Gated Dissipative Dynamic Artificial Photosynthetic Model Systems

Aptamer-Modified Homogeneous Catalysts, Heterogenous Nanoparticle Catalysts, and Photocatalysts: Functional "Nucleoapzymes", "Aptananozymes", and "Photoaptazymes"

Conjugation of aptamers to homogeneous catalysts ("nucleoapzymes"), heterogeneous nanoparticle catalysts ("aptananozymes"), and photocatalysts ("photoaptazymes") yields superior catalytic/photocatalytic hybrid nanostructures emulating functions of native enzymes and photosystems. The concentration of the substrate in proximity to the catalytic sites ("molarity effect") or spatial concentration of electron-acceptor units in spatial proximity to the photosensitizers, by aptamer-ligand complexes, leads to enhanced catalytic/photocatalytic efficacies of the hybrid nanostructures. This is exemplified by sets of "nucleoapzymes" composed of aptamers conjugated to the hemin/G-quadruplex DNAzymes or metal-ligand complexes as catalysts, catalyzing the oxidation of dopamine to aminochrome, oxygen-insertion into the Ar─H moiety of tyrosinamide and the subsequent oxidation of the catechol product into aminochrome, or the hydrolysis of esters or ATP. Also, aptananozymes consisting of aptamers conjugated to Cu2+ - or Ce4+ -ion-modified C-dots or polyadenine-stabilized Au nanoparticles acting as catalysts oxidizing dopamine or operating bioreactor biocatalytic cascades, are demonstrated. In addition, aptamers conjugated to the Ru(II)-tris-bipyridine photosensitizer or the Zn(II) protoporphyrin IX photosensitizer provide supramolecular photoaptazyme assemblies emulating native photosynthetic reaction centers. Effective photoinduced electron transfer followed by the catalyzed synthesis of NADPH or the evolution of H2 is demonstrated by the photosystems. Structure-function relationships dictate the catalytic and photocatalytic efficacies of the systems.

Cascaded dissipative DNAzyme-driven layered networks guide transient replication of coded-strands as gene models

Dynamic, transient, out-of-equilibrium networks guide cellular genetic, metabolic or signaling processes. Designing synthetic networks emulating natural processes imposes important challenges including the ordered connectivity of transient reaction modules, engineering of the appropriate balance between production and depletion of reaction constituents, and coupling of the reaction modules with emerging chemical functions dictated by the networks. Here we introduce the assembly of three coupled reaction modules executing a cascaded dynamic process leading to the transient formation and depletion of three different Mg²⁺-ion-dependent DNAzymes. The transient operation of the DNAzyme in one layer triggers the dynamic activation of the DNAzyme in the subsequent layer, leading to a three-layer transient catalytic cascade. The kinetics of the transient cascade is computationally simulated. The cascaded network is coupled to a polymerization/nicking DNA machinery guiding transient synthesis of three coded strands acting as “gene models”, and to the rolling circle polymerization machinery leading to the transient synthesis of fluorescent Zn(II)-PPIX/G-quadruplex chains or hemin/G-quadruplex catalytic wires.

A reaction network executing a cascaded transient formation and depletion of three different catalytic strands is introduced. The system is coupled to the secondary temporal synthesis of different coded strands as gene models.

Dissipative DNA nanotechnology

DNA nanotechnology has emerged as a powerful tool to precisely design and control molecular circuits, machines and nanostructures. A major goal in this field is to build devices with life-like properties, such as directional motion, transport, communication and adaptation. Here we provide an overview of the nascent field of dissipative DNA nanotechnology, which aims at developing life-like systems by combining programmable nucleic-acid reactions with energy-dissipating processes. We first delineate the notions, terminology and characteristic features of dissipative DNA-based systems and then we survey DNA-based circuits, devices and materials whose functions are controlled by chemical fuels. We emphasize how energy consumption enables these systems to perform work and cyclical tasks, in contrast with DNA devices that operate without dissipative processes. The ability to take advantage of chemical fuel molecules brings dissipative DNA systems closer to the active molecular devices that exist in nature.

Dissipative Organization of DNA Oligomers for Transient Catalytic Function

The development of synthetic non-equilibrium systems opens doors for man-made life-like materials. Yet, creating distinct transient functions from artificial fuel-driven structures remains a challenge. Building on our ATP-driven dynamic covalent DNA assembly in an enzymatic reaction network of concurrent ATP-powered ligation and restriction, we introduce ATP-fueled transient organization of functional subunits for various functions. The programmability of the ligation/restriction site allows to precisely organize multiple sticky-end-encoded oligo segments into double-stranded (ds) DNA complexes. We demonstrate principles of ATP-driven organization into sequence-defined oligomers by sensing barcode-embedded targets with different defects. Furthermore, ATP-fueled DNAzymes for substrate cleavage are achieved by transiently ligating two DNAzyme subunits into a dsDNA complex, rendering ATP-fueled transient catalytic function.

Molecular Photocatalytic Water Splitting by Mimicking Photosystems I and II

In nature, water is oxidized by plastoquinone to evolve O₂ and form plastoquinol in Photosystem II (PSII), whereas NADP⁺ is reduced by plastoquinol to produce NADPH and regenerate plastoquinone in Photosystem I (PSI), using homogeneous molecular photocatalysts. However, water splitting to evolve H₂ and O₂ in a 2:1 stoichiometric ratio has yet to be achieved using homogeneous molecular photocatalysts, remaining as one of the biggest challenges in science. Herein, we demonstrate overall water splitting to evolve H₂ and O₂ in a 2:1 ratio using a two liquid membranes system composed of two toluene phases, which are separated by a solvent mixture of water and trifluoroethanol (H₂O/TFE, 3:1 v/v), with a glass membrane to combine PSI and PSII molecular models. A PSII model contains plastoquinone analogs [p-benzoquinone derivatives (X-Q)] in toluene and an iron(II) complex as a molecular oxidation catalyst in H₂O/TFE (3:1 v/v), which evolves a stoichiometric amount of O₂ and forms plastoquinol analogs (X-QH₂) under photoirradiation. On the other hand, a PSI model contains nothing in toluene but contains X-QH₂, 9-mesityl-10-methylacridinium ion (Acr⁺-Mes) as a photocatalyst, and a cobalt(III) complex as an H₂ evolution catalyst in H₂O/TFE (3:1 v/v), which evolves a stoichiometric amount of H₂ and forms X-Q under photoirradiation. When a PSII model system is combined with a PSI model system with two glass membranes and two liquid membranes, photocatalytic water splitting with homogeneous molecular photocatalysts is achieved to evolve hydrogen and oxygen with the turnover number (TON) of >100.

Self-Assembled Porphyrin Nanoleaves with Unique Crossed Transportation of Photogenerated Carriers to Enhance Photocatalytic Hydrogen Production

The preparation of self-assembled porphyrins with orderly stacked nanostructures for emulating natural photosynthesis has stimulated extensive efforts to optimize the energy conversion efficiency. However, the elucidation of how orderly stacked structures promote photocatalysis at the molecular level remains a great challenge. Here, unique porphyrin nanoleaves with designed and ordered structure are synthesized and show a hydrogen evolution rate higher than that of commercial powder. Photodeposition of cocatalysts and Kelvin probe force microscopy measurement suggest selective aggregation of photogenerated electrons and holes at different active sites. Combined with theoretical calculations, we find that the orderly packing changes molecular symmetry and induces a molecular dipole, which increases linearly along the π-π stacking direction and forms a strong built-in electric field. The built-in electric field drives photogenerated electrons and holes for the unique crossed transportation along different directions. These findings reveal how orderly stacked structures promote photocatalysis and provide a novel approach for highly efficient water splitting.

Photoresponsive DNA materials and their applications

Photoresponsive nucleic acids attract growing interest as functional constituents in materials science. Integration of photoisomerizable units into DNA strands provides an ideal handle for the reversible reconfiguration of nucleic acid architectures by light irradiation, triggering changes in the chemical and structural properties of the nanostructures that can be exploited in the development of photoresponsive functional devices such as machines, origami structures and ion channels, as well as environmentally adaptable 'smart' materials including nanoparticle aggregates and hydrogels. Moreover, photoresponsive DNA components allow control over the composition of dynamic supramolecular ensembles that mimic native networks. Beyond this, the modification of nucleic acids with photosensitizer functionality enables these biopolymers to act as scaffolds for spatial organization of electron transfer reactions mimicking natural photosynthesis. This review provides a comprehensive overview of these exciting developments in the design of photoresponsive DNA materials, and showcases a range of applications in catalysis, sensing and drug delivery/release. The key challenges facing the development of the field in the coming years are addressed, and exciting emergent research directions are identified.

Bioinspired Artificial Photosynthetic Systems

Mimicking photosynthesis using artificial systems, as a means for solar energy conversion and green fuel generation, is one of the holy grails of modern science. This perspective presents recent advances towards developing artificial photosynthetic systems. In one approach, native photosystems are interfaced with electrodes to yield photobioelectrochemical cells that transform light energy into electrical power. This is exemplified by interfacing photosystem I (PSI) and photosystem II (PSII) as an electrically contacted assembly mimicking the native Z-scheme, and by the assembly of an electrically wired PSI/glucose oxidase biocatalytic conjugate on an electrode support. Illumination of the functionalized electrodes led to light-induced generation of electrical power, or to the generation of photocurrents using glucose as the fuel. The second approach introduces supramolecular photosensitizer nucleic acid/electron acceptor complexes as functional modules for effective photoinduced electron transfer stimulating the subsequent biocatalyzed generation of NADPH or the Pt-nanoparticle-catalyzed evolution of molecular hydrogen. Application of the DNA machineries for scaling-up the photosystems is demonstrated. A third approach presents the integration of artificial photosynthetic modules into dynamic nucleic acid networks undergoing reversible reconfiguration or dissipative transient operation in the presence of auxiliary triggers. Control over photoinduced electron transfer reactions and photosynthetic transformations by means of the dynamic networks is demonstrated.