence of the respective miRNAs on the sensing interface. The pH-induced displacement of reporter units triggers stepwise SPR reflectivity changes: at pH 5.0 for sensing miR-183 and at pH 8.3 for sensing miR-155. The reflectivity changes relate quantitatively to the concentrations of miRNAs. This sensing platform enables the detection of two miRNAs with detection limits as low as 0.57 pM for miR-183 and 0.83 pM for miR-155, highlighting its powerful utility for precise biomarker analysis. Moreover, this platform distinguishes BC patients from healthy individuals in urine samples. The method offers a versatile, noninvasive method for detecting any two miRNAs associated with other diseases.

Photochemically triggered, transient, and temporally oscillatory-modulated transcription machineries are introduced. The resulting dynamic transcription circuits are implemented to guide photochemically triggered, transient, and oscillatory modulation of thrombin toward temporal control over fibrinogenesis. One system describes the assembly of a reaction module leading to the photochemically triggered formation of an active transcription machinery that, in the presence of RNase H, guides the transient activation of thrombin toward fibrinogenesis. A second system introduces photochemical triggering of a reaction circuit consisting of two coupled transcription machineries, leading to the temporally oscillatory formation and depletion of an intermediate reaction product. The concept is applied to develop a photochemically triggered transcription circuit that, in the presence of RNase H, leads to the oscillatory generation of an intermediate anti-thrombin aptamer-modified product. The oscillating aptamer-modified product induces the rhythmic inhibition of thrombin, accompanied by the cyclic activation and deactivation of the fibrinogenesis process. The operation of the transient and oscillatory-modulated transcription machinery reaction circuits is accompanied by computational kinetic models, allowing to predict the dynamic behaviors of the system under different auxiliary conditions. The phototriggered transient transcription machinery and oscillatory circuit-guided fibrinogenesis is examined under physiological-like conditions and within a human plasma environment.

The primer-guided entropy-driven high-throughput evolution of the DNA-based constitutional dynamic network, CDN, is introduced. The entropy gain associated with the process provides a catalytic principle for the amplified emergence of the CDN. The concept is applied to develop a programmable, spatially localized DNA circuit for effective in vitro and in vivo theranostic, gene-regulated treatment of cancer cells. The localized circuit consists of a DNA tetrahedron core modified at its corners with four tethers that include encoded base sequences exhibiting the capacity to emerge and assemble into a [2 × 2] CDN. Two of the tethers are caged by a pair of siRNA subunits, blocking the circuit into a mute, dynamically inactive configuration. In the presence of miRNA-21 as primer, the siRNA subunits are displaced, resulting in amplified release of the siRNAs silencing the HIF-1α mRNA and fast dynamic reconfiguration of the tethers into a CDN. The resulting CDN is, however, engineered to be dynamically reconfigured by miRNA-155 into an equilibrated mixture enriched with a DNAzyme component, catalyzing the cleavage of EGR-1 mRNA. The DNA tetrahedron nanostructure stimulates enhanced permeation into cancer cells. The miRNA-triggered entropy-driven reconfiguration of the spatially localized circuit leads to the programmable, cooperative bis-gene-silencing of HIF-1α and EGR-1 mRNAs, resulting in the effective and selective apoptosis of breast cancer cells and effective inhibition of tumors in tumor bearing mice.

Expanding the functions and applications of DNA by integrating noncanonical bases and structures into biopolymers is a continuous scientific effort. An adenine-rich strand (A-strand) is introduced as functional scaffold revealing, in the presence of the low-molecular-weight cofactor cyanuric acid (CA, p K a 6.9), supramolecular hydrogel-forming efficacies demonstrating multiple pH-responsiveness. At pH 1.2, the A-strand transforms into a parallel A-motif duplex hydrogel cross-linked by AH + -H + A units due to the protonation of adenine (p K a 3.5). At pH 5.2, and in the presence of coadded CA, a helicene-like configuration is formed between adenine and protonated CA, generating a parallel A-CA triplex cross-linked hydrogel. At pH 8.0, the hydrogel undergoes transition into a liquid state by deprotonation of CA cofactor units and disassembly of A-CA triplex into its constituent components. Density functional theory calculations and molecular dynamics simulations, supporting the structural reconfigurations of A-strand in the presence of CA, are performed. The sequential pH-stimulated hydrogel states are rheometrically characterized. The hydrogel framework is loaded with fluorescein-labeled insulin, and the pH-stimulated release of insulin from the hydrogel across the pH barriers present in the gastrointestinal tract is demonstrated. The results provide principles for future application of the hydrogel for oral insulin administration for diabetes.

DNA is an ideal template for the design of nanoarchitectures with molecular-like features. Here, we present an optimized assembly strategy for the concatenation of DNA quasi-rings into long scaffolds. Ionic strength, which played a major role during self-assembly, produced the expected high quality only at 15 mM MgCl 2 . Atomic force microscopy (AFM) characterization showed several micrometer long tubular structures that were used as templates for the positioning of plasmonic nanoparticles (NPs) along a three-dimensional helical path using DNA tethers. As imaged by high-resolution scanning transmission electron microscopy (HR-STEM) and modeled by theoretical calculations, the NPs distributed into a "fusilli" fashion (i.e., a helical pasta shape), displaying chiroptical activity as revealed by a bisignated CD absorption, centered at the plasmon resonance wavelength. The present structures contribute to enrich the ever-developing arena of chiroplasmonic DNA-based nanomaterials and demonstrate that large assemblies are attainable for their future application to develop metamaterials.

A Fe 3+ -ion cross-linked carboxymethyl cellulose, Fe 3+ -CMC, redox-active gel exhibiting dissipative, transient stiffness properties is introduced. Chemical or photosensitized reduction of the higher-stiffness Fe 3+ -CMC to the lower-stiffness Fe 2+ -CMC gel, accompanied by the aerobic reoxidation of the Fe 2+ -CMC matrix, leads to the dissipative, transient stiffness, functional matrix. The light-induced, temporal, transient release of a load (Texas red dextran) and the light-triggered, transient mechanical bending of a poly- N -isopropylacrylamide (p-NIPAM)/Fe 3+ -CMC bilayer construct are introduced, thus demonstrating the potential use of the dissipative Fe 3+ -CMC gel for controlled drug release or soft robotic applications.

The photochemical deprotection of structurally engineered o -nitrobenzylphosphate-caged hairpin nucleic acids is introduced as a versatile method to evolve constitutional dynamic networks, CDNs. The photogenerated CDNs, in the presence of fuel strands, interact with auxiliary CDNs, resulting in their dynamically equilibrated reconfiguration. By modification of the constituents associated with the auxiliary CDNs with glucose oxidase (GOx)/horseradish peroxidase (HRP) or the lactate dehydrogenase (LDH)/nicotinamide adenine dinucleotide (NAD + ) cofactor, the photogenerated CDN drives the orthogonal operation upregulated/downregulated operation of the GOx/HRP and LDH/NAD + biocatalytic cascade in the conjugate mixture of auxiliary CDNs. Also, the photogenerated CDN was applied to control the reconfiguration of coupled CDNs, leading to upregulated/downregulated formation of the antithrombin aptamer units, resulting in the dictated inhibition of thrombin activity (fibrinogen coagulation). Moreover, a reaction module consisting of GOx/HRP-modified o -nitrobenzyl phosphate-caged DNA hairpins, photoresponsive caged auxiliary duplexes, and nickase leads upon irradiation to the emergence of a transient, dissipative CDN activating in the presence of two alternate auxiliary triggers, achieving transient operation of up- and downregulated GOx/HRP biocatalytic cascades.

DNA frameworks, consisting of constitutional dynamic networks (CDNs) undergoing fuel-driven reconfiguration, are coupled to a dissipative reaction module that triggers the reconfigured CDNs into a transient intermediate CDNs recovering the parent CDN state. Biocatalytic cascades consisting of the glucose oxidase (GOx)/horseradish peroxidase (HRP) couple or the lactate dehydrogenase (LDH)/nicotinamide adenine dinucleotide (NAD + ) couple are tethered to the constituents of two different CDNs, allowing the CDNs-guided operation of the spatially confined GOx/HRP or LDH/NAD + biocatalytic cascades. By applying two different fuel triggers, the directional transient CDN-guided upregulation/downregulation of the two biocatalytic cascades are demonstrated. By mixing the GOx/HRP-biocatalyst-modified CDN with the LDH/NAD + -biocatalyst-functionalized CDN, a composite CDN is assembled. Triggering the composite CDN with two different fuel strands results in orthogonal transient upregulation of the GOx/HRP cascade and transient downregulation of the LDH/NAD + cascade or vice versa . The transient CDNs-guided biocatalytic cascades are computationally simulated by kinetic models, and the computational analyses allow the prediction of the performance of transient biocatalytic cascades under different auxiliary conditions. The concept of orthogonally triggered temporal, transient, biocatalytic cascades by means of CDN frameworks is applied to design an orthogonally operating CDN for the temporal upregulated or downregulated transient thrombin-induced coagulation of fibrinogen to fibrin.

Glucose oxidase-loaded ZIF-90 metal-organic framework nanoparticles conjugated to hemin-G-quadruplexes act as functional bioreactor hybrids operating transient dissipative biocatalytic cascaded transformations consisting of the glucose-driven H 2 O 2 -mediated oxidation of Amplex-Red to resorufin or the glucose-driven generation of chemiluminescence by the H 2 O 2 -mediated oxidation of luminol. One system involves the fueled activation of a reaction module leading to the temporal formation and depletion of the bioreactor conjugate operating the nickase-guided transient biocatalytic cascades. The second system demonstrates the fueled activation of a reaction module yielding a bioreactor conjugate operating the exonuclease III-dictated transient operation of the two biocatalytic cascades. The temporal operations of the bioreactor circuits are accompanied by kinetic models and computational simulations enabling us to predict the dynamic behavior of the systems subjected to different auxiliary conditions.

Emulating native transient transcription machineries modulating temporal gene expression by synthetic circuits is a major challenge in the area of systems chemistry. Three different methods to operate transient transcription machineries and to modulate the gated transcription processes of target RNAs are introduced. One method involves the design of a reaction module consisting of transcription templates being triggered by promoter fuel strands transcribing target RNAs and in parallel generating functional DNAzymes in the transcription templates, modulating the dissipative depletion of the active templates and the transient operation of transcription circuits. The second approach involves the application of a reaction module consisting of two transcription templates being activated by a common fuel promoter strand. While one transcription template triggers the transcription of the target RNA, the second transcription template transcribes the anti-fuel strand, displacing the promoter strand associated with the transcription templates, leading to the depletion of the transcription templates and to the dynamic transient modulation of the transcription process. The third strategy involves the assembly of a reaction module consisting of a reaction template triggered by a fuel promoter strand transcribing the target RNA. The concomitant nickase-stimulated depletion of the promoter strand guides the transient modulation of the transcription process. Via integration of two parallel fuel-triggered transcription templates in the three transcription reaction modules and application of template-specific blocker units, the parallel and gated transiently modulated transcription of two different RNA aptamers is demonstrated. The nickase-stimulated transiently modulated transcription reaction module is applied as a functional circuit guiding the dynamic expression of gated, transiently operating, catalytic DNAzymes.

Membrane fusion processes play key roles in biological transformations, such as endocytosis/exocytosis, signal transduction, neurotransmission, or viral infections, and substantial research efforts have been directed to emulate these functions by artificial means. The recognition and dynamic reconfiguration properties of nucleic acids provide a versatile means to induce membrane fusion. Here we address recent advances in the functionalization of liposomes or membranes with structurally engineered lipidated nucleic acids guiding the fusion of cell-like containments, and the biophysical and chemical parameters controlling the fusion of the liposomes will be discussed. Intermembrane bridging by duplex or triplex nucleic acids and light-induced activation of membrane-associated nucleic acid constituents provide the means for spatiotemporal fusion of liposomes or nucleic acid modified liposome fusion with native cell membranes. The membrane fusion processes lead to exchange of loads in the fused containments and are a means to integrate functional assemblies. This is exemplified with the operation of biocatalytic cascades and dynamic DNA polymerization/nicking or transcription machineries in fused protocell systems. Membrane fusion processes of protocell assemblies are found to have important drug-delivery, therapeutic, sensing, and biocatalytic applications. The future challenges and perspectives of DNA-guided fused containments and membranes are addressed.

The assembly of enzyme [glucose oxidase (GOx)]-loaded stimuli-responsive DNA-based hydrogels on electrode surfaces, and the triggered control over the stiffness of the hydrogels, provides a means to switch the bioelectrocatalytic functions of the hydrogels. One system includes the assembly of GOx-loaded, pH-responsive, hydrogel matrices cross-linked by two cooperative nucleic acid motives comprising permanent duplex nucleic acids and "caged" i-motif pH-responsive duplexes. Bioelectrocatalyzed oxidation of glucose leads to the formation of gluconic acid that acidifies the hydrogel resulting in the separation of the i-motif constituents and lowering the hydrogel stiffness. Loading of the hydrogel matrices with insulin results in the potential-triggered, glucose concentration-controlled, switchable release of insulin from the hydrogel-modified electrodes. The switchable bioelectrocatalyzed release of insulin is demonstrated in the presence of ferrocenemethanol as a diffusional electron mediator or by applying an electrically wired integrated matrix that includes ferrocenyl-modified GOx embedded in the hydrogel. The second GOx-loaded, stimuli-responsive, DNA-based hydrogel matrix associated with the electrode includes a polyacrylamide hydrogel cooperatively cross-linked by duplex nucleic acids and "caged" G-quadruplex-responsive duplexes. The hydrogel matrix undergoes K + -ions/crown ether-triggered stiffness changes by the cyclic K + -ion-stimulated formation of G-quadruplexes (lower stiffness) and the crown ether-induced separation of the G-quadruplexes (higher stiffness). The hydrogel matrices demonstrate switchable bioelectrocatalytic functions guided by the stiffness properties of the hydrogels.

The enzyme-free catalytic hairpin assembly (CHA) process is introduced as a functional reaction module for guided, high-throughput, emergence, and evolution of constitutional dynamic networks, CDNs, from a set of nucleic acids. The process is applied to assemble networks of variable complexities, functionalities, and spatial confinement, and the systems provide possible mechanistic pathways for the evolution of dynamic networks under prebiotic conditions. Subjecting a set of four or six structurally engineered hairpins to a promoter P 1 leads to the CHA-guided emergence of a [2 × 2] CDN or the evolution of a [3 × 3] CDN, respectively. Reacting of a set of branched three-arm DNA-hairpin-functionalized junctions to the promoter strand activates the CHA-induced emergence of a three-dimensional (3D) CDN framework emulating native gene regulatory networks. In addition, activation of a two-layer CHA cascade circuit or a cross-catalytic CHA circuit and cascaded driving feedback-driven evolution of CDNs are demonstrated. Also, subjecting a four-hairpin-modified DNA tetrahedron nanostructure to an auxiliary promoter strand simulates the evolution of a dynamically equilibrated DNA tetrahedron-based CDN that undergoes secondary fueled dynamic reconfiguration. Finally, the effective permeation of DNA tetrahedron structures into cells is utilized to integrate the four-hairpin-functionalized tetrahedron reaction module into cells. The spatially localized miRNA-triggered CHA evolution and reconfiguration of CDNs allowed the logic-gated imaging of intracellular RNAs. Beyond the bioanalytical applications of the systems, the study introduces possible mechanistic pathways for the evolution of functional networks under prebiotic conditions.

This review article introduces mechanistic aspects and applications of photochemically deprotected ortho -nitrobenzyl (ONB)-functionalized nucleic acids and their impact on diverse research fields including DNA nanotechnology and materials chemistry, biological chemistry, and systems chemistry. Specific topics addressed include the synthesis of the ONB-modified nucleic acids, the mechanisms involved in the photochemical deprotection of the ONB units, and the photophysical and chemical means to tune the irradiation wavelength required for the photodeprotection process. Principles to activate ONB-caged nanostructures, ONB-protected DNAzymes and aptamer frameworks are introduced. Specifically, the use of ONB-protected nucleic acids for the phototriggered spatiotemporal amplified sensing and imaging of intracellular mRNAs at the single-cell level are addressed, and control over transcription machineries, protein translation and spatiotemporal silencing of gene expression by ONB-deprotected nucleic acids are demonstrated. In addition, photodeprotection of ONB-modified nucleic acids finds important applications in controlling material properties and functions. These are introduced by the phototriggered fusion of ONB nucleic acid functionalized liposomes as models for cell-cell fusion, the light-stimulated fusion of ONB nucleic acid functionalized drug-loaded liposomes with cells for therapeutic applications, and the photolithographic patterning of ONB nucleic acid-modified interfaces. Particularly, the photolithographic control of the stiffness of membrane-like interfaces for the guided patterned growth of cells is realized. Moreover, ONB-functionalized microcapsules act as light-responsive carriers for the controlled release of drugs, and ONB-modified DNA origami frameworks act as mechanical devices or stimuli-responsive containments for the operation of DNA machineries such as the CRISPR-Cas9 system. The future challenges and potential applications of photoprotected DNA structures are discussed.

Nucleic acid networks conjugated to native enzymes and supramolecular DNA nanostructures modified with enzymes or DNAzymes act as functional reaction modules for guiding dynamic catalytic transformations. These systems are exemplified with the assembly of constitutional dynamic networks (CDNs) composed of nucleic acid-functionalized enzymes, as constituents, undergoing triggered structural reconfiguration, leading to dynamically switched biocatalytic cascades. By coupling two nucleic acid/enzyme networks, the intercommunicated feedback-driven dynamic biocatalytic operation of the system is demonstrated. In addition, the tailoring of a nucleic acid/enzyme reaction network driving a dissipative, transient, biocatalytic cascade is introduced as a model system for out-of-equilibrium dynamically modulated biocatalytic transformation in nature. Also, supramolecular nucleic acid machines or DNA nanostructures, modified with DNAzyme or enzyme constituents, act as functional reaction modules driving temporal dynamic catalysis. The design of dynamic supramolecular machines is exemplified with the introduction of an interlocked two-ring catenane device that is dynamically reversibly switched between two states operating two different DNAzymes, and with the tailoring of a DNA-tweezers device functionalized with enzyme/DNAzyme constituents that guides the dynamic ON/OFF operation of a biocatalytic cascade by opening and closing the molecular device. In addition, DNA origami nanostructures provide functional scaffolds for the programmed positioning of enzymes or DNAzyme for the switchable operation of catalytic transformations. This is introduced by the tailored functionalization of the edges of origami tiles with nucleic acids guiding the switchable formation of DNAzyme catalysts through the dimerization/separation of the tiles. In addition, the programmed deposition of two-enzyme/cofactor constituents on the origami raft allowed the dynamic photochemical activation of the cofactor-mediated biocatalytic cascade on the spatially biocatalytic assembly on the scaffold. Furthermore, photoinduced "mechanical" switchable and reversible unlocking and closing of nanoholes in the origami frameworks allow the "ON" and "OFF" operation of DNAzyme units in the nanoholes, confined environments. The future challenges and potential applications of dynamic nucleic acid/enzyme and DNAzyme conjugates are discussed in the conclusion paragraph.

Transient transcription machineries play important roles in the dynamic modulation of gene expression and the sequestered regulation of cellular networks. The present study emulates such processes by designing artificial reaction modules consisting of transcription machineries that guide the transient synthesis of catalytic DNAzymes, the transient operation of gated DNAzymes, and the temporal activation of an intercommunicated DNAzyme cascade. The reaction modules rely on functional constituents that lead to the triggered activation of transcription machineries in the presence of the nucleoside triphosphates oligonucleotide fuel, yielding the transient formation and dissipative depletion of the intermediate DNAzyme(s) products. The kinetics of the transient DNAzyme networks are computationally simulated, allowing to predict and experimentally validate the performance of the systems under different auxiliary conditions. The study advances the field of systems chemistry by introducing transcription machinery-based networks for the dynamic control over transient catalysis─a primary step toward life-like cellular assemblies.

Aptamer-functionalized Ce 4+ -ion-modified C-dots act as catalytic hybrid systems, aptananozymes, catalyzing the H 2 O 2 oxidation of dopamine. A series of aptananozymes functionalized with different configurations of the dopamine binding aptamer, DBA, are introduced. All aptananozymes reveal substantially enhanced catalytic activities as compared to the separated Ce 4+ -ion-modified C-dots and aptamer constituents, and structure-catalytic functions between the structure and binding modes of the aptamers linked to the C-dots are demonstrated. The enhanced catalytic functions of the aptananozymes are attributed to the aptamer-induced concentration of the reaction substrates in spatial proximity to the Ce 4+ -ion-modified C-dots catalytic sites. The oxidation processes driven by the Ce 4+ -ion-modified C-dots involve the formation of reactive oxygen species ( • OH radicals). Accordingly, Ce 4+ -ion-modified C-dots with the AS1411 aptamer or MUC1 aptamer, recognizing specific biomarkers associated with cancer cells, are employed as targeted catalytic agents for chemodynamic treatment of cancer cells. Treatment of MDA-MB-231 breast cancer cells and MCF-10A epithelial breast cells, as control, with the AS1411 aptamer- or MUC1 aptamer-modified Ce 4+ -ion-modified C-dots reveals selective cytotoxicity toward the cancer cells. In vivo experiments reveal that the aptamer-functionalized nanoparticles inhibit MDA-MB-231 tumor growth.

Polyadenine-stabilized Au nanoparticles (pA-AuNPs) reveal dual nanozyme catalytic activities toward the H 2 O 2 -mediated oxidation of dopamine to aminochrome and toward the aerobic oxidation of glucose to gluconic acid and H 2 O 2 . The conjugation of a dopamine-binding aptamer (DBA) to the pA-AuNPs yields aptananozyme structures catalyzing simultaneously the H 2 O 2 -mediated oxidation of dopamine to aminochrome through the aerobic oxidation of glucose. A set of aptananozymes consisting of DBA conjugated through the 5'- or 3'-end directly or spacer bridges to pA-AuNPs were synthesized. The set of aptananozymes revealed enhanced catalytic activities toward the H 2 O 2 -catalyzed oxidation of dopamine to dopachrome, as compared to the separated pA-AuNPs and DBA constituents, and structure-function relationships within the series of aptananozymes were demonstrated. The enhanced catalytic function of the aptananozymes was attributed to the concentration of the dopamine at the catalytic interfaces by means of aptamer-dopamine complexes. The dual catalytic activities of aptananozymes were further applied to design bioreactors catalyzing the effective aerobic oxidation of dopamine in the presence of glucose. Mechanistic studies demonstrated that the aptananozymes generate reactive oxygen species. Accordingly, the AS1411 aptamer, recognizing the nucleolin receptor associated with cancer cells, was conjugated to the pA-AuNPs, yielding a nanozyme for the chemodynamic treatment of cancer cells. The AS1411 aptamer targets the aptananozyme to the cancer cells and facilitates the selective permeation of the nanozyme into the cells. Selective cytotoxicity toward MDA-MB-231 breast cancer cells ( ca . 70% cell death) as compared to MCF-10A epithelial cells ( ca . 2% cell death) is demonstrated.

A method to computationally and experimentally identify aptamers against short peptides or amino acid clusters is introduced. The method involves the selection of a well-defined protein aptamer complex and the extraction of the peptide sequence participating in the binding of the protein to the aptamer. The subsequent fragmentation of the peptide sequence into short peptides and the in silico docking-guided identification of affinity complexes between the miniaturized peptides and the antiprotein aptamer, followed by experimental validation of the binding features of the short peptides with the antiprotein aptamers, leads to the identification of new short peptide-aptamer complexes. This is exemplified with the identification of the pentapeptide RYERN as the scaffold that binds thrombin to the DNA thrombin aptamer (DNA TA). In silico docking studies followed by microscale thermophoresis (MST) experiments demonstrate that the miniaturized tripeptides RYE, YER, and ERN reveal selective binding affinities toward the DNA TA. In addition, docking and MST experiments show that the ribonucleotide-translated RNA TA shows related binding affinities of YER to the DNA TA. Most importantly, we demonstrate that the separated amino acids Y/E/R assemble as a three amino acid cluster on the DNA TA and RNA TA aptamers in spatial configurations similar to the tripeptide YER on the respective aptamers. The clustering phenomenon is selective for the YER tripeptide system. The method to identify binding affinities of miniaturized peptides to known antiprotein aptamers and the specific clustering of single amino acids on the aptamers is further demonstrated by in silico and experimental identification of the binding of the tripeptide RET and the selective clustering of the separated amino acids R/E/T onto a derivative of the AS1411 aptamer against the nucleolin receptor protein.

The dynamic transient formation and depletion of G-quadruplexes regulate gene replication and transcription. This process was found to be related to various diseases such as cancer and premature aging. We report on the engineering of nucleic acid modules revealing dynamic, transient assembly and disassembly of G-quadruplex structures and G-quadruplex-based DNAzymes, gated transient processes, and cascaded dynamic transient reactions that involve G-quadruplex and DNAzyme structures. The dynamic transient processes are driven by functional DNA reaction modules activated by a fuel strand and guided toward dissipative operation by a nicking enzyme (Nt.BbvCI). The dynamic networks were further characterized by computational simulation of the experiments using kinetic models, allowing us to predict the dynamic performance of the networks under different auxiliary conditions applied to the systems. The systems reported herein could provide functional DNA machineries for the spatiotemporal control of G-quadruplex structures perturbing gene expression and thus provide a therapeutic means for related emergent diseases.

Nanozymes have emerged as a class of novel catalytic nanomaterials that show great potential to substitute natural enzymes in various applications. Nevertheless, spatial organization of multiple subunits in a nanozyme to rationally engineer its catalytic properties remains to be a grand challenge. Here, we report a DNA-based approach to encode the organization of gold nanoparticle clusters (GNCs) for the construction of programmable enzyme equivalents (PEEs). We find that single-stranded (ss-) DNA scaffolds can self-fold into nanostructures with prescribed poly-adenine (polyA) loops and double-stranded stems and that the polyA loops serve as specific sites for seed-free nucleation and growth of GNCs with well-defined particle numbers and interparticle spaces. A spectrum of GNCs, ranging from oligomers with discrete particle numbers (2-4) to polymer-like chains, are in situ synthesized in this manner. The polymeric GNCs with multiple spatially organized nanoparticles as subunits show programmable peroxidase-like catalytic activity that can be tuned by the scaffold size and the inter-polyA spacer length. This study thus opens new routes to the rational design of nanozymes for various biological and biomedical applications.

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.

An analytical platform for the selective miRNA-21-guided imaging of breast cancer cells and miRNA-221-guided imaging of ovarian cancer cells and the selective photodynamic therapy (PDT) of these cancer cells is introduced. The method is based on Zn(II)-protoporphyrin IX, Zn(II)-PPIX-loaded UiO-66 metal-organic framework nanoparticles, NMOFs, gated by two hairpins H i /H j through ligation of their phosphate residues to the vacant Zr 4+ -ions associated with the NMOFs. The hairpins are engineered to include the miRNA recognition sequence in the stem domain of H i , and in the H i and H j , partial locked stem regions of G-quadruplex subunits. Intracellular phosphate-ions displace the hairpins, resulting in the release of the Zn(II)-PPIX and intracellular miRNAs open H i , and this triggers the autonomous cross-opening of H i and H j . This activates the interhairpin hybridization chain reaction and leads to the assembly of highly fluorescent Zn(II)-PPIX-loaded G-quadruplex chains. The miRNA-guided fluorescent chains allow selective imaging of cancer cells. Moreover, PDT with visible light selectively kills cancer cells and tumor cells through the formation of toxic reactive oxygen species.

Transient, dissipative, aggregation and deaggregation of Au nanoparticles (NPs) or semiconductor quantum dots (QDs) leading to control over their transient optical properties are introduced. The systems consist of nucleic acid-modified pairs of Au NPs or pairs of CdSe/ZnS QDs, an auxiliary duplex L 1 /T 1 , and the nicking enzyme Nt.BbvCI as functional modules yielding transient aggregation/deaggregation of the NPs and dynamically controlling over their optical properties. In the presence of a fuel strand L 1 ', the duplex L 1 /T 1 is separated, leading to the release of T 1 and the formation of duplex L 1 /L 1 '. The released T 1 leads to aggregation of the Au NPs or to the T 1 -induced G-quadruplex bridged aggregated CdSe/ZnS QDs. Biocatalytic nicking of the L 1 /L 1 ' duplex fragments L 1 ' and the released L 1 displaces T 1 bridging the aggregated NPs or QDs, resulting in the dynamic recovery of the original NPs or QDs modules. The dynamic aggregation/deaggregation of the Au NPs is followed by the transient interparticle plasmon coupling spectral changes. The dynamic aggregation/deaggregation of the CdSe/ZnS QDs is probed by following the transient chemiluminescence generated by the hemin/G-quadruplexes bridging the QDs and by the accompanying transient chemiluminescence resonance energy transfer proceeding in the dynamically formed QDs aggregates. A third system demonstrating transient, dissipative, luminescence properties of a reaction module consisting of nucleic acid-stabilized Ag nanoclusters (NCs) is introduced. Transient dynamic formation and depletion of the supramolecular luminescent Ag NCs system via strand displacement accompanied by a nicking process are demonstrated.

Gated dissipative artificial photosynthetic systems modeling dynamically modulated environmental effects on the photosynthetic apparatus are presented. Two photochemical systems composed of a supramolecular duplex scaffold, a photosensitizer-functionalized strand (photosensitizer is Zn(II)protoporphyrin IX, Zn(II)PPIX, or pyrene), an electron acceptor bipyridinium (V 2+ )-modified strand, and a nicking enzyme (Nt.BbvCI) act as functional assemblies driving transient photosynthetic-like processes. In the presence of a fuel strand, the transient electron transfer quenching of the photosensitizers, in each of the photochemical systems, is activated. In the presence of a sacrificial electron donor (mercaptoethanol) and continuous irradiation, the resulting electron transfer process in the Zn(II)PPIX/V 2+ photochemical module leads to the transient accumulation and depletion of the bipyridinium radical-cation (V· + ) product, and in the presence of ferredoxin-NADP + reductase and NADP + , to the kinetically modulated photosynthesis of NADPH. By subjecting the mixture of two photochemical modules to one of two inhibitors, the gated transient photoinduced electron transfer in the two modules is demonstrated. Such gated dissipative process highlights its potential as an important pathway to protect artificial photosynthetic module against overdose of irradiance and to minimize photodamage.

The covalent linkage of aptamer binding sites to nanoparticle nanozymes is introduced as a versatile method to improve the catalytic activity of nanozymes by concentrating the reaction substrates at the catalytic nanozyme core, thereby emulating the binding and catalytic active-site functions of native enzymes. The concept is exemplified with the synthesis of Cu 2+ ion-functionalized carbon dots (C-dots), modified with the dopamine binding aptamer (DBA) or the tyrosinamide binding aptamer (TBA), for the catalyzed oxidation of dopamine to aminochrome by H 2 O 2 or the oxygenation of l-tyrosinamide to the catechol product, which is subsequently oxidized to amidodopachrome, in the presence of H 2 O 2 /ascorbate mixture. Sets of structurally functionalized DBA-modified Cu 2+ ion-functionalized C-dots or sets of structurally functionalized TBA-modified Cu 2+ ion-functionalized C-dots are introduced as nanozymes of superior catalytic activities (aptananozymes) toward the oxidation of dopamine or the oxygenation of l-tyrosinamide, respectively. The aptananozymes reveal enhanced catalytic activities as compared to the separated catalyst and respective aptamer constituents. The catalytic functions of the aptananozymes are controlled by the structure of the aptamer units linked to the Cu 2+ ion-functionalized C-dots. In addition, the aptananozyme shows chiroselective catalytic functions demonstrated by the chiroselective-catalyzed oxidation of l/d-DOPA to l/d-dopachrome. Binding studies of the substrates to the different aptananozymes and mechanistic studies associated with the catalytic transformations are discussed.

The synthesis of stimuli-responsive hybrid structures composed of drug-loaded UiO-66 metal-organic framework nanoparticles, NMOFs, locked by DNA tetrahedra gates is presented. The hybrid systems combine the high loading capacity of drugs in the porous NMOFs and the effective cell permeation properties of the DNA tetrahedra. The nucleic acid-functionalized UiO-66 NMOFs are loaded with drugs (doxorubicin, DOX, or camptothecin, CPT) or with dyes as drug models (Rhodamine 6G or fluorescein) and used to prepare stimuli-responsive carriers. In this study, two different stimuli-responsive NMOFs are presented. One system introduces the drug-loaded NMOFs locked by pH-responsive DNA tetrahedra. At acidic pH values, the gating tetrahedra are dissociated from the NMOFs through the formation of i-motif structures, resulting in the unlocking of the NMOFs and the release of the drugs. In addition, the tetrahedra gates are modified with AS1411 aptamer tethers, and these target the drug-loaded NMOFs to nucleolin receptors overexpressed in certain malignant cells. A second system involves the preparation of NMOFs loaded with drugs/dyes and gated by the microRNA (miRNA)-responsive tetrahedra (miRNA-21 or miRNA-155). In the presence of miRNAs, the dissociation of miRNA-responsive tetrahedra from the NMOFs leads to the unlocking of the NMOFs and the release of the loads. Further developments of the miRNA-responsive tetrahedra-gated hybrid carriers include the following. (i) By appropriate engineering of the miRNA gating units, the exonuclease III (Exo III)-amplified unlocking of the carriers, through the regeneration of the miRNA triggers, and the enhanced release of the loaded drugs are demonstrated. (ii) By applying mixtures of miRNA-21-responsive DNA tetrahedra-gated DOX-loaded NMOFs and miRNA-155-responsive DNA tetrahedra-gated CPT-loaded NMOFs, the multiplexed miRNA-21/miRNA-155-dictated release of the drugs is demonstrated. As compared to the analog DNA duplex-modified NMOFs, DNA tetrahedra-gated, drug-loaded NMOFs permeation into malignant MDA-MB-231 breast cancer cells presents more effective cell permeation. Effective and selective cytotoxicity toward the malignant cells, as compared to nonmalignant epithelial MCF-10A breast cells, is demonstrated due to the acidic pH, present in cancer cells, or the miRNA-21, present in MDA-MB-231 malignant cells.

Nucleic acid based, out-of-equilibrium, dissipative networks driven by nucleic acid fuels coupled to the nicking enzyme, Nt.BbvCI, are presented. One set of experiments includes a functional module consisting of a duplex and two fluorophore-labeled strands. The fuel-triggered activation of the functional module leads to a supramolecular intermediate composed of a template bound to the two fluorophore-labeled strands. Nicking of the fuel strand by Nt.BbvCI yields "waste" products, resulting in the regeneration of original system. The transient dissipative behavior of the systems is probed by following the FRET signal generated by the fluorophore labels associated with the intermediate supramolecular complex. The second set of experiments introduces two functional modules activated in parallel by the fuel strand. Using two inhibitors, I 1 or I 2 , the selective gated dissipative operation of the networks is demonstrated. Finally, experiments presenting the intercommunication and cascading of two dissipative networks are introduced. Subjecting the networks to the fuel strands leads to intercommunication between the networks by strand-transfer and strand-feedback processes, allowing the cascaded dissipative operation of the assembly. The experimental results of the different dissipative systems are accompanied by kinetic models and computational simulations. The computational simulations provide useful means to predict the dissipative transient patterns of the systems at different auxiliary conditions.

The covalent linkage of catalytic units to aptamer sequence-specific nucleic acids exhibiting selective binding affinities for substrates leads to functional scaffolds mimicking native enzymes, nucleoapzymes. The binding of the substrates to the aptamer and their structural orientation with respect to the catalytic units duplicate the functions of the active center of enzymes. The possibility of linking the catalytic sites directly, or through spacer units, to the 5'-end, 3'-end, and middle positions of the aptamers allows the design of nucleoapzyme libraries, revealing structure-functions diversities, and these can be modeled by molecular dynamics simulations. Catalytic sites integrated into nucleoapzymes include DNAzymes, transition metal complexes, and organic ligands. Catalytic transformations driven by nucleoapzymes are exemplified by the oxidation of dopamine or l-arginine, hydroxylation of tyrosine to l-DOPA, hydrolysis of ATP, and cholic acid-modified esters. The covalent linkage of photosensitizers to the tyrosinamide aptamer leads to a photonucleoapzyme scaffold that binds the N -methyl- N '-(3-aminopropane)-4,4'-bipyridinium-functionalized tyrosinamide to the aptamer. By linking the photosensitizer directly, or through a spacer bridge to the 5'-end or 3'-end of the aptamer, we demonstrate a library of supramolecular photosensitizer/electron acceptor photonucleoapzymes mimicking the functions of photosystem I in the photosynthetic apparatus. The photonucleoapzymes catalyze the photoinduced generation of NADPH, in the presence of ferredoxin-NADP + -reductase (FNR), or the photoinduced H 2 evolution catalyzed by Pt nanoparticles. The future prospects of nucleoapzymes and photonucleoapzymes are discussed.

Sequence-specific nucleic acids recognizing low-molecular-weight ligands or macromolecules (aptamers) have found growing interest for biomedical applications. The present review article summarizes recent applications of aptamers as stimuli-responsive gating units of drug (or dye)-loaded nano- or microcarriers for controlled and targeted drug release. In the presence of cellular biomarkers, the nano-/microcarriers are unlocked by forming aptamer-ligand complexes. Different aptamer-functinalized nano-/microcarriers are presented, including inorganic nanomaterials, metal-organic framework nanoparticles, and soft materials. The chemistries associated with the preparation of the carriers and the mechanisms to unlock the carriers are discussed. Stimuli-responsive gated drug-loaded micro-/nanocarriers hold great promise as functional sense-and-treat materials for the targeted and selective release of drugs.

The emergence of nucleic acid-based constitutional dynamic networks, CDNs, from a pool of nucleic acids is a key process for the understanding and modality of the evolution of biological networks. We present a versatile method that applies a library of nucleic acids coupled to biocatalytic DNA machineries as functional modules for the emergence of CDNs of diverse composition, complexity, and structural diversity. A set of four DNA template/blocker scaffolds coupled to the polymerase/dNTP replication machinery leads, in the presence of a primer, P 1 , to the gated replication of the scaffolds and to the displacement of four components that reconfigure into a [2 × 2] CDN. Using six template/blocker scaffolds and the polymerase/dNTPs, the P 1 -guided emergence of a [3 × 3] CDN is demonstrated. In addition, by further engineering the template/blocker scaffolds, the hierarchical control over the composition of the P 1 -guided emergence of [3 × 3] CDNs is accomplished. Also, sequence-engineered template/blocker scaffolds, coupled to the polymerase/dNTP machinery, lead, in the presence of two primers P 1 and/or P 2 , to the selective emergence of two different [2 × 2] CDNs or to a [3 × 3] CDN. Also, a set of six appropriately engineered template/blocker scaffolds, coupled to the polymerase/dNTP machinery, leads to the emergence of a CDN composed of four equilibrated DNA tetrahedra constituents. Finally, by further sequence engineering of the set of template/blocker scaffolds and their coupling to a nicking/polymerization/dNTP replication machinery, the amplified high-throughput emergence of CDNs is demonstrated.

Inspired by nature where intracellular dynamic interactions between DNA, RNA and proteins processed within complex networks leading to programmed reaction patterns, extensive research efforts are directed to mimic these processes by chemical means, "Systems Chemistry". The present perspective introduces nucleic acids as functional modules to construct constitutional dynamic networks, CDNs, mimicking natural networks. The base sequences comprising nucleic acids provide a rich "tool box" to assemble signal-triggered reconfigurable CDNs revealing adaptive and hierarchically adaptive properties, intercommunication between CDNs, and feedback-driven reaction pathways similar to natural systems. Pathways for the evolution of CDNs and the formation of networks of enhanced complexities are discussed. Different applications of constitutional dynamic networks are introduced including programmed catalysis, CDN-guided optical and catalytic functions of nanoparticle aggregates, and CDN-dictated stiffness and self-healing functions of hydrogels. Future perspectives of the field in designing dissipative transient CDNs, CDNs-guided transcription/translation synthesis of selective proteins, and the challenging integration of CDNs into cell-like containments aiming to assemble "artificial cells" are addressed.

Inspired by nature, where dynamic networks control the levels of gene expression and the activities of transcribed/translated proteins, we introduce nucleic acid-based constitutional dynamic networks (CDNs) as functional modules mimicking native circuits by demonstrating CDNs-guided programmed synthesis of genes, controlled transcription of RNAs, and dictated transcription/translation synthesis of proteins. An auxiliary CDN consisting of four dynamically equilibrated constituents AA', AB', BA', and BB' is orthogonally triggered by two different inputs yielding two different compositionally reconfigured CDNs. Subjecting the parent auxiliary CDN to two hairpins, H A and H B , and two templates T A and T B and a nicking/replication machinery leads to the cleavage of the hairpins and to the activation of the nicking/replication machineries that synthesize two "genes", e.g., the histidine-dependent DNAzyme g1 and the Zn 2+ -ion-dependent DNAzyme g2. The triggered orthogonal reconfiguration of the parent CDN to the respective CDNs leads to the programmed preferred CDN-guided synthesis of g1 or g2. Similarly, the triggered reconfigured CDNs are subjected to two hairpins H C and H D , the templates I'/I and J'/J, and the RNA polymerase (RNAp)/NTPs machinery. While the cleavage of the hairpins by the constituents associated with the parent CDN leads to the transcription of the broccoli aptamer recognizing the DFHBI ligand and of the aptamer recognizing the malachite green (MG) ligand, the orthogonally triggered CDNs lead to the CDNs-guided enhanced transcription of either the DFHBI aptamer or the MG aptamer. In addition, subjecting the triggered reconfigured CDNs to predesigned hairpins H E and H F , the templates M'/M and N'/N, the RNAp/NTPs machinery, and the cell-free ribosome t-RNA machinery leads to the CDNs-guided transcription/translation of the green fluorescence protein (GFP) or red fluorescence protein (RFP).

Following the significance of dissipative, out-of-equilibrium biological processes controlling living systems, we introduce nucleic acid-based dissipative constitutional dynamic networks (CDNs) that exhibit tunable transient composition changes of the networks dictated by auxiliary fuel strands. CDN "X" composed of four equilibrated nucleic acid constituents, AA', AB', BA', and BB', and the accompanying "dormant" structures T 1 L 1 and T 2 L 2 and nicking enzyme Nt.BbvCI, undergoes dissipative orthogonal transitions to CDN "Y" and back or to CDN "Z" and back. In the presence of the fuel strand L 1 ' or L 2 ', the displacement of the respective "dormant" structure releases the trigger T 1 or T 2 that activates the reconfiguration of CDN "X" to CDN "Y" or CDN "X" to CDN "Z". The generated duplex L 1 L 1 ' or L 2 L 2 ' is designed to be nicked by Nt.BbvCI, leading to the regeneration of L 1 or L 2 that rebinds to T 1 or T 2 , resulting in the dissipative cyclic recovery of CDN "X". Kinetic simulations of the dissipative processes allow us to predict the dissipative behavior of the systems under different auxiliary conditions. Subjecting CDN "X" to altering sets of the fuel strands L 1 ' and L 2 ' yields programmed reconfiguration patterns of dissipative reaction cycles. By engineering functional nucleic acid tethers on the constituents and the triggering strands, orthogonal dissipative emerging catalytic transformations dictated by the dissipative CDNs are demonstrated.

Within the broad research efforts to engineer chemical pathways to yield high-throughput evolutionary synthesis of genes and their screening for dictated functionalities, we introduce the evolution of nucleic-acid-based constitutional dynamic networks (CDNs) that follow reproduction/variation/selection principles. These fundamental principles are demonstrated by assembling a library of nucleic-acid strands and hairpins as functional modules for evolving networks. Primary T 1 -initiated selection of components from the library assembles a parent CDN X, where the evolved constituents exhibit catalytic properties to cleave the hairpins in the library. Cleavage of the hairpins yields fragments, which reproduces T 1 to replicate CDN X, whereas the other fragments T 2 and T 3 select other components to evolve two other CDNs, Y and Z (variation). By applying appropriate counter triggers, we demonstrate the guided selection of networks from the evolved CDNs. By integrating additional hairpin substrates into the system, CDN-dictated emergent catalytic transformations are accomplished. The study provides pathways to construct evolutionary dynamic networks revealing enhanced gated and cascaded functions.

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, Eco RI, and Hin dIII) 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.

A method to assemble loaded stimuli-responsive DNA-polyacrylamide hydrogel-stabilized microcapsules is presented. The method involves coating substrate-loaded CaCO 3 microparticles, functionalized with nucleic acid promoter units, and cross-linking DNA-modified polyacrylamide chains on the microcapsules, using the hybridization chain reaction (HCR) to yield the DNA-cross-linked hydrogel coating. Dissolution of the CaCO 3 particles generated the substrate-loaded hydrogel-protected microcapsules. The microcapsule-hydrogel shells include engineered stimuli-responsive oligonucleotide cross-linkers that control the stiffness of the hydrogel shells, allowing the triggered release of the loads. One approach includes the incorporation of cofactor-dependent DNAzyme units into the cross-linked hydrogel layers (cofactor = Mg 2+ ions, Zn 2+ ions, or histidine) as stimuli-responsive units. Cleavage of the cross-linking DNAzyme substrates by the respective cofactors yields hydrogel coatings with a reduced stiffness and higher porosity that allow the release of the loads. A further approach involved the application of the HCR process to assemble the bilayer hydrogel microcapsules that are unlocked by two cooperative triggers. Bilayer microcapsules consisting of a K + ions-stabilized G-quadruplex/18-crown-6-ether (CE) responsive layer and a Mg 2+ ion DNAzyme-responsive layers are presented. Unlocking and locking of the G-quadruplex cross-linked layer by 18-crown-6-ether and K + ions, respectively, in the presence of Mg 2+ ions allow the switchable controlled release of the load. In addition, the intercommunication of two kinds of stimuli-responsive bilayer hydrogel microcapsules carrying two different loads (tetramethylrhodamine-dextran, TMR-D, and CdSe/ZnS quantum dots) is demonstrated. The intercommunication process involves the stimuli-triggered generation of "information transfer" strands from one microcapsule to another that activate the release of the loads.

Enzymes (endonucleases) are coupled to constitutional dynamic networks to stimulate the selection of a constituent and cascaded emergence of a new network. This is exemplified with the Eco RI-dictated depletion of a network and selection of a constituent that activates the cascaded emergence of a new network. The new network is further depleted by Hin dIII to a selected constituent that can be coupled to the cascaded emergence of a dynamic network. In addition, upon subjecting a [3 × 3] constitutional dynamic network to endonucleases Eco RI and Hin dIII, the programmed hierarchical selection of [2 × 2] constitutional dynamic networks followed by the biocatalytic selection of a constituent for the subsequent emergence of new networks is demonstrated.

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 Sr 2+ -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.

A method to assemble stimuli-responsive nucleic acid-based hydrogel-stabilized microcapsule-in-microcapsule systems is introduced. An inner aqueous compartment stabilized by a stimuli-responsive hydrogel-layer (∼150 nm) provides the inner microcapsule (diameter ∼2.5 μm). The inner microcapsule is separated from an outer aqueous compartment stabilized by an outer stimuli-responsive hydrogel layer (thickness of ∼150 nm) that yields the microcapsule-in-microcapsule system. Different loads, e.g., tetramethyl rhodamine-dextran (TMR-D) and CdSe/ZnS quantum dots (QDs), are loaded in the inner and outer aqueous compartments. The hydrogel layers exist in a higher stiffness state that prevents inter-reservoir or leakage of the loads from the respective aqueous compartments. Subjecting the inner hydrogel layer to Zn 2+ -ions and/or the outer hydrogel layer to acidic pH or crown ether leads to the triggered separation of the bridging units associated with the respective hydrogel layers. This results in the hydrogel layers of lower stiffness allowing either the mixing of the loads occupying the two aqueous compartments, the guided release of the load from the outer aqueous compartment, or the release of the loads from the two aqueous compartments. In addition, a pH-responsive microcapsule-in-microcapsule system is loaded with glucose oxidase (GOx) in the inner aqueous compartment and insulin in the outer aqueous compartment. Glucose permeates across the two hydrogel layers resulting in the GOx catalyzed aerobic oxidation of glucose to gluconic acid. The acidification of the microcapsule-in-microcapsule system leads to the triggered unlocking of the outer, pH-responsive hydrogel layer and to the release of insulin. The pH-stimulated release of insulin is controlled by the concentration of glucose. While at normal glucose levels, the release of insulin is practically prohibited, the dose-controlled release of insulin in the entire diabetic range  is demonstrated. Also, switchable ON/OFF release of insulin is achieved highlighting an autonomous glucose-responsive microdevice operating as an "artificial pancreas" for the release of insulin.

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, H 1 and H 2 , 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 H 1 and H 2 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 H 2 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.

The broadband C 3 N 4 semiconductor absorbs in the UV region, λ = 330-380 nm, a feature limiting its application for light-to-energy conversion. The unique surface adsorption properties of C 3 N 4 allow, however, the binding of a photosensitizer, operating in the visible-solar spectrum to the surface of C 3 N 4 . Coupling of the energy levels of the photosensitizer with the energy levels of C 3 N 4 allows effective photoinduced electron-transfer quenching and subsequent charge separation in the hybrid structures. Two methods to adsorb a photosensitizer on the C 3 N 4 nanoparticles are described. One is exemplified by the adsorption of Zn(II)-protoporphyrin IX on C 3 N 4 using π-π interactions. The second method utilizes the specific binding interactions of single-stranded nucleic acids on C 3 N 4 and involves the binding of a Ru(II)-tris-bipyridine-modified nucleic acid on the C 3 N 4 nanoparticles. Effective electron-transfer quenching of the photoexcited photosensitizers by C 3 N 4 proceeds in the two hybrid systems. The two hybrid photosystems induce the effective photosensitized reduction of N , N '-dimethyl-4,4'-bipyridinium, MV 2+ , to MV +• , in the presence of Na 2 EDTA as a sacrificial electron donor. The generation of MV +• is ca. 5-fold higher as compared to the formation of MV +• in the presence of the photosensitizer alone (in the absence of C 3 N 4 ). The effective generation of MV +• in the photosystems is attributed to the efficient quenching of the photosensitizers, followed by effective charge separation of the electrons in the conduction band of C 3 N 4 and the holes in the oxidized photosensitizer. The subsequent transfer of the conduction-band electrons to MV 2+ and the oxidation of Na 2 EDTA by the oxidized photosensitizers lead to the effective formation of MV +• . The photogenerated MV +• by the two hybrid photosystems is used to catalyze H 2 evolution in the presence of Pt nanoparticle catalysts and to mediate the reduction of NADP + to NADPH, in the presence of ferredoxin-NADP + reductase, FNR. The ability to couple the photogenerated NADPH to drive NADP + -dependent biocatalytic transformations is demonstrated.

Inspired by nature, where gene regulatory networks consisting of intercommunicating constituents, each composed of three or more components, play a central role in the development of living systems, we use the information encoded in the base sequences of nucleic acids to construct three-dimensional constitutional dynamic networks (3D CDNs) consisting of eight three-component constituents (A i B j C k ). Upon subjecting the parent 3D CDN I to four auxiliary nucleic acid triggers (T 1 , T 2 , T 3 , or T 4 ), the adaptive reconfiguration of CDN I into four different CDNs (II, III, IV, or V) is demonstrated, and by applying two consecutive triggers or counter triggers, the adaptive reversible hierarchical control over the compositions of new CDN systems (VI, VII, VIII, or IX) is demonstrated. The labeling of the constituents with nine different Mg 2+ -ion-dependent DNAzyme reporter units and the incorporation of a fluorescent dye/anticocaine aptamer complex into the structure of one of the constituents enable the quantitative evaluation of the contents of the constituents in the different CDNs. The quantification of the compositions of the CDNs is based on the activities of the DNAzymes conjugated to the constituents, the fluorescence signals upon the cocaine-induced separation of the dye/aptamer complex, appropriate calibration curves, and the set of equations. These assessments are further supported by quantitative electrophoretic experiments of the respective CDNs.

Constitutional dynamic networks (CDNs) consisting of DNA tetrahedra allow the dynamically triggered adaptive control over the compositions and structures of the constituents. In one system, a CDN consisting of four tetrahedra constituents is orthogonally triggered by two alternative triggers, T 1 or T 2 , to reconfigure into two different CDNs, revealing adaptive control-over the tetrahedra compositions in the two CDNs. In the presence of the counter triggers T 1 ' or T 2 ', the parent CDN is regenerated. In the second system, the assembly of a CDN consisting of four dimeric tetrahedra exhibiting variable sizes and shapes is described. The orthogonal triggering of the CDN by two different triggers T 3 or T 4 , leads to the adaptive reconfiguration of the CDN into new equilibrated CDNs exhibiting control-over the compositions and shapes of the dimeric tetrahedra comprising the CDNs. Mg 2+ -ion-dependent DNAzyme units conjugated to the tetrahedra nanostructures and complementary electrophoretic experiments provide means to quantitatively evaluate the compositions of the different CDN systems. By the functionalization of the four-tetrahedra-based CDN system with two fluorophor donor-acceptor pairs and the orthogonal reconfiguration of the CDN in the presence of two alternative triggers, the control-over the FRET functions of the CDN systems is demonstrated.

In this study, we report on a redox-controllable and reversible complete "ON"/"OFF"-switchable aptamer binding to ATP. A series of methylene blue-modified ATP-aptamers was synthesized, revealing improved binding affinities toward ATP as compared to the nonmodified aptamer. These binding affinities were dependent on the conjugation site of the redox label on the aptamer scaffold. Importantly, we find that the oxidized methylene blue-modified aptamers bind to ATP with micromolar affinity, while the reduced form lacks binding affinity toward ATP, resulting in an unprecedented complete "ON"/"OFF" redox-controllable aptamer switch. We demonstrate the cyclic "ON"/"OFF" binding of ATP to the methylene blue-functionalized aptamer through cyclic oxidation and reduction of the redox label using both chemical and electrochemical means. Molecular dynamics and docking simulations were performed to account for the redox-switchable properties of the conjugated aptamers and to rationalize the enhanced binding affinities of the different aptamer designs.