Dissipative Synthetic DNA‐Based Receptors for the Transient Loading and Release of Molecular Cargo

Phototriggered Equilibrated and Transient Orthogonally Operating Constitutional Dynamic Networks Guiding Biocatalytic Cascades

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.

Dynamic surface chemistry and interparticle interactions mediating chemically fueled dissipative assembly of colloids

HYPOTHESIS

Dissipative assembly of colloids involves using a chemical fuel to temporarily activate organic colloid surface ligands to an assembly prone state. Colloids assemble into transient aggregates that disintegrate after the fuel is consumed. The underlying colloidal interactions controlling dissipative assembly have not been rigorously identified or quantified. We expect that fuel concentration dependent dissipative assembly behavior can be reconciled with measurements of dynamic colloid surface chemistry and colloidal interactions.

EXPERIMENTS

Carbodiimide chemistry was utilized to induce dissipative assembly of carboxylic acid functionalized polystyrene colloids. We measured aggregation kinetics, colloid surface hydrophobicity, and zeta potential as a function of time, which established that colloids underwent dissipative assembly for fuel concentrations between 5 and 12.5 mM and irreversible aggregation at higher fuel concentrations due to transient changes in surface chemistry.

FINDINGS

We formulated a pairwise colloidal interaction potential model including hydrophobic interactions quantified by fluorescence binding experiments. Fuel concentrations causing dissipative assembly displayed a transient increase in secondary minimum depth and a primary maximum much larger than the thermal potential. Fuel concentrations leading to irreversible aggregation displayed a primary maximum smaller than the thermal potential. This is the first study to quantify surface chemistry and interparticle interactions during dissipative colloid assembly and represents a foundational step in rationally designing more complex dissipative assembly systems.

Dynamic DNA Networks-Guided Directional and Orthogonal Transient 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.

Mechanosensitive non-equilibrium supramolecular polymerization in closed chemical systems

Chemical fuel-driven supramolecular systems have been developed showing out-of-equilibrium functions such as transient gelation and oscillations. However, these systems suffer from undesired waste accumulation and they function only in open systems. Herein, we report non-equilibrium supramolecular polymerizations in a closed system, which is built by viologens and pyranine in the presence of hydrazine hydrate. On shaking, the viologens are quickly oxidated by air followed by self-assembly of pyranine into micrometer-sized nanotubes. The self-assembled nanotubes disassemble spontaneously over time by the reduced agent, with nitrogen as the only waste product. Our mechanosensitive dissipative system can be extended to fabricate a chiral transient supramolecular helix by introducing chiral-charged small molecules. Moreover, we show that shaking induces transient fluorescence enhancement or quenching depending on substitution of viologens. Ultrasound is introduced as a specific shaking way to generate template-free reproducible patterns. Additionally, the shake-driven transient polymerization of amphiphilic naphthalenetetracarboxylic diimide serves as further evidence of the versatility of our mechanosensitive non-equilibrium system.

Dynamic Transcription Machineries Guide the Synthesis of Temporally Operating DNAzymes, Gated and Cascaded DNAzyme Catalysis

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.

Programming Non-Nucleic Acid Molecules into Computational Nucleic Acid Systems

Nucleic acid (NA) computation has been widely developed in the past years to solve kinds of logic and mathematic issues in both information technologies and biomedical analysis. However, the difficulty to integrate non-NA molecules limits its power as a universal platform for molecular computation. Here, we report a versatile prototype of hybridized computation integrated with both nucleic acids and non-NA molecules. Employing the conformationally controlled ligand converters, we demonstrate that non-NA molecules, including both small molecules and proteins, can be computed as nucleic acid strands to construct the circuitry with increased complexity and scalability, and can be even programmed to solve arithmetical calculations within the computational nucleic acid system. This study opens a new door for molecular computation in which all-NA circuits can be expanded with integration of various ligands, and meanwhile, ligands can be precisely programmed by the nuclei acid computation.

Orthogonal Enzyme-Driven Timers for DNA Strand Displacement Reactions

Here, we demonstrate a strategy to rationally program a delayed onset of toehold-mediated DNA strand displacement reactions (SDRs). The approach is based on blocker strands that efficiently inhibit the strand displacement by binding to the toehold domain of the target DNA. Specific enzymatic degradation of the blocker strand subsequently enables SDR. The kinetics of the blocker enzymatic degradation thus controls the time at which the SDR starts. By varying the concentration of the blocker strand and the concentration of the enzyme, we show that we can finely tune and modulate the delayed onset of SDR. Additionally, we show that the strategy is versatile and can be orthogonally controlled by different enzymes each specifically targeting a different blocker strand. We designed and established three different delayed SDRs using RNase H and two DNA repair enzymes (formamidopyrimidine DNA glycosylase and uracil-DNA glycosylase) and corresponding blockers. The achieved temporal delay can be programed with high flexibility without undesired leak and can be conveniently predicted using kinetic modeling. Finally, we show three possible applications of the delayed SDRs to temporally control the ligand release from a DNA nanodevice, the inhibition of a target protein by a DNA aptamer, and the output signal generated by a DNA logic circuit.

Programming Dissipation Systems by DNA Timer for Temporally Regulating Enzyme Catalysis and Nanostructure Assembly

Live cells precisely control their temporal pattern in energy dissipative processes such as catalysis and assembly. Here, we demonstrate a DNA-based artificial dissipative nonequilibrium system where the transient state is controlled by the processive digestion of λ-exonuclease (λ Exo). This enzyme reaction serves as an orthogonal and independent molecular timer allowing for the programmable regulation of the transient-state lifetime. This dissipation system is concatenated to enzyme catalysis and nanostructure assembly networks. Dynamic activation of enzyme catalysis and dynamic disassembly of DNA nanotubes (DNT) are realized, and the state lifetimes of these systems are accurately encoded by the DNA timer. This work demonstrates nontrivial dissipation systems with built-in molecular timers, which can be a useful tool for developing artificial reaction networks and nanostructures with enhanced complexities and intelligence.

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.

Ultra-specific fluorescence detection of DNA modifying enzymes by dissipation system

Abnormal expression of DNA modifying enzymes (DMEs) is linked to a variety of diseases including cancers. It is desirable to develop accurate methods for DME detection. However, the substrate-based probe for target DMEs is disturbed by various non-target DMEs that have similar activity resulting in a loss of specificity. Here we utilized dissipative DNA networks to develop an ultra-specific fluorescence assay for DME, absolutely distinguishing between target and non-target enzymes. Unlike the conventional sensors in which the discrimination of target and non-target relies on signal intensity, in our system, target DMEs exhibit featured fluorescence oscillatory signals, while non-target DMEs show irreversible 'one-way' fluorescence increase. These dissipation-enabled probes (DEPs) exhibit excellent generality for various types of DMEs including DNA repair enzyme apurinic/apyrimidinic endonuclease 1 (APE1), polynucleotide kinase (T4 PNK), and methyltransferase (Dam). DEPs provide a novel quantification mode based on area under curve which is more robust than those intensity-based quantifications. The detection limits of APE1, T4 PNK, and Dam reach 0.025 U/mL, 0.44 U/mL, and 0.113 U/mL, respectively. DEPs can accurately identify their corresponding DMEs with excellent specificity in cell extracts. Fluorescence sensors based on DEPs herein represent a conceptually new class of methods for enzyme detection, which can be easily adapted to other sensing platforms such as electrochemical sensors.

Dissipative Control over the Toehold-Mediated DNA Strand Displacement Reaction

Here we show a general approach to achieve dissipative control over toehold‐mediated strand‐displacement, the most widely employed reaction in the field of DNA nanotechnology. The approach relies on rationally re‐engineering the classic strand displacement reaction such that the high‐energy invader strand (fuel) is converted into a low‐energy waste product through an energy‐dissipating reaction allowing the spontaneous return to the original state over time. We show that such dissipative control over the toehold‐mediated strand displacement process is reversible (up to 10 cycles), highly controllable and enables unique temporal activation of DNA systems. We show here two possible applications of this strategy: the transient labelling of DNA structures and the additional temporal control of cascade reactions.

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.

Construction of Molecular Transporter Based on DNA Structure Regulation

This study aims to build a molecular transporter machine that is based on the microstructure regulation of DNA triplets, which can automatically search, load, target delivery, and unload target protein molecules. The design of the molecular transporter includes: (1) a DNA triplet, which can recognize and load of the target protein; (2) a similar DNA triplet realizing the target transport; and (3) the signal-indicating DNA, which is connected at the target destination to achieve fixation of the target protein at the target destination. The molecular transporter machine would provide research practice and theoretical guidance for the development of DNA-based molecular machines.

Dissipative biocatalytic cascades and gated transient biocatalytic cascades driven by nucleic acid networks

Living systems consist of complex transient cellular networks guiding structural, catalytic, and switchable functions driven by auxiliary triggers, such as chemical or light energy inputs. We introduce two different transient, dissipative, biocatalytic cascades, the coupled glucose oxidase (GOx)/horseradish peroxidase (HRP) glucose-driven oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS^2-) to the radical anion (ABTS^•-) and the lactate dehydrogenase (LDH)/nicotinamide adenine dinucleotide (NAD⁺) lactate-driven reduction of NAD⁺ to NADH. The transient biocatalytic systems are driven by nucleic acid reaction modules using a nucleic acid fuel strand L₁' and a nicking enzyme, Nt.BbvCI, as fuel-degrading catalyst, leading to the dynamic spatiotemporal transient formation of structurally proximate biocatalysts activating the biocatalytic cascades and transient coupled processes, including the generation of chemiluminescence and the synthesis of alanine. Subjecting the mixture of biocatalysts to selective inhibitors allows the gated transient operation of the biocatalysts. The kinetics of transient biocatalytic cascades are accompanied by kinetic models and computational simulations.

Assembly of Dynamic Gated and Cascaded Transient DNAzyme Networks

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.

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.

Chemical Fuel Mediated Self-Regulatory Polymer Brushes for Autonomous Fluorescence Modulator and Wettability Switcher

Synthetic systems of non-equilibrium self-assembly have made considerable progress, however, the achievement of innovative materials with self-regulated functions analogous to living systems remains a grand challenge. Herein, we report a versatile non-equilibrium system of polymer brushes with spatiotemporally programmable properties and functions driven by chemical fuels. By combining a responsive polymer with an autonomous pH regulator, the polymer brushes self-regulate their swelling and deswelling process with tunable lifetimes. By using patterned copolymer brushes with pH-responsive fluorescence moiety, we create an autonomous fluorescence modulator that self-regulates its fluorescence in spatiotemporally programmable fashion driven by a chemical or an enzymatic reaction. Furthermore, we implement a self-regulated wettability switcher of polymer brushes both in air and in an aqueous solution. The methodology and results in this work provide a useful avenue into the exploration of non-equilibrium synthetic materials with programmable functions and would accelerate the transformative developments of non-equilibrium materials and systems in practical applications. This article is protected by copyright. All rights reserved.

Dissipative control of the fluorescence of a 1,3-dipyrenyl calix[4]arene in the cone conformation

The temporal control (ON/OFF/ON) of the fluorescence of a dichloromethane/acetonitrile 1 : 1 solution of calixarene 3 decorated with two pyrenyl moieties at the upper rim is attained by the addition of CCl₃CO₂H used as a convenient chemical fuel.

Spontaneous Reorganization of DNA-Based Polymers in Higher Ordered Structures Fueled by RNA

We demonstrate a strategy that allows for the spontaneous reconfiguration of self-assembled DNA polymers exploiting RNA as chemical fuel. To do this, we have rationally designed orthogonally addressable DNA building blocks that can be transiently deactivated by RNA fuels and subtracted temporarily from participation in the self-assembly process. Through a fine modulation of the rate at which the building blocks are reactivated we can carefully control the final composition of the polymer and convert a disordered polymer in a higher order polymer, which is disfavored from a thermodynamic point of view. We measure the dynamic reconfiguration via fluorescent signals and confocal microscopy, and we derive a kinetic model that captures the experimental results. Our approach suggests a novel route toward the development of biomolecular materials in which engineered chemical reactions support the autonomous spatial reorganization of multiple components.

Self-resetting molecular probes for nucleic acids detection enabled by fuel dissipative systems

A once-in-a-century global public health crisis, the COVID-19 pandemic has damaged human health and world economy greatly. To help combat the virus, we report a self-resetting molecular probe capable of repeatedly detecting SARS-CoV-2 RNA, developed by orchestrating a fuel dissipative system via DNA nanotechnology. A set of simulation toolkits was utilized to design the probe, permitting highly consistent signal amplitudes across cyclic detections. Uniquely, full width at half maximum regulated by dissipative kinetics exhibits a fingerprint signal suitable for high confidential identifications of single-nucleotide variants. Further examination on multiple human-infectious RNA viruses, including ZIKV, MERS-CoV, and SARS-CoV, demonstrates the generic detection capability and superior orthogonality of the probe. It also correctly classified all the clinical samples from 55 COVID-19 patients and 55 controls. Greatly enhancing the screening capability for COVID-19 and other infectious diseases, this probe could help with disease control and build a broader global public health agenda.

Transient Dissipative Optical Properties of Aggregated Au Nanoparticles, CdSe/ZnS Quantum Dots, and Supramolecular Nucleic Acid-Stabilized Ag Nanoclusters

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 L₁/T₁, 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 L₁', the duplex L₁/T₁ is separated, leading to the release of T₁ and the formation of duplex L₁/L₁'. The released T₁ leads to aggregation of the Au NPs or to the T₁-induced G-quadruplex bridged aggregated CdSe/ZnS QDs. Biocatalytic nicking of the L₁/L₁' duplex fragments L₁' and the released L₁ displaces T₁ 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.

Dissipative operation of pH-responsive DNA-based nanodevices

We demonstrate here the use of 2-(4-chlorophenyl)-2-cyanopropanoic acid (CPA) and nitroacetic acid (NAA) as convenient chemical fuels to drive the dissipative operation of DNA-based nanodevices. Addition of either of the fuel acids to a water solution initially causes a rapid transient pH decrease, which is then followed by a slower pH increase. We have employed such low-to-high pH cycles to control in a dissipative way the operation of two model DNA-based nanodevices: a DNA nanoswitch undergoing time-programmable open–close–open cycles of motion, and a DNA-based receptor able to release-uptake a DNA cargo strand. The kinetics of the transient operation of both systems can be easily modulated by varying the concentration of the acid fuel added to the solution and both acid fuels show an efficient reversibility which further supports their versatility.

We demonstrate here the use of 2-(4-chlorophenyl)-2-cyanopropanoic acid (CPA) and nitroacetic acid (NAA) as convenient chemical fuels to drive the dissipative operation of DNA-based nanodevices.

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 Pb²⁺-ion-dependent DNAzyme fuel strand-driven network leading to the transient cleavage of the fuel strand to “waste” products. Applying the Pb²⁺-ion-dependent DNAzyme to two competitive fuel strand-driven systems yields two parallel operating networks. Blocking the competitively operating networks with selective inhibitors leads, however, to gated transient operation of dictated networks, yielding gated catalytic operations. A second system introduces a “non-waste” generating out-of-equilibrium, dissipative network driven by light. The system consists of a trans-azobenzene-functionalized photoactive module that is reconfigured by light to an intermediary state consisting of cis-azobenzene units that are thermally recovered to the original trans-azobenzene-modified module. The cyclic transient photoinduced operation of the device is demonstrated. The kinetic simulation of the systems allows the prediction of the transient behavior of the networks under different auxiliary conditions.

Functional DNA modules are triggered in the presence of appropriate inhibitors to yield transient gated catalytic functions, and a photoresponsive DNA module leads to “waste-free” operation of transient, dissipative dynamic transitions.

A dissipative pathway for the structural evolution of DNA fibres

Biochemical networks interconnect, grow and evolve to express new properties as different chemical pathways are selected during a continuous cycle of energy consumption and transformation. In contrast, synthetic systems that push away from equilibrium usually return to the same self-assembled state, often generating waste that limits system recyclability and prevents the formation of adaptable networks. Here we show that annealing by slow proton dissipation selects for otherwise inaccessible morphologies of fibres built from DNA and cyanuric acid. Using single-molecule fluorescence microscopy, we observe that proton dissipation influences the growth mechanism of supramolecular polymerization, healing gaps within fibres and converting highly branched, interwoven networks into nanocable superstructures. Just as the growth kinetics of natural fibres determine their structural attributes to modulate function, our system of photoacid-enabled depolymerization and repolymerization selects for healed materials to yield organized, robust fibres. Our method provides a chemical route for error-checking, distinct from thermal annealing, that improves the morphologies and properties of supramolecular materials using out-of-equilibrium systems.

Gated Dissipative Dynamic Artificial Photosynthetic Model Systems

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 (V²⁺)-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/V²⁺ 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.

Time-gated fluorescence signalling under dissipative conditions

Precise control over specific functions in the time domain is ubiquitous in biological systems. Here, we demonstrate time-gated fluorescence signalling under dissipative conditions exploiting an ATP-fueled self-assembly process. A temporal ATP-concentration gradient allows the system to pass through three states, among which only the intermediate state generates a fluorescent signal from a hydrophobic dye entrapped in the assemblies. The system can be reactivated by adding a new batch of ATP. The results indicate a strategy to rationally programme the temporal emergence of functions in complex chemical systems.

Active Bicomponent Nanoparticle Assembly with Temporal, Microstructural, and Functional Control

Transient supramolecular self-assembly has evolved as a tool to create temporally programmable smart materials. Yet, so far single-component self-assembly has been mostly explored. In contrast, multicomponent self-assembly provides an opportunity to create unique nanostructures exhibiting complex functional outcomes, newer and different than individual components. Even two-component can result in multiple organizations, such as self-sorted domains or co-assembled heterostructures, can occur, thus making it highly complex to predict and reversibly modulate these microstructures. In this study, we attempted to create active bicomponent nanoparticle assemblies of orthogonally pH-responsive-group-functionalized gold and cadmium selenide nanoparticles with temporal microstructural control on their composition (self-sorted or co-assembly) in order to harvest their emergent transient photocatalytic activity by coupling to temporal changes in pH. Moving towards multicomponent systems can deliver next level control in terms of structural and functional outcomes of supramolecular systems.

Synthesis of Complex Molecular Systems-The Foreseen Role of Organic Chemists

How to control the self-assembly of complex molecular systems is unknown. Yet, these complex molecular systems are fundamental for advances in material and biomedical sciences. A step forward is to transform one-step self-assembly into multistep synthesis involving covalent and noncovalent reactions. Key to this approach is to explore the chemical space at the frontiers of advanced covalent synthesis and supramolecular chemistry. Herein, we describe a selection of such reported cases and provide a guide for current limitations and insights for future directions. This outlook is meant to trigger collaborations between synthetic organic and supramolecular chemists, to expand the repertoire of organic syntheses working with supramolecular assemblies and thereby join forces to achieve stepwise emergence of molecular complexity in supramolecular systems.

Chemical-Fuel-Driven Assembly in Macromolecular Science: Recent Advances and Challenges

In the past decade, chemical-fuel-driven processes have been integrated with synthetic self-assembled systems, in which both the formation and properties can be carefully controlled. This strategy can drive systems far away from equilibrium, tailor the lifetime window of transient self-assembled systems, thus holding promise for future smart, adaptive, self-regulated, and life-like systems. By judging whether the building blocks or transient self-assembled systems participate in the fuel-to-waste conversion, the reported systems can be divided into two classes: dissipative self-assembly and self-assembly under dissipative conditions. Among these systems, the utilization of macromolecular building blocks to design non-equilibrium self-assemblied systems is becoming common. Macromolecular systems capable of dissipating energy with a programmed time domain have found widespread application, and have therefore been an active field of scientific inquiry. This Minireview aims to highlight the recent progress and opportunities of chemical-fuel-driven assembly in macromolecules. We envision that chemical-fuel-driven approach will play an increasingly important role in polymer science in the near future.

Scalable One-Pot-Liquid-Phase Oligonucleotide Synthesis for Model Network Hydrogels

Solid-phase oligonucleotide synthesis (SPOS) based on phosphoramidite chemistry is currently the most widespread technique for DNA and RNA synthesis but suffers from scalability limitations and high reagent consumption. Liquid-phase oligonucleotide synthesis (LPOS) uses soluble polymer supports and has the potential of being scalable. However, at present, LPOS requires 3 separate reaction steps and 4-5 precipitation steps per nucleotide addition. Moreover, long acid exposure times during the deprotection step degrade sequences with high A content (adenine) due to depurination and chain cleavage. In this work, we present the first one-pot liquid-phase DNA synthesis technique which allows the addition of one nucleotide in a one-pot reaction of sequential coupling, oxidation, and deprotection followed by a single precipitation step. Furthermore, we demonstrate how to suppress depurination during the addition of adenine nucleotides. We showcase the potential of this technique to prepare high-purity 4-arm PEG-T20 (T = thymine) and 4-arm PEG-A20 building blocks in multigram scale. Such complementary 4-arm PEG-DNA building blocks reversibly self-assemble into supramolecular model network hydrogels and facilitate the elucidation of bond lifetimes. These model network hydrogels exhibit new levels of mechanical properties (storage modulus, bond lifetimes) in DNA bonds at room temperature (melting at 44 °C) and thus open up pathways to next-generation DNA materials programmable through sequence recognition and available for macroscale applications.

Four-Dimensional Deoxyribonucleic Acid-Gold Nanoparticle Assemblies

Organization of gold nanoobjects by oligonucleotides has resulted in many three-dimensional colloidal assemblies with diverse size, shape, and complexity; nonetheless, autonomous and temporal control during formation remains challenging. In contrast, living systems temporally and spatially self-regulate formation of functional structures by internally orchestrating assembly and disassembly kinetics of dissipative biomacromolecular networks. We present a novel approach for fabricating four-dimensional gold nanostructures by adding an additional dimension: time. The dissipative character of our system is achieved using exonuclease III digestion of deoxyribonucleic acid (DNA) fuel as an energy-dissipating pathway. Temporal control over amorphous clusters composed of spherical gold nanoparticles (AuNPs) and well-defined core-satellite structures from gold nanorods (AuNRs) and AuNPs is demonstrated. Furthermore, the high specificity of DNA hybridization allowed us to demonstrate selective activation of the evolution of multiple architectures of higher complexity in a single mixture containing small and larger spherical AuNPs and AuNRs.

ATP-powered molecular recognition to engineer transient multivalency and self-sorting 4D hierarchical systems

Biological systems organize multiple hierarchical structures in parallel, and create dynamic assemblies and functions by energy dissipation. In contrast, emerging artificial non-equilibrium self-assembling systems have remained relatively simplistic concerning hierarchical design, and non-equilibrium multi-component systems are uncharted territory. Here we report a modular DNA toolbox allowing to program transient non-equilibrium multicomponent systems across hierarchical length scales by introducing chemically fueled molecular recognition orchestrated by reaction networks of concurrent ATP-powered ligation and cleavage of freely programmable DNA building blocks. Going across hierarchical levels, we demonstrate transient side-chain functionalized nucleic acid polymers, and further introduce the concept of transient cooperative multivalency as a key to bridge length scales to pioneer fuel-driven encapsulation, self-assembly of colloids, and non-equilibrium transient narcissistic colloidal self-sorting on a systems level. The fully programmable and functionalizable DNA components pave the way to design chemically fueled 4D (3 space, 1 time) molecular multicomponent systems and autonomous materials.

Controlling the liberation rate of the in situ release of a chemical fuel for the operationally autonomous motions of molecular machines

Second-order rate constants of the aminolysis of 2-cyano-2-phenylpropanoic anhydride 3 by a series of N-methylanilines differently substituted in the aromatic moiety (4a-d) were measured in dichloromethane. The common reaction product of aminolysis is 2-cyano-2-phenylpropanoic acid 1, which is known to be an effective fuel for acid-base driven molecular machines, but cannot be used in molar excess with respect to the machine. The motivation behind the kinetic study has been the prospect of using the aminolysis of 3 to supply the machine with fuel at a rate that is never so high as to overfeed the system, thus avoiding the malfunction of the machine with concomitant waste of fuel. Knowledge of the kinetic parameters dictated the choice of 4c as the best nucleophile in the lot for feeding acid 1 into a catenane-based molecular machine at a rate that ensured a correct operation.

Allosteric Regulation of DNAzyme Activities through Intrastrand Transformation Induced by Cu(II)-Mediated Artificial Base Pairing

Allosteric regulation is gaining increasing attention as a basis for the production of stimuli-responsive materials in many research areas including DNA nanotechnology. We expected that metal-mediated artificial base pairs, consisting of ligand-type nucleotides and a bridging metal ion, could serve as allosteric units that regulate the function of DNA molecules. In this study, we established a rational design strategy for developing Cu^II-responsive allosteric DNAzymes by incorporating artificial hydroxypyridone ligand-type nucleotides (H) that form a Cu^II-mediated base pair (H-Cu^II-H). We devised a new enzymatic method using a standard DNA polymerase and a ligase to prepare DNA strands containing H nucleotides. Previously reported DNAzymes were modified by introducing a H-H pair into the stem region, and the stem-loop sequences were altered so that the structure becomes catalytically inactive in the absence of Cu^II ions. The formation of a H-Cu^II-H base pair triggers intrastrand transformation from the inactive to the active structure, enabling allosteric regulation of the DNAzyme activity in response to Cu^II ions. The activity of the H-modified DNAzyme was reversibly switched by the addition and removal of Cu^II ions under isothermal conditions. Similarly, by incorporating a H-Cu^II-H pair into an in vitro-selected Ag^I-dependent DNAzyme, we have developed a DNAzyme that exhibits an AND logic-gate response to Cu^II and Ag^I ions. The rational design strategy and the easy enzymatic synthetic method presented here provide a versatile way to develop a variety of metal-responsive allosteric DNA materials, including molecular machines and logic circuits, based on metal-mediated artificial base pairing.

Sound-driven dissipative self-assembly of aromatic biomolecules into functional nanoparticles

Dissipative self-assembly processes were recently exploited to assemble synthetic materials into supramolecular structures. In most cases, chemical fuel or light driven self-assembly of synthetic molecules was reported. Herein, experimental and computational approaches were used to unveil the role of acoustic cavitation in the formation of supramolecular nanoaggregates by dissipative self-assembly. Acoustic cavitation bubbles were employed as an energy source and a transient interface to fuel and refuel the dissipative self-assembly of simple aromatic biomolecules into uniform nanoparticles. Molecular dynamics simulations were applied to predict the formation of metastable aggregates and the dynamic exchange of the interacting molecules in the nanoaggregates. The intracellular trafficking and dissipative dissolution of the nanoparticles were tracked by microscopy imaging.

Structure-Property Effects in the Generation of Transient Aqueous Benzoic Acid Anhydrides by Carbodiimide Fuels

The design of dissipative systems, which operate out-of-equilibrium by consuming chemical fuels, is challenging. As yet, there are a few examples of privileged fuel chemistries that can be broadly applied in abiotic systems in the same way that ATP hydrolysis is exploited throughout biochemistry. The key issue is that designing nonequilibrium systems is inherently about balancing the relative rates of coupled reactions. The use of carbodiimides as fuels to generate transient aqueous carboxylic anhydrides has recently been used in examples of new nonequilibrium materials and supramolecular assemblies. Here, we explore the kinetics of formation and decomposition of a series of benzoic anhydrides generated from the corresponding acids and EDC under typical conditions (EDC = N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide hydrochloride). The reactions can be described by a simple mechanism that merges known behavior for the two processes independently. Structure-property effects in these systems are dominated by differences in the anhydride decomposition rate. The kinetic parameters allow trends in concentration-dependent properties to be simulated, such as reaction lifetimes, peak anhydride concentrations, and yields. For key properties, there are diminishing returns with the addition of increasing amounts of fuel. These results should provide useful guidelines for the design of functional systems making use of this chemistry.