Pathway Complexity in Fuel-Driven DNA Nanostructures with Autonomous Reconfiguration of Multiple Dynamic Steady States

Complex Pathways Drive Pluripotent Fmoc-Leucine Self-Assemblies

Nature uses complex self-assembly pathways to access distinct functional non-equilibrium self-assemblies. This remarkable ability to steer same set of biomolecules into different self-assembly states is done by avoiding thermodynamic pit. In synthetic systems, on demand control over 'Pathway Complexity' to access self-assemblies different from equilibrium structures remains challenging. Here we show versatile non-equilibrium assemblies of the same monomer via alternate assembly pathways. The assemblies nucleate using non-classical or classical nucleation routes into distinct metastable (transient hydrogels), kinetic (stable hydrogels) and thermodynamic structures [(poly)-crystals and 2D sheets]. Initial chemical and thermal inputs force the monomers to follow different assembly pathways and form soft-materials with distinct molecular arrangements than at equilibrium. In many cases, equilibrium structures act as thermodynamic sink which consume monomers from metastable structures giving transiently formed materials. This dynamics can be tuned chemically or thermally to slow down the dissolution of transient hydrogel, or skip the intermediate hydrogel altogether to reach final equilibrium assemblies. If required this metastable state can be kinetically trapped to give strong hydrogel stable over days. This method to control different self-assembly states can find potential use in similar biomimetic systems to access new materials for various applications.

Enzyme-Programmed Self-Assembly of Nanoparticles

Nanoparticles are a hot topic in the field of nanomaterial research due to their excellent physical and chemical properties. In recent years, DNA-directed nanoparticle self-assembly technology has been widely applied to the development of numerous complex nanoparticle superstructures. Due to the inherent stability and surface electric repulsion of nanoparticles, it is difficult to make nanoparticle superstructures respond to molecular signals in the external environment. In fact, enzyme-programmed molecular systems are developed to allow diverse functions, including logical operations, signal amplification, and dynamic assembly control. Therefore, combining enzyme-controlled DNA systems may endow nanoparticle assembly systems with more flexibility in program design, allowing them to respond to a variety of external signals. In this review, we summarize the basic principles of enzyme-controlled DNA/nanoparticle self-assembly and introduce its applications in heavy metal detection, gene expression, proteins inside living cells, cancer cell therapy, and drug delivery. With the continuous development of new nanoparticle materials and the increasing functionality of enzyme DNA circuits, enzyme-directed DNA/nanoparticle self-assembled probe technology is expected to see significant future development.

Synthetic molecular switches driven by DNA-modifying enzymes

Taking inspiration from natural systems, in which molecular switches are ubiquitous in the biochemistry regulatory network, we aim to design and construct synthetic molecular switches driven by DNA-modifying enzymes, such as DNA polymerase and nicking endonuclease. The enzymatic treatments on our synthetic DNA constructs controllably switch ON or OFF the sticky end cohesion and in turn cascade to the structural association or disassociation. Here we showcase the concept in multiple DNA nanostructure systems with robust assembly/disassembly performance. The switch mechanisms are first illustrated in minimalist systems with a few DNA strands. Then the ON/OFF switches are realized in complex DNA lattice and origami systems with designated morphological changes responsive to the specific enzymatic treatments.

Dynamic monitoring of an enzymatically driven dissipative toehold-mediated strand displacement reaction

A general strategy to program self-resettable and dissipative toehold-mediated strand displacement reactions was proposed, using DNA strands as the fuel and lambda exonuclease as the fuel-consuming unit. This non-equilibrium system is reversible and temporally controllable. Furthermore, it can be well integrated into a DNA network to temporally control its cascade reaction or dynamic behaviour.

Dynamic supramolecular hydrogels mediated by chemical reactions

Supramolecular self-assembly in a biological system is usually dominated by sophisticated metabolic processes (chemical reactions) such as catalysis of enzymes and consumption of high energy chemicals, leading to groups of biomolecules with unique dynamics and functions in an aqueous environment. In recent years, increasing efforts have been made to couple chemical reactions to molecular self-assembly, with the aim of creating supramolecular materials with lifelike properties and functions. In this feature article, after summarising the work of chemical reaction mediated supramolecular hydrogels, we first focus on a typical example where dynamic self-assembly of molecular hydrogels is activated by in situ formation of a hydrazone bond in water. We discuss how the formation of the hydrazone-based supramolecular hydrogels can be controlled in time and space. After that, we describe transient assembly of supramolecular hydrogels powered by out-of-equilibrium chemical reaction networks regulated by chemical fuels, which show unique properties such as finite lifetime, dynamic structures, and regenerative capabilities. Finally, we provide a perspective on the future investigations that need to be done urgently, which range from fundamental research to real-life applications of dynamic supramolecular hydrogels.

Transient co-assemblies of micron-scale colloids regulated by ATP-fueled reaction networks

Self-assembly of colloidal particles offers an attractive bottom-up approach to functional materials. Current design strategies for colloidal assemblies are mostly based on thermodynamically controlled principles and lack autonomous behavior. The next advance in the properties of colloidal assemblies will come from coupling these structures to out-of-equilibrium chemical reaction networks furnishing them with autonomous and dynamic behavior. This, however, constitutes a major challenge of carefully modulating the interparticle potentials on a temporal circuit program and avoiding kinetic trapping and irreversible aggregation. Herein, we report the coupling of a fuel-driven DNA-based enzymatic reaction network (ERN) to micron-sized colloidal particles to achieve their transient co-assembly. The ERN operating on the molecular level transiently releases an Output strand which links two DNA functionalized microgel particles together into co-assemblies with a programmable assembly lifetime. The system generates minimal waste and recovers all components of the ERN after the consumption of the ATP fuel. The system can be reactivated by addition of new fuel as shown for up to three cycles. The design can be applied to organize other building blocks into hierarchical structures and materials with advanced biomimetic properties.

Pathway complexity in fibre assembly: from liquid crystals to hyper-helical gelmorphs

Pathway complexity results in unique materials from the same components according to the assembly conditions. Here a chiral acyl-semicarbazide gelator forms three different gels of contrasting fibre morphology (termed 'gelmorphs') as well as lyotropic liquid crystalline droplets depending on the assembly pathway. The gels have morphologies that are either hyperhelical (HH-Gel), tape-fibre (TF-Gel) or thin fibril derived from the liquid crystalline phase (LC-Gels) and exhibit very different rheological properties. The gelator exists as three slowly interconverting conformers in solution. All three gels are comprised of an unsymmetrical, intramolecular hydrogen bonded conformer. The kinetics show that formation of the remarkable HH-Gel is cooperative and is postulated to involve association of the growing fibril with a non-gelling conformer. This single molecule dynamic conformational library shows how very different materials with different morphology and hence very contrasting materials properties can arise from pathway complexity as a result of emergent interactions during the assembly process.

Timed Pulses in DNA Strand Displacement Reactions

Inspired by naturally occurring regulatory mechanisms that allow complex temporal pulse features with programmable delays, we demonstrate here a strategy to achieve temporally programmed pulse output signals in DNA-based strand displacement reactions (SDRs). To achieve this, we rationally designed input strands that, once bound to their target duplex, can be gradually degraded, resulting in a pulse output signal. We also designed blocker strands that suppress strand displacement and determine the time at which the pulse reaction is generated. We show that by controlling the degradation rate of blocker and input strands, we can finely control the delayed pulse output over a range of 10 h. We also prove that it is possible to orthogonally delay two different pulse reactions in the same solution by taking advantage of the specificity of the degradation reactions for the input and blocker strands. Finally, we show here two possible applications of such delayed pulse SDRs: the time-programmed pulse decoration of DNA nanostructures and the sequentially appearing and self-erasing formation of DNA-based patterns.

Alternate Strategies to Induce Dynamically Modulated Transient Transcription Machineries

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.

Mechanics of dynamic and deformable DNA nanostructures

In DNA nanotechnology, DNA molecules are designed, engineered, and assembled into arbitrary-shaped architectures with predesigned functions. Static DNA assemblies often have delicate designs with structural rigidity to overcome thermal fluctuations. Dynamic structures reconfigure in response to external cues, which have been explored to create functional nanodevices for environmental sensing and other applications. However, the precise control of reconfiguration dynamics has been a challenge due partly to flexible single-stranded DNA connections between moving parts. Deformable structures are special dynamic constructs with deformation on double-stranded parts and single-stranded hinges during transformation. These structures often have better control in programmed deformation. However, related deformability and mechanics including transformation mechanisms are not well understood or documented. In this review, we summarize the development of dynamic and deformable DNA nanostructures from a mechanical perspective. We present deformation mechanisms such as single-stranded DNA hinges with lock-and-release pairs, jack edges, helicity modulation, and external loading. Theoretical and computational models are discussed for understanding their associated deformations and mechanics. We elucidate the pros and cons of each model and recommend design processes based on the models. The design guidelines should be useful for those who have limited knowledge in mechanics as well as expert DNA designers.

Modulating the Lifetime of DNA Motifs Using Visible Light and Small Molecules

Here we regulate the formation of dissipative assemblies built from DNA using a merocyanine photoacid that responds to visible light. The operation of our system and the relative distribution of species within it are controlled by irradiation time, initial pH value, and the concentration of a small-molecule binder that inhibits the reaction cycle. This approach is modular, does not require DNA modification, and can be used for several DNA sequences and lengths. Our system design allows for waste-free control of dissipative DNA nanotechnology, toward the generation of nonequilibrium, life-like nanodevices.

Communication and Cross-Regulation between Chemically Fueled Sender and Receiver Reaction Networks

Nature connects multiple fuel-driven chemical/enzymatic reaction networks (CRNs/ERNs) via cross-regulation to hierarchically control biofunctions for a tailored adaption in complex sensory landscapes. Herein, we introduce a facile example of communication and cross-regulation among two fuel-driven DNA-based ERNs regulated by a concatenated RNA transcription regulator. ERN1 ("sender") is designed for the fuel-driven promoter formation for T7 RNA polymerase, which activates RNA transcription. The produced RNA can deactivate or activate DNA in ERN2 ("receiver") by toehold-mediated strand displacement, leading to a communication between two ERNs. The RNA from ERN1 can repress or promote the fuel-driven state of ERN2; ERN2 in turn feedbacks to regulate the lifetime of ERN1. Furthermore, the incorporation of RNase H allows for RNA degradation and enables the autonomous recovery of ERN2. We believe that concatenation of multiple CRNs/ERNs provides a basis for the design of more elaborate autonomous regulatory mechanisms in systems chemistry and synthetic biology.

Regulating DNA-Hybridization Using a Chemically Fueled Reaction Cycle

Molecular machines, such as ATPases or motor proteins, couple the catalysis of a chemical reaction, most commonly hydrolysis of nucleotide triphosphates, to their conformational change. In essence, they continuously convert a chemical fuel to drive their motion. An outstanding goal of nanotechnology remains to synthesize a nanomachine with similar functions, precision, and speed. The field of DNA nanotechnology has given rise to the engineering precision required for such a device. Simultaneously, the field of systems chemistry developed fast chemical reaction cycles that convert fuel to change the function of molecules. In this work, we thus combined a chemical reaction cycle with the precision of DNA nanotechnology to yield kinetic control over the conformational state of a DNA hairpin. Future work on such systems will result in out-of-equilibrium DNA nanodevices with precise functions.

Density-tunable pathway complexity in a minimalistic self-assembly model

An open challenge in self-assembly is learning how to design systems that can be conditionally guided towards different target structures depending on externally-controlled conditions. Using a theoretical and numerical approach, here we discuss a minimalistic self-assembly model that can be steered towards different types of ordered constructs at the equilibrium by solely tuning a facile selection parameter, namely the density of building blocks. Metadynamics and Langevin dynamics simulations allow us to explore the behavior of the system in and out of equilibrium conditions. We show that the density-driven tunability is encoded in the pathway complexity of the system, and specifically in the competition between two different main self-assembly routes. A comprehensive set of simulations provides insight into key factors allowing to make one self-assembling pathway prevailing on the other (or vice versa), determining the selection of the final self-assembled products. We formulate and validate a practical criterion for checking whether a specific molecular design is predisposed for such density-driven tunability of the products, thus offering a new, broader perspective to realize and harness this facile extrinsic control of conditional self-assembly.

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.

Dissipative self-assembly of a proline catalyst for temporal regulation of the aldol reaction

The spatiotemporal regulation of chemical reactivity in biological systems permits a network of metabolic reactions to take place within the same cellular environment. The exquisite control of reactivity is often mediated by out-of-equilibrium structures that remain functional only as long as fuel is present to maintain the higher energy, active state. An important goal in supramolecular chemistry aims to develop functional, energy dissipating systems that approach the sophistication of biological machinery. The challenge is to create strategies that couple the energy consumption needed to promote a molecule to a higher energy, assembled state to a functional property such as catalytic activity. In this work, we demonstrated that the assembly of a spiropyran (SP) dipeptide (1) transiently promoted the proline-catalyzed aldol reaction in water when visible light was present as fuel. The transient catalytic activity emerged from 1 under light illumination due to the photoisomerization of the monomeric, O-protonated (1-MCH⁺) merocyanine form to the spiropyran (1-SP) state, which rapidly assembled into nanosheets capable of catalyzing the aldol reaction in water. When the light source was removed, thermal isomerization to the more stable MCH⁺ form caused the nanosheets to dissociate into a catalytically inactive, monomeric state. Under these conditions, the aldol reaction could be repeatedly activated and deactivated by switching the light source on and off.

Hierarchically supramolecular polymerization of anthraquinone dye to chiral aggregates via 2D-monolayered nanosheets: the unanticipated role of pathway complexity

An anthraquinone dye underwent supramolecular polymerization, affording 2D-monolayered nanosheets in a kinetically controlled state. The nanosheets then transformed into hierarchically chiral aggregates in a thermodynamically controlled step. The unanticipated role played by pathway complexity was clearly unravelled in this work, highlighting the diversified pathways in the supramolecular polymerization of various building blocks.

Design, Mechanical Properties, and Dynamics of Synthetic DNA Filaments

Over the past 40 years, structural and dynamic DNA nanotechnologies have undoubtedly demonstrated to be effective means for organizing matter at the nanoscale and reconfiguring equilibrium structures, in a predictable fashion and with an accuracy of a few nanometers. Recently, novel concepts and methodologies have been developed to integrate nonequilibrium dynamics into DNA nanostructures, opening the way to the construction of synthetic materials that can adapt to environmental changes and thus acquire new properties. In this Review, we summarize the strategies currently applied for the construction of synthetic DNA filaments and conclude by reporting some recent and most relevant examples of DNA filaments that can emulate typical structural and dynamic features of the cytoskeleton, such as compartmentalization in cell-like vesicles, support for active transport of cargos, sustained or transient growth, and responsiveness to external stimuli.

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 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.

Self-Regulating Colloidal Co-Assemblies That Accelerate Their Own Destruction via Chemo-Structural Feedback

Biological self‐assemblies self‐ and cross‐regulate each other via chemical reaction networks (CRNs) and feedback. Although artificial transient self‐assemblies have been realized via activation/deactivation CRNs, the transient structures themselves do mostly not engage in the CRN. We introduce a rational design approach for chemo‐structural feedback, and present a transient colloidal co‐assembly system, where the formed co‐assemblies accelerate their destruction autonomously. We achieve this by immobilizing enzymes of a deactivating acid‐producing enzymatic cascade on pH‐switchable microgels that can form co‐assemblies at high pH. Since the enzyme partners are immobilized on individual microgels, the co‐assembled state brings them close enough for enhanced acid generation. The amplified deactivator production (acid) leads to an almost two‐fold reduction in the lifetime of the transiently formed pH‐state. Our study thus introduces versatile mechanisms for chemo‐structural feedback.

Gated Transient Dissipative Dimerization of DNA Tetrahedra Nanostructures for Programmed DNAzymes Catalysis

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.

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.

Temporal Control of the Host-Guest Properties of a Calix[6]arene Receptor by the Use of a Chemical Fuel

The host–guest interaction of a 1,3,5-trisaminocalix[6]arene receptor with N-methylisoquinolinium trifluoromethanesulfonate (K_ass of 500 ± 30 M^–1 in CD₂Cl₂) can be dissipatively driven by means of 2-cyano-2-(4′-chloro)phenylpropanoic acid used as a convenient chemical fuel. When the fuel is added to a dichloromethane solution containing the above complex, the host is induced to immediately release the guest in the bulk solution. Consumption of the fuel allows the guest to be re-uptaken by the host. The operation can be satisfactorily reiterated with four subsequent additions of fuel, producing four successive release–reuptake cycles. The percentage of the guest temporarily released in the bulk solution by the host and the time required for the reuptake process can be finely regulated by varying the quantities of added fuel.

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.

Light-driven dissipative self-assembly of a peptide hydrogel

Light energy provides an attractive fuel source for energy dissipating systems because of the lack of waste production, wavelength tunability and the potential for spatial and temporal resolution. In this work, we describe a peptide-spiropyran conjugate that assembled into a transient nanofiber hydrogel in the presence of visible light, and dissociated when the light source was removed.

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.

Molecular communication relays for dynamic cross-regulation of self-sorting fibrillar self-assemblies

Structures in living systems cross-regulate via exchange of molecular information to assemble or disassemble on demand and in a coordinated, signal-triggered fashion. DNA strand displacement (DSD) reaction networks allow rational design of signaling and feedback loops, but combining DSD with structural nanotechnology to achieve self-reconfiguring hierarchical system states is still in its infancy. We introduce modular DSD networks with increasing amounts of regulatory functions, such as negative feedback, signal amplification, and signal thresholding, to cross-regulate the transient polymerization/depolymerization of two self-sorting DNA origami nanofibrils and nanotubes. This is achieved by concatenation of the DSD network with molecular information relays embedded on the origami tips. The two origamis exchange information and display programmable transient states observable by TEM and fluorescence spectroscopy. The programmability on the DSD and the origami level is a viable starting point toward more complex lifelike behavior of colloidal multicomponent systems featuring advanced signal processing functions.

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.

Autonomous DNA nanostructures instructed by hierarchically concatenated chemical reaction networks

Concatenation and communication between chemically distinct chemical reaction networks (CRNs) is an essential principle in biology for controlling dynamics of hierarchical structures. Here, to provide a model system for such biological systems, we demonstrate autonomous lifecycles of DNA nanotubes (DNTs) by two concatenated CRNs using different thermodynamic principles: (1) ATP-powered ligation/restriction of DNA components and (2) input strand-mediated DNA strand displacement (DSD) using energy gains provided in DNA toeholds. This allows to achieve hierarchical non-equilibrium systems by concurrent ATP-powered ligation-induced DSD for activating DNT self-assembly and restriction-induced backward DSD reactions for triggering DNT degradation. We introduce indirect and direct activation of DNT self-assemblies, and orthogonal molecular recognition allows ATP-fueled self-sorting of transient multicomponent DNTs. Coupling ATP dissipation to DNA nanostructures via programmable DSD is a generic concept which should be widely applicable to organize other DNA nanostructures, and enable the design of automatons and life-like systems of higher structural complexity.

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.

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.

Synthesis and characterization of chemically fueled supramolecular materials driven by carbodiimide-based fuels

Many supramolecular materials in biological systems are driven to a nonequilibrium state by the irreversible consumption of high-energy molecules such as ATP or GTP. As a result, they exhibit unique dynamic properties such as a tunable lifetime, adaptivity or the ability to self-heal. In contrast, synthetic counterparts that exist in or close to equilibrium are controlled by thermodynamic parameters and therefore lack these dynamic properties. To mimic biological materials more closely, synthetic self-assembling systems have been developed that are driven out of equilibrium by chemical reactions. This protocol describes the synthesis and characterization of such an assembly, which is driven by carbodiimide fuels. Depending on the amount of chemical fuel added to the material, its lifetime can be tuned. In the first step, the protocol details the synthesis and purification of the peptide-based precursors for the fuel-driven assemblies by solid-phase peptide synthesis. Then, we explain how to analyze the kinetic response of the precursors to a carbodiimide-based chemical fuel by HPLC and kinetic models. Finally, we detail how to study the emerging assembly's macro- and microscopic properties by time-lapse photography, UV-visible spectroscopy, shear rheology, confocal laser scanning microscopy and electron microscopy. The procedure is described using the example of a colloid-forming precursor Fmoc-E-OH and a fiber-forming precursor Fmoc-AAD-OH to emphasize the differences in characterization depending on the type of assembly. The characterization of a precursor's transient assembly can be done within 5 d. The synthesis and purification of a peptide precursor requires 2 d of work.

Autonomous Transient pH Flips Shaped by Layered Compartmentalization of Antagonistic Enzymatic Reactions

Transient signaling orchestrates complex spatiotemporal behaviour in living organisms via (bio)chemical reaction networks (CRNs). Compartmentalization of signal processing is an important aspect for controlling such networks. However, artificial CRNs mostly focus on homogeneous solutions to program autonomous self-assembling systems, which limits their accessible behaviour and tuneability. Here, we introduce layered compartments housing antagonistic pH-modulating enzymes and demonstrate that transient pH signals in a supernatant solution can be programmed based on spatial delays. This overcomes limitations of activity mismatches of antagonistic enzymes in solution and allows to flexibly program acidic and alkaline pH lifecycles beyond the possibilities of homogeneous solutions. Lag time, lifetime, and the pH minima and maxima can be precisely programmed by adjusting spatial and kinetic conditions. We integrate these spatially controlled pH flips with switchable peptides, furnishing time-programmed self-assemblies and hydrogel material system.

On the use of catalysis to bias reaction pathways in out-of-equilibrium systems

Catalysis is an essential function in living systems and provides a way to control complex reaction networks. In natural out-of-equilibrium chemical reaction networks (CRNs) driven by the consumption of chemical fuels, enzymes provide catalytic control over pathway kinetics, giving rise to complex functions. Catalytic regulation of man-made fuel-driven systems is far less common and mostly deals with enzyme catalysis instead of synthetic catalysts. Here, we show via simulations, illustrated by literature examples, how any catalyst can be incorporated in a non-equilibrium CRN and what their effect is on the behavior of the system. Alteration of the catalysts' concentrations in batch and flow gives rise to responses in maximum conversion, lifetime (i.e. product half-lives and t90 - time to recover 90% of the reactant) and steady states. In situ up or downregulation of catalysts' levels temporarily changes the product steady state, whereas feedback elements can give unusual concentration profiles as a function of time and self-regulation in a CRN. We show that simulations can be highly effective in predicting CRN behavior. In the future, shifting the focus from enzyme catalysis towards small molecule and metal catalysis in out-of-equilibrium systems can provide us with new reaction networks and enhance their application potential in synthetic materials, overall advancing the design of man-made responsive and interactive systems.

Supramolecular polymorphism in aggregates of a boron-difluoride complex of peri-naphthoindigo via solvent- and pathway-dependent self-assembly

Supramolecular polymorphism, a rare phenomenon, has been demonstrated using BF2-coordinated peri-naphthoindigo.

Programmable and Chemically Fueled DNA Coacervates by Transient Liquid-Liquid Phase Separation

Multivalency-driven liquid-liquid phase separation (LLPS) is essential in biomolecular condensates to facilitate spatiotemporal regulation of biological functions. Providing programmable model systems would help to better understand the LLPS processes in biology, and furnish new types of compartmentalized synthetic reaction crucibles that exploit biological principles. Herein, we demonstrate a concept for programming LLPS using transient multivalency between ATP-driven sequence-defined functionalized nucleic acid polymers (SfNAPs), which serve as simple models for membrane-less organelles. The ATP-driven SfNAPs are transiently formed by an enzymatic reaction network (ERN) of concurrent ATP-powered DNA ligation and DNA restriction. The lifetimes can be programmed by the ATP concentration, which manifests on the LLPS length scale in tunable lifetimes for the all-DNA coacervates. Critically, the prominent programmability of the DNA-based building blocks allows to encode distinct molecular recognitions for multiple multivalent systems, enabling sorted LLPS and thus multicomponent DNA coacervates, reminiscent of the diverse membraneless organelles in biological systems. The ATP-driven coacervates are capable for multivalent trapping of micron-scale colloids and biomolecules to generate functions as emphasized for rate enhancements in enzymatic cascades. This work supports ATP-driven multivalent coacervation as a valuable mechanism for dynamic multicomponent and function biomolecular condensate mimics and for autonomous materials design in general.

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.

Polymer Transformers: Interdigitating Reaction Networks of Fueled Monomer Species to Reconfigure Functional Polymer States

Adaptivity is an essential trait of life. One type of adaptivity is the reconfiguration of a functional system states by correlating sensory inputs. We report polymer transformers, which can adaptively reconfigure their composition from a state of a mixed copolymer to being enriched in either monomer A or B. This is achieved by embedding and hierarchically interconnecting two chemically fueled activation/deactivation enzymatic reaction networks for both monomers via a joint activation pathway (network level) and an AB linker monomer reactive to both A and B (species level). The ratio of enzymes governing the individual deactivation pathways (our external signals) control the enrichment behavior in the dynamic state. The method shows high programmability of the reconfigured state, rejuvenation of transformation cycles, and quick in situ adaptation. As a proof-of-concept, we showcase this dynamic reconfiguration for colloidal surface functionalities.

ATP-Responsive and ATP-Fueled Self-Assembling Systems and Materials

Adenosine triphosphate (ATP) is a central metabolite that plays an indispensable role in various cellular processes, from energy supply to cell-to-cell signaling. Nature has developed sophisticated strategies to use the energy stored in ATP for many metabolic and non-equilibrium processes, and to sense and bind ATP for biological signaling. The variations in the ATP concentrations from one organelle to another, from extracellular to intracellular environments, and from normal cells to cancer cells are one motivation for designing ATP-triggered and ATP-fueled systems and materials, because they show great potential for applications in biological systems by using ATP as a trigger or chemical fuel. Over the last decade, ATP has been emerging as an attractive co-assembling component for man-made stimuli-responsive as well as for fuel-driven active systems and materials. Herein, current advances and emerging concepts for ATP-triggered and ATP-fueled self-assemblies and materials are discussed, shedding light on applications and highlighting future developments. By bringing together concepts of different domains, that is from supramolecular chemistry to DNA nanoscience, from equilibrium to non-equilibrium self-assembly, and from fundamental sciences to applications, the aim is to cross-fertilize current approaches with the ultimate aim to bring synthetic ATP-dependent systems closer to living systems.

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.