Threshold sensing through a synthetic enzymatic reaction-diffusion network

Exploring Emergent Properties in Enzymatic Reaction Networks: Design and Control of Dynamic Functional Systems

The intricate and complex features of enzymatic reaction networks (ERNs) play a key role in the emergence and sustenance of life. Constructing such networks in vitro enables stepwise build up in complexity and introduces the opportunity to control enzymatic activity using physicochemical stimuli. Rational design and modulation of network motifs enable the engineering of artificial systems with emergent functionalities. Such functional systems are useful for a variety of reasons such as creating new-to-nature dynamic materials, producing value-added chemicals, constructing metabolic modules for synthetic cells, and even enabling molecular computation. In this review, we offer insights into the chemical characteristics of ERNs while also delving into their potential applications and associated challenges.

Regulating Spatial Localization and Reactivity Biasness of DNAzymes by Metal Ions and Oligonucleotides

Chemical gradient sensing behavior of catalytically active colloids and enzymes is an area of immense interest owing to their importance in understanding fundamental spatiotemporal complexity pattern in living systems and designing of dynamic materials. Herein, we have shown peroxidase activity of DNAzyme (G-quadruplex-hemin complex tagged in a micron-sized glass bead) can be modulated by metal ions and metal ion-binding oligonucleotides. Next we demonstrated both experimentally and theoretically that the localization and product formation ability of the DNAzyme containing particle remains biased to the more catalytically active zone where concentration of metal ion (Hg2+) inhibitor is low. Interestingly, this biased localization can be broken by introduction of Hg2+ binding oligonucleotide in the system. Additionally, macroscopically asymmetric catalytic product distributed zone has also been achieved on this process, showing possibility in regulation in autonomous spatially controlled chemical process. This demonstration of autonomous modulation of the localization pattern and spatially specific enhanced product forming ability of DNAzymes will further enable in designing of responsive nucleic acid-based motile materials and surfaces.

Spatiotemporal Regulation of Hydrogel Actuators by Autocatalytic Reaction Networks

Regulating hydrogel actuators with chemical reaction networks is instrumental for constructing life-inspired smart materials. Herein, hydrogel actuators are engineered that are regulated by the autocatalytic front of thiols. The actuators consist of two layers. The first layer, which is regular polyacrylamide hydrogel, is in a strained conformation. The second layer, which is polyacrylamide hydrogel with disulfide crosslinks, maintains strain in the first layer. When thiols released by the autocatalytic front reduce disulfide crosslinks, the hydrogel actuates by releasing the mechanical strain in the first layer. The autocatalytic front is sustained by the reaction network, which uses thiouronium salts, disulfides of β-aminothiols, and maleimide as starting components. The gradual actuation by the autocatalytic front enables movements such as gradual unrolling, screwing, and sequential closing of "fingers." This actuation also allows the transmission of chemical signals in a relay fashion and the conversion of a chemical signal to an electrical signal. Locations and times of spontaneous initiation of autocatalytic fronts can be preprogrammed in the spatial distribution of the reactants in the hydrogel. To approach the functionality of living matter, the actuators triggered by an autocatalytic front can be integrated into smart materials regulated by chemical circuits.

Thylakoid Membrane-Inspired Capsules with Fortified Cofactor Shuttling for Enzyme-Photocoupled Catalysis

Enzyme-photocoupled catalytic systems (EPCSs), combining the natural enzyme with a library of semiconductor photocatalysts, may break the constraint of natural evolution, realizing sustainable solar-to-chemical conversion and non-natural reactivity of the enzyme. The overall efficiency of EPCSs strongly relies on the shuttling of energy-carrying molecules, e.g., NAD⁺/NADH cofactor, between active centers of enzyme and photocatalyst. However, few efforts have been devoted to NAD⁺/NADH shuttling. Herein, we propose a strategy of constructing a thylakoid membrane-inspired capsule (TMC) with fortified and tunable NAD⁺/NADH shuttling to boost the enzyme-photocoupled catalytic process. The apparent shuttling number (ASN) of NAD⁺/NADH for TMC could reach 17.1, ∼8 times as high as that of non-integrated EPCS. Accordingly, our TMC exhibits a turnover frequency (TOF) of 38 000 ± 365 h^-1 with a solar-to-chemical efficiency (STC) of 0.69 ± 0.12%, ∼6 times higher than that of non-integrated EPCS.

Trade-off between carbohydrates and metal ions regulates the chemotactic directionality of alkaline phosphatase

The role of the Hofmeister interaction in governing the chemotactic behavior of alkaline phosphatase in the presence of carbohydrate and metal ion gradients has been established.

Spatiotemporal dynamics of self-assembled structures in enzymatically induced agonistic and antagonistic conditions

Predicting and designing systems with dynamic self-assembly properties in a spatiotemporal fashion is an important research area across disciplines ranging from understanding the fundamental non-equilibrium features of life to the fabrication of next-generation materials with life-like properties. Herein, we demonstrate a spatiotemporal dynamics pattern in the self-assembly behavior of a surfactant from an unorganized assembly, induced by adenosine triphosphate (ATP) and enzymes responsible for the degradation or conversion of ATP. We report the different behavior of two enzymes, alkaline phosphatase (ALP) and hexokinase (HK), towards adenosine triphosphate (ATP)-driven surfactant assembly, which also results in contrasting spatiotemporal dynamic assembly behavior. Here, ALP acts antagonistically, resulting in transient self-assemblies, whereas HK shows agonistic action with the ability to sustain the assemblies. This dynamic assembly behavior was then used to program the time-dependent emergence of a self-assembled structure in a two-dimensional space by maintaining concentration gradients of the enzymes and surfactant at different locations, demonstrating a new route for obtaining 'spatial' organizational adaptability in a self-organized system of interacting components for the incorporation of programmed functionality.

Spatial localisation meets biomolecular networks

Spatial organisation through localisation/compartmentalisation of species is a ubiquitous but poorly understood feature of cellular biomolecular networks. Current technologies in systems and synthetic biology (spatial proteomics, imaging, synthetic compartmentalisation) necessitate a systematic approach to elucidating the interplay of networks and spatial organisation. We develop a systems framework towards this end and focus on the effect of spatial localisation of network components revealing its multiple facets: (i) As a key distinct regulator of network behaviour, and an enabler of new network capabilities (ii) As a potent new regulator of pattern formation and self-organisation (iii) As an often hidden factor impacting inference of temporal networks from data (iv) As an engineering tool for rewiring networks and network/circuit design. These insights, transparently arising from the most basic considerations of networks and spatial organisation, have broad relevance in natural and engineered biology and in related areas such as cell-free systems, systems chemistry and bionanotechnology.

Complex biomolecular networks are fundamental to the functioning of living systems, both at the cellular level and beyond. In this paper, the authors develop a systems framework to elucidate the interplay of networks and the spatial localisation of network components.

Reaction-diffusion hydrogels from urease enzyme particles for patterned coatings

The reaction and diffusion of small molecules is used to initiate the formation of protective polymeric layers, or biofilms, that attach cells to surfaces. Here, inspired by biofilm formation, we present a general method for the growth of hydrogels from urease enzyme-particles by combining production of ammonia with a pH-regulated polymerization reaction in solution. We show through experiments and simulations how the propagating basic front and thiol-acrylate polymerization were continuously maintained by the localized urease reaction in the presence of urea, resulting in hydrogel layers around the enzyme particles at surfaces, interfaces or in motion. The hydrogels adhere the enzyme-particles to surfaces and have a tunable growth rate of the order of 10 µm min^-1 that depends on the size and spatial distribution of particles. This approach can be exploited to create enzyme-hydrogels or chemically patterned coatings for applications in biocatalytic flow reactors.

Viewpoint: Homeostasis as Inspiration-Toward Interactive Materials

Homeostatic systems combine an ability to maintain integrity over time with an incredible capacity for interactive behavior. Fundamental to such systems are building blocks of "mini-homeostasis": feedback loops in which one component responds to a stimulus and another opposes the response, pushing the module to restore its original configuration. Particularly when they cross time and length scales, perturbation of these loops by external changes can generate diverse and complex phenomena. Here, it is proposed that by recognizing and implementing mini-homeostatic modules-often composed of very different physical and chemical processes-into synthetic materials, numerous interactive behaviors can be obtained, opening avenues for designing multifunctional materials. How a variety of controlled, nontrivial material responses can be evoked from even simple versions of such synthetic feedback modules is illustrated. Moreover, random events causing seemingly random responses give insights into how one can further explore, understand and control the full interaction space. Ultimately, material fabrication and exploration of interactivity become inseparable in the rational design of such materials. Homeostasis provides a lens through which one can learn how to combine and perturb coupled processes across time and length scales to conjure up exciting behaviors for new materials that are both robust and interactive.

Amplification of Salt-Induced Protein Diffusiophoresis by Varying Salt from Potassium to Sodium to Magnesium Chloride in Water

Salt-induced diffusiophoresis is the migration of a macromolecule or a colloidal particle induced by a concentration gradient of salt in water. Here, the effect of salt type on salt-induced diffusiophoresis of the protein lysozyme at pH 4.5 and 25 °C was examined as a function of salt concentration for three chloride salts: NaCl, KCl, and MgCl₂. Diffusiophoresis coefficients were calculated from experimental ternary diffusion coefficients on lysozyme-salt-water mixtures. In all cases, diffusiophoresis of this positively charged protein occurs from high to low salt concentration. An appropriate mass transfer process was theoretically examined to show that concentration gradients of MgCl₂ produce significant lysozyme diffusiophoresis. This is attributed to the relatively low mobility of Mg²⁺ ions compared to that of Cl^- ions at low salt concentration and a strong thermodynamic nonideality of this salt at high salt concentration. These findings indicate that MgCl₂ concentration gradients could be exploited for protein manipulation in solution (e.g., using microfluidic technologies) with applications to protein adsorption and purification. The dependence of lysozyme diffusiophoresis on salt type was theoretically examined and linked to protein charge. The effect of salts on hydrogen-ion titration curves was experimentally characterized to understand the role of salt type on protein charge. Our results indicate that binding of Mg²⁺ ions to lysozyme further enhances protein diffusiophoresis.

Artificial morphogen-mediated differentiation in synthetic protocells

The design and assembly of artificial protocell consortia displaying dynamical behaviours and systems-based properties are emerging challenges in bottom-up synthetic biology. Cellular processes such as morphogenesis and differentiation rely in part on reaction-diffusion gradients, and the ability to mimic rudimentary aspects of these non-equilibrium processes in communities of artificial cells could provide a step to life-like systems capable of complex spatiotemporal transformations. Here we expose acoustically formed arrays of initially identical coacervate micro-droplets to uni-directional or counter-directional reaction-diffusion gradients of artificial morphogens to induce morphological differentiation and spatial patterning in single populations of model protocells. Dynamic reconfiguration of the droplets in the morphogen gradients produces a diversity of membrane-bounded vesicles that are spontaneously segregated into multimodal populations with differentiated enzyme activities. Our results highlight the opportunities for constructing protocell arrays with graded structure and functionality and provide a step towards the development of artificial cell platforms capable of multiple operations.

The ability to mimic aspects of cellular process that rely on reaction-diffusion gradients could provide a step to building life-like systems capable of complex behaviour. Here the authors demonstrate morphological differentiation in coacervate micro-droplets.

Control over the formation of supramolecular material objects using reaction-diffusion

Controlled diffusion, reaction and assembly of hydrogelator precursors can be used to create soft hydrogel objects of defined shape and size. In this study we show that controlling local reaction kinetics by means of pH, diffusion length and the concentrations of reactants allows control over the dimensions of formed supramolecular structures. By correlating a reaction diffusion model to experimental results, we show that the influence of all these control parameters can be unified using the Damköhler number, thus providing an easy-to-use relation between experimental parameters and structure dimensions. Finally, our study suggests that control over concentration gradients and chemical reactivity in combination with supramolecular chemistry is a promising platform for the design of soft matter objects of defined sizes, a concept that has received little attention up until now.

Propagation of Oscillating Chemical Signals through Reaction Networks

Akin to electronic systems that can tune to and process signals of select frequencies, systems/networks of chemical reactions also "propagate" time-varying concentration inputs in a frequency-dependent manner. Whereas signals of low frequencies are transmitted, higher frequency inputs are dampened and converted into steady-concentration outputs. Such behavior is observed in both idealized reaction chains as well as realistic signaling cascades, in the latter case explaining the experimentally observed responses of such cascades to input calcium oscillations. These and other results are supported by numerical simulations within the freely available Kinetix web application we developed to study chemical systems of arbitrary architectures, reaction kinetics, and boundary conditions.

Two Synthetic Replicators Compete To Process a Dynamic Reagent Pool

Complementary building blocks, comprising a set of four aromatic aldehydes and a set of four nucleophiles-three anilines and one hydroxylamine-combine through condensation reactions to afford a dynamic covalent library (DCL) consisting of the eight starting materials and 16 condensation products. One of the aldehydes and, consequently, all of the DCL members derived from this compound bear an amidopyridine recognition site. Exposure of this DCL to two maleimides, M^p and M^m, each equipped with a carboxylic acid recognition site, results in the formation of a series of products through irreversible 1,3-dipolar cycloaddition reactions with the four nitrones present in the DCL. However, only the two cycloadducts in the product pool that incorporate both recognition sites, T^p and T^m, are self-replicators that can harness the DCL as feedstock for their own formation, facilitating their own synthesis via autocatalytic and cross-catalytic pathways. The ability of these replicators to direct their own formation from the components present in the dynamic reagent pool in response to the input of instructions in the form of preformed replicators is demonstrated through a series of quantitative ¹⁹F{¹H} NMR spectroscopy experiments. Simulations establish the critical relationships between the kinetic and thermodynamic parameters of the replicators, the initial reagent concentrations, and the presence or absence of the DCL and their influence on the competition between T^p and T^m. Thus, we establish the rules that govern the behavior of the competing replicators under conditions where their formation is coupled tightly to the processing of a DCL.

Immobilization adjusted clock reaction in the urea–urease–H+ reaction system

The bell-shaped reactivity-pH curve is the fundamental reason that the temporal programmable kinetic switch in clock reactions can be obtained in bio-competitive enzymatic reactions. In this work, urease was loaded on small resin particles through ionic binding. Experimental results reveal that the immobilization not only increased the stability of the enzyme and the reproducibility of the clock reaction, but also shifted the bell-shaped activity curve to lower pHs. The latter change enables the clock reaction to occur from an initial pH of 2.3, where the free enzyme had already lost its activity. Two mechanisms explain the influence of the immobilization on the clock reaction. Immobilization modified the pH sensitive functional groups on the enzyme, shifting the activity curve to a more acidic region, and reduced diffusion alters the enzyme dynamics.

The reported immobilization shifts the bell-shaped reactivity-pH curve to lower pHs and enables the clock reaction to occur from a very low initial pH, where the free enzyme had already lost its activity.

Nonequilibrium Spatiotemporal Sensing within Acoustically Patterned Two-Dimensional Protocell Arrays

Acoustically trapped periodic arrays of horseradish peroxidase (HRP)-loaded poly(diallydimethylammonium chloride) / adenosine 5'-triphosphate coacervate microdroplet-based protocells exhibit a spatiotemporal biochemical response when exposed to a codiffusing mixture of substrate molecules (o-phenylenediamine (o-PD) and hydrogen peroxide (H₂O₂)) under nonequilibrium conditions. Unidirectional propagation of the chemical concentration gradients gives rise to time- and position-dependent fluorescence signal outputs from individual coacervate microdroplets, indicating that the organized protocell assembly can dynamically sense encoded information in the advancing reaction-diffusion front. The methodology is extended to arrays comprising spatially separated binary populations of HRP- or glucose oxidase-containing coacervate microdroplets to internally generate a H₂O₂ signal that chemically connects the two protocell communities via a concerted biochemical cascade reaction. Our results provide a step toward establishing a systematic approach to study dynamic interactions between organized protocell consortia and propagating reaction-diffusion gradients, and offer a new methodology for exploring the complexity of protocellular communication networks operating under nonequilibrium conditions.

Free-standing supramolecular hydrogel objects by reaction-diffusion

Self-assembly provides access to a variety of molecular materials, yet spatial control over structure formation remains difficult to achieve. Here we show how reaction-diffusion (RD) can be coupled to a molecular self-assembly process to generate macroscopic free-standing objects with control over shape, size, and functionality. In RD, two or more reactants diffuse from different positions to give rise to spatially defined structures on reaction. We demonstrate that RD can be used to locally control formation and self-assembly of hydrazone molecular gelators from their non-assembling precursors, leading to soft, free-standing hydrogel objects with sizes ranging from several hundred micrometres up to centimeters. Different chemical functionalities and gradients can easily be integrated in the hydrogel objects by using different reactants. Our methodology, together with the vast range of organic reactions and self-assembling building blocks, provides a general approach towards the programmed fabrication of soft microscale objects with controlled functionality and shape.

Synthesis and materialization of a reaction-diffusion French flag pattern

During embryo development, patterns of protein concentration appear in response to morphogen gradients. These patterns provide spatial and chemical information that directs the fate of the underlying cells. Here, we emulate this process within non-living matter and demonstrate the autonomous structuration of a synthetic material. First, we use DNA-based reaction networks to synthesize a French flag, an archetypal pattern composed of three chemically distinct zones with sharp borders whose synthetic analogue has remained elusive. A bistable network within a shallow concentration gradient creates an immobile, sharp and long-lasting concentration front through a reaction-diffusion mechanism. The combination of two bistable circuits generates a French flag pattern whose 'phenotype' can be reprogrammed by network mutation. Second, these concentration patterns control the macroscopic organization of DNA-decorated particles, inducing a French flag pattern of colloidal aggregation. This experimental framework could be used to test reaction-diffusion models and fabricate soft materials following an autonomous developmental programme.

Materials learning from life: concepts for active, adaptive and autonomous molecular systems

A broad overview of functional aspects in biological and synthetic out-of-equilibrium systems.

Stable DNA-based reaction–diffusion patterns

This paper demonstrates the generation of enzyme free DNA reaction–diffusion gradientsin vitrothat remain stable for tens of hours.

The nanotechnology of life-inspired systems

For some decades now, nanotechnology has been touted as the 'next big thing' with potential impact comparable to the steam, electricity or Internet revolutions - but has it lived up to these expectations? While advances in top-down nanolithography, now reaching 10-nm resolution, have resulted in devices that are rapidly approaching mass production, attempts to produce nanoscale devices using bottom-up approaches have met with only limited success. We have been inundated with nanoparticles of almost any shape, material and composition, but their societal impact has been far from revolutionary, with growing concerns over their toxicity. Despite nebulous hopes that making hierarchical nanomaterials will lead to new, emergent properties, no breakthrough applications seem imminent. In this Perspective, we argue that the time is ripe to look beyond individual nano-objects and their static assemblies, and instead focus on systems comprising different types of 'nanoparts' interacting and/or communicating with one another to perform desired functions. Such systems are interesting for a variety of reasons: they can act autonomously without external electrical or optical connections, can be dynamic and reconfigurable, and can act as 'nanomachines' by directing the flow of mass, energy or information . In thinking how this systems nanoscience approach could be implemented to design useful - as opposed to toy-model - nanosystems, our choice of applications and our nanoengineering should be inspired by living matter.

Reaction-diffusion processes at the nano- and microscales

The bottom-up fabrication of nano- and microscale structures from primary building blocks (molecules, colloidal particles) has made remarkable progress over the past two decades, but most research has focused on structural aspects, leaving our understanding of the dynamic and spatiotemporal aspects at a relatively primitive stage. In this Review, we draw inspiration from living cells to argue that it is now time to move beyond the generation of structures and explore dynamic processes at the nanoscale. We first introduce nanoscale self-assembly, self-organization and reaction-diffusion processes as essential features of cells. Then, we highlight recent progress towards designing and controlling these fundamental features of life in abiological systems. Specifically, we discuss examples of reaction-diffusion processes that lead to such outcomes as self-assembly, self-organization, unique nanostructures, chemical waves and dynamic order to illustrate their ubiquity within a unifying context of dynamic oscillations and energy dissipation. Finally, we suggest future directions for research on reaction-diffusion processes at the nano- and microscales that we find hold particular promise for a new understanding of science at the nanoscale and the development of new kinds of nanotechnologies for chemical transport, chemical communication and integration with living systems.

Temporal Control of Gelation and Polymerization Fronts Driven by an Autocatalytic Enzyme Reaction

Chemical systems that remain kinetically dormant until activated have numerous applications in materials science. Herein we present a method for the control of gelation that exploits an inbuilt switch: the increase in pH after an induction period in the urease-catalyzed hydrolysis of urea was used to trigger the base-catalyzed Michael addition of a water-soluble trithiol to a polyethylene glycol diacrylate. The time to gelation (minutes to hours) was either preset through the initial concentrations or the reaction was initiated locally by a base, thus resulting in polymerization fronts that converted the mixture from a liquid into a gel (ca. 0.1 mm min(-1)). The rate of hydrolytic degradation of the hydrogel depended on the initial concentrations, thus resulting in a gel lifetime of hours to months. In this way, temporal programming of gelation was possible under mild conditions by using the output of an autocatalytic enzyme reaction to drive both the polymerization and subsequent degradation of a hydrogel.

Temporal Control of Gelation and Polymerization Fronts Driven by an Autocatalytic Enzyme Reaction

Chemical systems that remain kinetically dormant until activated have numerous applications in materials science. Herein we present a method for the control of gelation that exploits an inbuilt switch: the increase in pH after an induction period in the urease-catalyzed hydrolysis of urea was used to trigger the base-catalyzed Michael addition of a water-soluble trithiol to a polyethylene glycol diacrylate. The time to gelation (minutes to hours) was either preset through the initial concentrations or the reaction was initiated locally by a base, thus resulting in polymerization fronts that converted the mixture from a liquid into a gel (ca. 0.1 mm min-1). The rate of hydrolytic degradation of the hydrogel depended on the initial concentrations, thus resulting in a gel lifetime of hours to months. In this way, temporal programming of gelation was possible under mild conditions by using the output of an autocatalytic enzyme reaction to drive both the polymerization and subsequent degradation of a hydrogel.

Automated design of programmable enzyme-driven DNA circuits

Molecular programming allows for the bottom-up engineering of biochemical reaction networks in a controlled in vitro setting. These engineered biochemical reaction networks yield important insight in the design principles of biological systems and can potentially enrich molecular diagnostic systems. The DNA polymerase-nickase-exonuclease (PEN) toolbox has recently been used to program oscillatory and bistable biochemical networks using a minimal number of components. Previous work has reported the automatic construction of in silico descriptions of biochemical networks derived from the PEN toolbox, paving the way for generating networks of arbitrary size and complexity in vitro. Here, we report an automated approach that further bridges the gap between an in silico description and in vitro realization. A biochemical network of arbitrary complexity can be globally screened for parameter values that display the desired function and combining this approach with robustness analysis further increases the chance of successful in vitro implementation. Moreover, we present an automated design procedure for generating optimal DNA sequences, exhibiting key characteristics deduced from the in silico analysis. Our in silico method has been tested on a previously reported network, the Oligator, and has also been applied to the design of a reaction network capable of displaying adaptation in one of its components. Finally, we experimentally characterize unproductive sequestration of the exonuclease to phosphorothioate protected ssDNA strands. The strong nonlinearities in the degradation of active components caused by this unintended cross-coupling are shown computationally to have a positive effect on adaptation quality.

A bistable switch in pH in urease-loaded alginate beads

A bistable switch from a low pH (unreacted "off") state to a high pH (reacted "on") state was obtained in enzyme-loaded gel beads in response to supra-threshold substrate concentrations.

Programmable chemical reaction networks: emulating regulatory functions in living cells using a bottom-up approach

Living cells are able to produce a wide variety of biological responses when subjected to biochemical stimuli.