DNA-based communication in populations of synthetic protocells

Living cells and biological mechanisms as prototypes for developing chemical artificial intelligence

Artificial Intelligence (AI) is having a revolutionary impact on our societies. It is helping humans in facing the global challenges of this century. Traditionally, AI is developed in software or through neuromorphic engineering in hardware. More recently, a brand-new strategy has been proposed. It is the so-called Chemical AI (CAI), which exploits molecular, supramolecular, and systems chemistry in wetware to mimic human intelligence. In this work, two promising approaches for boosting CAI are described. One regards designing and implementing neural surrogates that can communicate through optical or chemical signals and give rise to networks for computational purposes and to develop micro/nanorobotics. The other approach concerns "bottom-up synthetic cells" that can be exploited for applications in various scenarios, including future nano-medicine. Both topics are presented at a basic level, mainly to inform the broader audience of non-specialists, and so favour the rise of interest in these frontier subjects.

Chemotactic Interactions Drive Migration of Membraneless Active Droplets

In nature, chemotactic interactions are ubiquitous and play a critical role in driving the collective behavior of living organisms. Reproducing these interactions in vitro is still a paramount challenge due to the complexity of mimicking and controlling cellular features, such as tangled metabolic networks, cytosolic macromolecular crowding, and cellular migration, on a microorganism size scale. Here, we generate enzymatically active cell-sized droplets able to move freely, and by following a chemical gradient, able to interact with the surrounding droplets in a collective manner. The enzyme within the droplets generates a pH gradient that extends outside the edge of the droplets. We discovered that the external pH gradient triggers droplet migration and controls its directionality, which is selectively toward the neighboring droplets. Hence, by changing the enzyme activity inside the droplet, we tuned the droplet migration speed. Furthermore, we showed that these cellular-like features can facilitate the reconstitution of a simple and linear protometabolic pathway and increase the final reaction product generation. Our work suggests that simple and stable membraneless droplets can reproduce complex biological phenomena, opening new perspectives as bioinspired materials and synthetic biology tools.

Chemomechanical Communication between Liposomes Based on Enzyme Cascades

Communication between cells is crucial to the survival of both uni- and multicellular organisms. The primary mode of communication involves chemical cues. There is great current interest in mimicking this behavior in synthetic cells to understand the physical basis of intercellular communication and design collective functional behavior. Using liposomal cell mimics, we demonstrate how a chemical input can elicit a mechanical response (enhanced motility). We employed a single substrate to trigger enzyme cascade-induced control of the diffusion of up to three different liposome populations. Furthermore, substrate competition allows temporal control over enhanced diffusion. The use of enzyme cascades to propagate chemical signals provides a robust and efficient mechanism for diverse populations of protocells to coordinate their motion in response to signals from each other.

A Methylation-Gated DNAzyme Circuit for Spatially Controlled Imaging of MicroRNA in Cells and Animals

Epigenetic modification plays an indispensable role in regulating routine molecular signaling pathways, yet it is rarely used to modulate molecular self-assembly networks. Herein, we constructed a bioorthogonal demethylase-stimulated DNA circuitry (DSC) system for high-fidelity imaging of microRNA (miRNA) in live cells and mice by eliminating undesired off-site signal leakage. The simple and robust DSC system is composed of a primary cell-specific circuitry regulation (CR) module and an ultimate signal-transducing amplifier (SA) module. After the modularly designed DSC system was delivered into target live cells, the DNAzyme of the CR module was site-specifically activated by endogenous demethylase to produce fuel strands for the subsequent miRNA-targeting SA module. Through the on-site and multiply guaranteed molecular recognitions, the lucid yet efficient DSC system realized the reliably amplified in vivo miRNA sensing and enabled the in-depth exploration of the demethylase-involved signal pathway with miRNA in live cells. Our bioorthogonally on-site-activated DSC system represents a universal and versatile biomolecular sensing platform via various demethylase regulations and shows more prospects for more different personalized theragnostics.

Target-promoted autocatalytic hairpin assembly of bivalent DNAzymes for sensitive and label-free electrochemical metallothionein assay

Metallothionein (MT) has shown to be an important biomarker for environmental monitoring and various diseases, due to its significant binding ability to heavy metal ions. On the basis of such a characteristic and the Hg2+-stabilized DNA duplex (Hg2+-dsDNA) probe, as well as a new autocatalytic hairpin assembly (aCHA)/DNAzyme cascaded signal enhancement strategy, the construction of a highly sensitive and label-free electrochemical MT biosensor is described. Target MT molecules bind Hg2+ in Hg2+-dsDNA to disrupt the duplex structure and to release ssDNA sequences, which trigger subsequent aCHA for efficient production of mimic aCHA triggering strands and many bivalent DNAzymes. The signal hairpins on the electrode are then cyclically cleaved by DNAzyme amplification cascade to liberate plenty G-quadruplex sequences, which bind hemin and yield largely enhanced currents for sensitive assay of MT with a detection limit of 0.217 nM in a label-free approach. Such sensor also shows selective discrimination capability to MT against other interfering proteins and assay of MT in normal serums with dilution has also been verified, indicating its potential for highly sensitive detection of different heavy metal ion binding molecules for various application scenarios.

DNA-empowered synthetic cells as minimalistic life forms

Cells, the fundamental units of life, orchestrate intricate functions - motility, adaptation, replication, communication, and self-organization within tissues. Originating from spatiotemporally organized structures and machinery, coupled with information processing in signalling networks, cells embody the 'sensor-processor-actuator' paradigm. Can we glean insights from these processes to construct primitive artificial systems with life-like properties? Using de novo design approaches, what can we uncover about the evolutionary path of life? This Review discusses the strides made in crafting synthetic cells, utilizing the powerful toolbox of structural and dynamic DNA nanoscience. We describe how DNA can serve as a versatile tool for engineering entire synthetic cells or subcellular entities, and how DNA enables complex behaviour, including motility and information processing for adaptive and interactive processes. We chart future directions for DNA-empowered synthetic cells, envisioning interactive systems wherein synthetic cells communicate within communities and with living cells.

Circular single-stranded DNA as a programmable vector for gene regulation in cell-free protein expression systems

Cell-free protein expression (CFE) systems have emerged as a critical platform for synthetic biology research. The vectors for protein expression in CFE systems mainly rely on double-stranded DNA and single-stranded RNA for transcription and translation processing. Here, we introduce a programmable vector - circular single-stranded DNA (CssDNA), which is shown to be processed by DNA and RNA polymerases for gene expression in a yeast-based CFE system. CssDNA is already widely employed in DNA nanotechnology due to its addressability and programmability. To apply above methods in the context of synthetic biology, CssDNA can not only be engineered for gene regulation via the different pathways of sense CssDNA and antisense CssDNA, but also be constructed into several gene regulatory logic gates in CFE systems. Our findings advance the understanding of how CssDNA can be utilized in gene expression and gene regulation, and thus enrich the synthetic biology toolbox.

Recent advances in enzyme-free and enzyme-mediated single-nucleotide variation assay in vitro

Single-nucleotide variants (SNVs) are the most common type variation of sequence alterations at a specific location in the genome, thus involving significant clinical and biological information. The assay of SNVs has engaged great awareness, because many genome-wide association studies demonstrated that SNVs are highly associated with serious human diseases. Moreover, the investigation of SNV expression levels in single cells are capable of visualizing genetic information and revealing the complexity and heterogeneity of single-nucleotide mutation-related diseases. Thus, developing SNV assay approaches in vitro, particularly in single cells, is becoming increasingly in demand. In this review, we summarized recent progress in the enzyme-free and enzyme-mediated strategies enabling SNV assay transition from sensing interface to the test tube and single cells, which will potentially delve deeper into the knowledge of SNV functions and disease associations, as well as discovering new pathways to diagnose and treat diseases based on individual genetic profiles. The leap of SNV assay achievements will motivate observation and measurement genetic variations in single cells, even within living organisms, delve into the knowledge of SNV functions and disease associations, as well as open up entirely new avenues in the diagnosis and treatment of diseases based on individual genetic profiles.

Dampened Transient Actuation of Hydrogels Autonomously Controlled by pH-Responsive Bicontinuous Nanospheres

The fabrication of a soft actuator with a dampened actuation response is presented. This was achieved via the incorporation into an actuating hydrogel of urease-loaded pH-responsive bicontinuous nanospheres (BCNs), whose membrane was able to regulate the permeability and thus conversion of fuel urea into ammonia. The dampened response of these nanoreactors to the enzymatically induced pH change was translated to a pH-responsive soft actuator. In hydrogels composed of a pH-responsive and nonresponsive layer, the transient pH gradient yielded an asymmetric swelling behavior, which induced a bending response. The transient actuation profile could be controlled by varying the external fuel concentrations. Furthermore, we showed that the spatial organization of the BCNs within the actuator had a great influence on the actuation response. Embedding the urease-loaded nanoreactors within the active, pH-responsive layer resulted in a reduced response due to local substrate conversion in comparison to embedding them within the passive layer of the bilayer hydrogel. Finally, we were able to induce transient actuation in a hydrogel comprising two identical active layers by the immobilization of the BCNs within one specific layer. Upon addition of urea, a local pH gradient was generated, which caused accelerated swelling in the BCN layer and transient bending of the device before the pH gradient was attenuated over time.

Artificial Homeostasis Systems Based on Feedback Reaction Networks: Design Principles and Future Promises

Feedback-controlled chemical reaction networks (FCRNs) are indispensable for various biological processes, such as cellular mechanisms, patterns, and signaling pathways. Through the intricate interplay of many feedback loops (FLs), FCRNs maintain a stable internal cellular environment. Currently, creating minimalistic synthetic cells is the long-term objective of systems chemistry, which is motivated by such natural integrity. The design, kinetic optimization, and analysis of FCRNs to exhibit functions akin to those of a cell still pose significant challenges. Indeed, reaching synthetic homeostasis is essential for engineering synthetic cell components. However, maintaining homeostasis in artificial systems against various agitations is a difficult task. Several biological events can provide us with guidelines for a conceptual understanding of homeostasis, which can be further applicable in designing artificial synthetic systems. In this regard, we organize our review with artificial homeostasis systems driven by FCRNs at different length scales, including homogeneous, compartmentalized, and soft material systems. First, we stretch a quick overview of FCRNs in different molecular and supramolecular systems, which are the essential toolbox for engineering different nonlinear functions and homeostatic systems. Moreover, the existing history of synthetic homeostasis in chemical and material systems and their advanced functions with self-correcting, and regulating properties are also emphasized.

Models of Chemical Communication for Micro/Nanoparticles

Engineering chemical communication between micro/nanosystems (via the exchange of chemical messengers) is receiving increasing attention from the scientific community. Although a number of micro- and nanodevices (e.g., drug carriers, sensors, and artificial cells) have been developed in the last decades, engineering communication at the micro/nanoscale is a recent emergent topic. In fact, most of the studies in this research area have been published within the last 10 years. Inspired by nature─where information is exchanged by means of molecules─the development of chemical communication strategies holds wide implications as it may provide breakthroughs in many areas including nanotechnology, artificial cell research, biomedicine, biotechnology, and ICT. Published examples rely on nanotechnology and synthetic biology for the creation of micro- and nanodevices that can communicate. Communication enables the construction of new complex systems capable of performing advanced coordinated tasks that go beyond those carried out by individual entities. In addition, the possibility to communicate between synthetic and living systems can further advance our understanding of biochemical processes and provide completely new tailored therapeutic and diagnostic strategies, ways to tune cellular behavior, and new biotechnological tools. In this Account, we summarize advances by our laboratories (and others) in the engineering of chemical communication of micro- and nanoparticles. This Account is structured to provide researchers from different fields with general strategies and common ground for the rational design of future communication networks at the micro/nanoscale. First, we cover the basis of and describe enabling technologies to engineer particles with communication capabilities. Next, we rationalize general models of chemical communication. These models vary from simple linear communication (transmission of information between two points) to more complex pathways such as interactive communication and multicomponent communication (involving several entities). Using illustrative experimental designs, we demonstrate the realization of these models which involve communication not only between engineered micro/nanoparticles but also between particles and living systems. Finally, we discuss the current state of the topic and the future challenges to be addressed.

DNA as a universal chemical substrate for computing and data storage

DNA computing and DNA data storage are emerging fields that are unlocking new possibilities in information technology and diagnostics. These approaches use DNA molecules as a computing substrate or a storage medium, offering nanoscale compactness and operation in unconventional media (including aqueous solutions, water-in-oil microemulsions and self-assembled membranized compartments) for applications beyond traditional silicon-based computing systems. To build a functional DNA computer that can process and store molecular information necessitates the continued development of strategies for computing and data storage, as well as bridging the gap between these fields. In this Review, we explore how DNA can be leveraged in the context of DNA computing with a focus on neural networks and compartmentalized DNA circuits. We also discuss emerging approaches to the storage of data in DNA and associated topics such as the writing, reading, retrieval and post-synthesis editing of DNA-encoded data. Finally, we provide insights into how DNA computing can be integrated with DNA data storage and explore the use of DNA for near-memory computing for future information technology and health analysis applications.

Cell Free Expression in Proteinosomes Prepared from Native Protein-PNIPAAm Conjugates

Towards the goal of building synthetic cells from the bottom-up, the establishment of micrometer-sized compartments that contain and support cell free transcription and translation that couple cellular structure to function is of critical importance. Proteinosomes, formed from crosslinked cationized protein-polymer conjugates offer a promising solution to membrane-bound compartmentalization with an open, semi-permeable membrane. Critically, to date, there has been no demonstration of cell free transcription and translation within water-in-water proteinosomes. Herein, a novel approach to generate proteinosomes that can support cell free transcription and translation is presented. This approach generates proteinosomes directly from native protein-polymer (BSA-PNIPAAm) conjugates. These native proteinosomes offer an excellent alternative as a synthetic cell chassis to other membrane bound compartments. Significantly, the native proteinosomes are stable under high salt conditions that enables the ability to support cell free transcription and translation and offer enhanced protein expression compared to proteinosomes prepared from traditional methodologies. Furthermore, the integration of native proteinosomes into higher order synthetic cellular architectures with membrane free compartments such as liposomes is demonstrated. The integration of bioinspired architectural elements with the central dogma is an essential building block for realizing minimal synthetic cells and is key for exploiting artificial cells in real-world applications.

Lipid vesicle-based molecular robots

A molecular robot, which is a system comprised of one or more molecular machines and computers, can execute sophisticated tasks in many fields that span from nanomedicine to green nanotechnology. The core parts of molecular robots are fairly consistent from system to system and always include (i) a body to encapsulate molecular machines, (ii) sensors to capture signals, (iii) computers to make decisions, and (iv) actuators to perform tasks. This review aims to provide an overview of approaches and considerations to develop molecular robots. We first introduce the basic technologies required for constructing the core parts of molecular robots, describe the recent progress towards achieving higher functionality, and subsequently discuss the current challenges and outlook. We also highlight the applications of molecular robots in sensing biomarkers, signal communications with living cells, and conversion of energy. Although molecular robots are still in their infancy, they will unquestionably initiate massive change in biomedical and environmental technology in the not too distant future.

DNA Reaction System That Acquires Classical Conditioning

Biochemical reaction networks can exhibit plastic adaptation to alter their functions in response to environmental changes. This capability is derived from the structure and dynamics of the reaction networks and the functionality of the biomolecule. This plastic adaptation in biochemical reaction systems is essentially related to memory and learning capabilities, which have been studied in DNA computing applications for the past decade. However, designing DNA reaction systems with memory and learning capabilities using the dynamic properties of biochemical reactions remains challenging. In this study, we propose a basic DNA reaction system design that acquires classical conditioning, a phenomenon underlying memory and learning, as a typical learning task. Our design is based on a simple mechanism of five DNA strand displacement reactions and two degradative reactions. The proposed DNA circuit can acquire or lose a new function under specific conditions, depending on the input history formed by repetitive stimuli, by exploiting the dynamic properties of biochemical reactions induced by different input timings.

Cell-Like Synthetic Supramolecular Soft Materials Realized in Multicomponent, Non-/Out-of-Equilibrium Dynamic Systems

Living cells are complex, nonequilibrium supramolecular systems capable of independently and/or cooperatively integrating multiple bio-supramolecules to execute intricate physiological functions that cannot be accomplished by individual biomolecules. These biological design strategies offer valuable insights for the development of synthetic supramolecular systems with spatially controlled hierarchical structures, which, importantly, exhibit cell-like responses and functions. The next grand challenge in supramolecular chemistry is to control the organization of multiple types of supramolecules in a single system, thus integrating the functions of these supramolecules in an orthogonal and/or cooperative manner. In this perspective, the recent progress in constructing multicomponent supramolecular soft materials through the hybridization of supramolecules, such as self-assembled nanofibers/gels and coacervates, with other functional molecules, including polymer gels and enzymes is highlighted. Moreover, results show that these materials exhibit bioinspired responses to stimuli, such as bidirectional rheological responses of supramolecular double-network hydrogels, temporal stimulus pattern-dependent responses of synthetic coacervates, and 3D hydrogel patterning in response to reaction-diffusion processes are presented. Autonomous active soft materials with cell-like responses and spatially controlled structures hold promise for diverse applications, including soft robotics with directional motion, point-of-care disease diagnosis, and tissue regeneration.

Tuning of Cationic Polymer Functionality in Complex Coacervate Artificial Cells for Optimized Enzyme Activity

Complex coacervates are a versatile platform to mimic the structure of living cells. In both living systems and artificial cells, a macromolecularly crowded condensate phase has been shown to be able to modulate enzyme activity. Yet, how enzyme activity is affected by interactions (particularly with cationic charges) inside coacervates is not well studied. Here, we synthesized a series of amino-functional polymers to investigate the effect of the type of amine and charge density on coacervate formation, stability, protein partitioning, and enzyme function. The polymers were prepared by RAFT polymerization using as monomers aminoethyl methacrylate (AEAM), 2-(dimethylamino)ethyl methacrylate (DMAEMA), imidazolepropyl methacrylamide (IPMAm), and [2-(methacryloyloxy)ethyl] trimethylammonium chloride (TMAEMA). Membranized complex coacervate artificial cells were formed with these polycations and an anionic amylose derivative. Results show that polycations with reduced charge density result in higher protein mobility in the condensates and also higher enzyme activity. Insights described here could help guide the use of coacervate artificial cells in applications such as sensing, catalysis, and therapeutic formulations.

Artificial cells with viscoadaptive behavior based on hydrogel-loaded giant unilamellar vesicles

Viscoadaptation is an essential process in natural cells, where supramolecular interactions between cytosolic components drive adaptation of the cellular mechanical features to regulate metabolic function. This important relationship between mechanical properties and function has until now been underexplored in artificial cell research. Here, we have created an artificial cell platform that exploits internal supramolecular interactions to display viscoadaptive behavior. As supramolecular material to mimic the cytosolic component of these artificial cells, we employed a pH-switchable hydrogelator based on poly(ethylene glycol) coupled to ureido-pyrimidinone units. The hydrogelator was membranized in its sol state in giant unilamellar lipid vesicles to include a cell-membrane mimetic component. The resulting hydrogelator-loaded giant unilamellar vesicles (designated as HL-GUVs) displayed reversible pH-switchable sol-gel behavior through multiple cycles. Furthermore, incorporation of the regulatory enzyme urease enabled us to increase the cytosolic pH upon conversion of its substrate urea. The system was able to switch between a high viscosity (at neutral pH) and a low viscosity (at basic pH) state upon addition of substrate. Finally, viscoadaptation was achieved via the incorporation of a second enzyme of which the activity was governed by the viscosity of the artificial cell. This work represents a new approach to install functional self-regulation in artificial cells, and opens new possibilities for the creation of complex artificial cells that mimic the structural and functional interplay found in biological systems.

Hierarchical Structuration in Protocellular System

Spatial control is one of the ubiquitous features in biological systems and the key to the functional complexity of living cells. The strategies to achieve such precise spatial control in protocellular systems are crucial to constructing complex artificial living systems with functional collective behavior. Herein, the authors review recent advances in the spatial control within a single protocell or between different protocells and discuss how such hierarchical structured protocellular system can be used to understand complex living systems or to advance the development of functional microreactors with the programmable release of various biomacromolecular payloads, or smart protocell-biological cell hybrid system.

Signal Transduction in Artificial Cells

In recent years, significant progress has been made in the emerging field of constructing biomimetic soft compartments with life-like behaviors. Given that biological activities occur under a flux of energy and matter exchange, the implementation of rudimentary signaling pathways in artificial cells (protocells) is a prerequisite for the development of adaptive sense-response phenotypes in cytomimetic models. Herein, recent approaches to the integration of signal transduction modules in model protocells prepared by bottom-up construction are discussed. The approaches are classified into two categories involving invasive biochemical signals or non-invasive physical stimuli. In the former mechanism, transducers with intrinsic recognition capability respond with high specificity, while in the latter, artificial cells respond through intra-protocellular energy transduction. Although major challenges remain in the pursuit of a sophisticated artificial signaling network for the orchestration of higher-order cytomimetic models, significant advances have been made in establishing rudimentary protocell communication networks, providing novel organizational models for the development of life-like microsystems and new avenues in protoliving technologies.

Synthetic-Cell-Based Multi-Compartmentalized Hierarchical Systems

In the extant lifeforms, the self-sustaining behaviors refer to various well-organized biochemical reactions in spatial confinement, which rely on compartmentalization to integrate and coordinate the molecularly crowded intracellular environment and complicated reaction networks in living/synthetic cells. Therefore, the biological phenomenon of compartmentalization has become an essential theme in the field of synthetic cell engineering. Recent progress in the state-of-the-art of synthetic cells has indicated that multi-compartmentalized synthetic cells should be developed to obtain more advanced structures and functions. Herein, two ways of developing multi-compartmentalized hierarchical systems, namely interior compartmentalization of synthetic cells (organelles) and integration of synthetic cell communities (synthetic tissues), are summarized. Examples are provided for different construction strategies employed in the above-mentioned engineering ways, including spontaneous compartmentalization in vesicles, host-guest nesting, phase separation mediated multiphase, adhesion-mediated assembly, programmed arrays, and 3D printing. Apart from exhibiting advanced structures and functions, synthetic cells are also applied as biomimetic materials. Finally, key challenges and future directions regarding the development of multi-compartmentalized hierarchical systems are summarized; these are expected to lay the foundation for the creation of a "living" synthetic cell as well as provide a larger platform for developing new biomimetic materials in the future.

Coacervate Microdroplets as Synthetic Protocells for Cell Mimicking and Signaling Communications

Synthetic protocells are minimal systems that mimic certain properties of natural cells and are used to research the emergence of life from a nonliving chemical network. Currently, coacervate microdroplets, which are formed via liquid-liquid phase separation, are receiving wide attention in the context of cell biology and protocell research; these microdroplets are notable because they can provide liquid-like compartment structures for biochemical reactions by creating highly macromolecular crowded local environments. In this review, an overview of recent research on the formation of coacervate microdroplets through phase separation; the design of coacervate-based stimuli-responsive protocells, multichamber protocells, and membranized protocells; and their cell mimic behaviors, is provided. The simplified protocell models with precisely defined and tunable compositions advance the understanding of the requirements for cellular structure and function. Efforts are then discussed to establish signal communication systems in protocell and protocell consortia, as communication is a fundamental feature of life that coordinates matter exchanges and energy fluxes dynamically in space and time. Finally, some perspectives on the challenges and future developments of synthetic protocell research in biomimetic science and biomedical applications are provided.

A Photo-degradable Crosslinker for the Development of Light-responsive Protocell Membranes

The achievement of light-responsive behaviours is an important target for protocell engineering to allow control of fundamental protocellular processes such as communication via diffusible chemical signals, shape changes or even motility at the flick of a switch. As a step towards this ambitious goal, here we describe the synthesis of a novel poly(ethylene glycol)-based crosslinker, reactive towards nucleophiles, that effectively degrades with UV light (405 nm). We demonstrate its utility for the fabrication of the first protocell membranes capable of light-induced disassembly, for the photo-generation of patterns of protocells, and for the modulation of protocell membrane permeability. Overall, our results not only open up new avenues towards the engineering of spatially organised, communicating networks of protocells, and of micro-compartmentalised systems for information storage and release, but also have important implications for other research fields such as drug delivery and soft materials chemistry.

Micro-compartmentalized strand displacement reactions with a random pool background

Toehold-mediated strand displacement (TMSD) is a widely used process in dynamic DNA nanotechnology, which has been applied for the actuation of molecular devices, in biosensor applications, and for DNA-based molecular computation. Similar processes also occur in a biological context, when RNA strands invade secondary structures or duplexes of other RNA or DNA molecules. Complex reaction environments-inside cells or synthetic cells-potentially contain a large number of competing nucleic acid molecules that transiently bind to the components of the strand displacement reaction of interest and thus slow down its kinetics. Here, we investigate the kinetics of TMSD reactions compartmentalized into water-in-oil emulsion droplets-in both the presence and absence of a random sequence background-using a droplet microfluidic 'stopped flow' set-up. The set-up enables one to determine the kinetics within thousands of droplets and easily vary experimental parameters such as the stoichiometry of the TMSD components. While the average kinetics in the droplets coincides precisely with the bulk behaviour, we observe considerable variability among the droplets. This variability is partially explained by the encapsulation procedure itself, but appears to be more pronounced in reactions involving a random pool background.

DNA-based programmable gate arrays for general-purpose DNA computing

The past decades have witnessed the evolution of electronic and photonic integrated circuits, from application specific to programmable1,2. Although liquid-phase DNA circuitry holds the potential for massive parallelism in the encoding and execution of algorithms3,4, the development of general-purpose DNA integrated circuits (DICs) has yet to be explored. Here we demonstrate a DIC system by integration of multilayer DNA-based programmable gate arrays (DPGAs). We find that the use of generic single-stranded oligonucleotides as a uniform transmission signal can reliably integrate large-scale DICs with minimal leakage and high fidelity for general-purpose computing. Reconfiguration of a single DPGA with 24 addressable dual-rail gates can be programmed with wiring instructions to implement over 100 billion distinct circuits. Furthermore, to control the intrinsically random collision of molecules, we designed DNA origami registers to provide the directionality for asynchronous execution of cascaded DPGAs. We exemplify this by a quadratic equation-solving DIC assembled with three layers of cascade DPGAs comprising 30 logic gates with around 500 DNA strands. We further show that integration of a DPGA with an analog-to-digital converter can classify disease-related microRNAs. The ability to integrate large-scale DPGA networks without apparent signal attenuation marks a key step towards general-purpose DNA computing.

Engineering global and local signal generators for probing temporal and spatial cellular signaling dynamics

Cells constantly encounter a wide range of environmental signals and rely on their signaling pathways to initiate reliable responses. Understanding the underlying signaling mechanisms and cellular behaviors requires signal generators capable of providing diverse input signals to deliver to cell systems. Current research efforts are primarily focused on exploring cellular responses to global or local signals, which enable us to understand cellular signaling and behavior in distinct dimensions. This review presents recent advancements in global and local signal generators, highlighting their applications in studying temporal and spatial signaling activity. Global signals can be generated using microfluidic or photochemical approaches. Local signal sources can be created using living or artificial cells in combination with different control methods. We also address the strengths and limitations of each signal generator type, discussing challenges and potential extensions for future research. These approaches are expected to continue to facilitate on-going research to discover novel and intriguing cellular signaling mechanisms.

A DNA Nanodevice-Based Platform with Diverse Capabilities

Social biotic colonies often perform intricate tasks by interindividual communication and cooperation. Inspired by these biotic behaviors, a DNA nanodevice community is proposed as a universal and scalable platform. The modular nanodevice as the infrastructure of platform contains a DNA origami triangular prism framework and a hairpin-swing arm machinery core. By coding and decoding a signal domain on the shuttled output strand in different nanodevices, an orthogonal inter-nanodevice communication network is established to connect multi-nanodevices into a functional platform. The nanodevice platform enables implementation of diverse tasks, including signal cascading and feedback, molecular input recording, distributed logic computing, and modeling of simulation for virus transmission. The nanodevice platform with powerful compatibility and programmability presents an elegant example of the combination of the distributed operation of multiple devices and the complicated interdevice communication network, and may become a new generation of intelligent DNA nanosystems.

DNA-Based Signaling Networks for Transient Colloidal Co-Assemblies

Programmable chemical circuits inspired by signaling networks in living cells are a promising approach for the development of adaptive and autonomous self-assembling molecular systems and material functions. Progress has been made at the molecular level, but connecting molecular control circuits to self-assembling larger elements such as colloids that enable real-space studies and access to functional materials is sparse and can suffer from kinetic traps, flocculation, or difficult system integration protocols. Herein, we report a toehold-mediated DNA strand displacement reaction network capable of autonomously directing two different microgels into transient and self-regulating co-assemblies. The microgels are functionalized with DNA and become elemental components of the network. The flexibility of the circuit design allows the installation of delay phases or accelerators by chaining additional circuit modules upstream or downstream of the core circuit. The design provides an adaptable and robust route to regulate other building blocks for advanced biomimetic functions.

A Synthetic Signaling Network Imitating the Action of Immune Cells in Response to Bacterial Metabolism

State-of-the-art bottom-up synthetic biology allows to replicate many basic biological functions in artificial-cell-like devices. To mimic more complex behaviors, however, artificial cells would need to perform many of these functions in a synergistic and coordinated fashion, which remains elusive. Here, a sophisticated biological response is considered, namely the capture and deactivation of pathogens by neutrophil immune cells, through the process of netosis. A consortium consisting of two synthetic agents is designed-responsive DNA-based particles and antibiotic-loaded lipid vesicles-whose coordinated action mimics the sought immune-like response when triggered by bacterial metabolism. The artificial netosis-like response emerges from a series of interlinked sensing and communication pathways between the live and synthetic agents, and translates into both physical and chemical antimicrobial actions, namely bacteria immobilization and exposure to antibiotics. The results demonstrate how advanced life-like responses can be prescribed with a relatively small number of synthetic molecular components, and outlines a new strategy for artificial-cell-based antimicrobial solutions.

A Role for Bottom-Up Synthetic Cells in the Internet of Bio-Nano Things?

The potential role of bottom-up Synthetic Cells (SCs) in the Internet of Bio-Nano Things (IoBNT) is discussed. In particular, this perspective paper focuses on the growing interest in networks of biological and/or artificial objects at the micro- and nanoscale (cells and subcellular parts, microelectrodes, microvessels, etc.), whereby communication takes place in an unconventional manner, i.e., via chemical signaling. The resulting "molecular communication" (MC) scenario paves the way to the development of innovative technologies that have the potential to impact biotechnology, nanomedicine, and related fields. The scenario that relies on the interconnection of natural and artificial entities is briefly introduced, highlighting how Synthetic Biology (SB) plays a central role. SB allows the construction of various types of SCs that can be designed, tailored, and programmed according to specific predefined requirements. In particular, "bottom-up" SCs are briefly described by commenting on the principles of their design and fabrication and their features (in particular, the capacity to exchange chemicals with other SCs or with natural biological cells). Although bottom-up SCs still have low complexity and thus basic functionalities, here, we introduce their potential role in the IoBNT. This perspective paper aims to stimulate interest in and discussion on the presented topics. The article also includes commentaries on MC, semantic information, minimal cognition, wetware neuromorphic engineering, and chemical social robotics, with the specific potential they can bring to the IoBNT.

Autonomic Integration in Nested Protocell Communities

The self-driven organization of model protocells into higher-order nested cytomimetic systems with coordinated structural and functional relationships offers a step toward the autonomic implementation of artificial multicellularity. Here, we describe an endosymbiotic-like pathway in which proteinosomes are captured within membranized alginate/silk fibroin coacervate vesicles by guest-mediated reconfiguration of the host protocells. We demonstrate that interchange of coacervate vesicle and droplet morphologies through proteinosome-mediated urease/glucose oxidase activity produces discrete nested communities capable of integrated catalytic activity and selective disintegration. The self-driving capacity is modulated by an internalized fuel-driven process using starch hydrolases sequestered within the host coacervate phase, and structural stabilization of the integrated protocell populations can be achieved by on-site enzyme-mediated matrix reinforcement involving dipeptide supramolecular assembly or tyramine-alginate covalent cross-linking. Our work highlights a semi-autonomous mechanism for constructing symbiotic cell-like nested communities and provides opportunities for the development of reconfigurable cytomimetic materials with structural, functional, and organizational complexity.

Plant Cell-Inspired Membranization of Coacervate Protocells with a Structured Polysaccharide Layer

The design of compartmentalized colloids that exhibit biomimetic properties is providing model systems for developing synthetic cell-like entities (protocells). Inspired by the cell walls in plant cells, we developed a method to prepare membranized coacervates as protocell models by coating membraneless liquid-like microdroplets with a protective layer of rigid polysaccharides. Membranization not only endowed colloidal stability and prevented aggregation and coalescence but also facilitated selective biomolecule sequestration and chemical exchange across the membrane. The polysaccharide wall surrounding coacervate protocells acted as a stimuli-responsive structural barrier that enabled enzyme-triggered membrane lysis to initiate internalization and killing of Escherichia coli. The membranized coacervates were capable of spatial organization into structured tissue-like protocell assemblages, offering a means to mimic metabolism and cell-to-cell communication. We envision that surface engineering of protocells as developed in this work generates a platform for constructing advanced synthetic cell mimetics and sophisticated cell-like behaviors.

Autonomic self-regulating systems based on polyelectrolyte microcapsules and microgel particles

Biological systems possess unique non-equilibrium functions, maintaining tight manipulation of their surroundings through inter-communication of multiple components and self-regulatory capability organized over different length scales. However, most artificial materials are incapable of communicating and self-regulating behavior due to their limited number of component and direct responsive modes. Herein, a new integrated self-regulation system is developed utilizing stimuli-responsive polyelectrolyte capsules as building blocks. The combination of stimuli-responsive capsules and enzyme immobilized microgels is designed to mimic life systems and its programmable interactive communications and self-regulation behavior is demonstrated through communication-feedback mechanism. Polyelectrolyte capsules can sense changes of their surrounding, then start the internal communication by releasing energy-rich cargo mimicking the behavior of the cells. The microgel particles subsequently complete closed-loop communication through providing negative feedback on capsules by enzymatic reaction and actuating pH-regulation of the whole system. Different communication modes and pH-regulation behaviors could be achieved by adjusting spatial and kinetic conditions. Proposed intelligent system is highly customizable due to the wide selection of encapsulated cargos, stimuli-responsive blocks and reaction networks, and would have broad influences in areas ranging from medical implants that assist in stabilizing body functions to microreactor system that regulate catalytic reactions.

Self-Regulated and Bidirectional Communication in Synthetic Cell Communities

Cell-to-cell communication is not limited to a sender releasing a signaling molecule and a receiver perceiving it but is often self-regulated and bidirectional. Yet, in communities of synthetic cells, such features that render communication efficient and adaptive are missing. Here, we report the design and implementation of adaptive two-way signaling with lipid-vesicle-based synthetic cells. The first layer of self-regulation derives from coupling the temporal dynamics of the signal, H₂O₂, production in the sender to adhesions between sender and receiver cells. This way the receiver stays within the signaling range for the duration sender produces the signal and detaches once the signal fades. Specifically, H₂O₂ acts as both a forward signal and a regulator of the adhesions by activating photoswitchable proteins at the surface for the duration of the chemiluminescence. The second layer of self-regulation arises when the adhesions render the receiver permeable and trigger the release of a backward signal, resulting in bidirectional exchange. These design rules provide a concept for engineering multicellular systems with adaptive communication.

Orthogonal Light-Activated DNA for Patterned Biocomputing within Synthetic Cells

Cell-free gene expression is a vital research tool to study biological systems in defined minimal environments and has promising applications in biotechnology. Developing methods to control DNA templates for cell-free expression will be important for precise regulation of complex biological pathways and use with synthetic cells, particularly using remote, nondamaging stimuli such as visible light. Here, we have synthesized blue light-activatable DNA parts that tightly regulate cell-free RNA and protein synthesis. We found that this blue light-activated DNA could initiate expression orthogonally to our previously generated ultraviolet (UV) light-activated DNA, which we used to generate a dual-wavelength light-controlled cell-free AND-gate. By encapsulating these orthogonal light-activated DNAs into synthetic cells, we used two overlapping patterns of blue and UV light to provide precise spatiotemporal control over the logic gate. Our blue and UV orthogonal light-activated DNAs will open the door for precise control of cell-free systems in biology and medicine.

Trumpet is an operating system for simple and robust cell-free biocomputing

Biological computation is becoming a viable and fast-growing alternative to traditional electronic computing. Here we present a biocomputing technology called Trumpet: Transcriptional RNA Universal Multi-Purpose GatE PlaTform. Trumpet combines the simplicity and robustness of the simplest in vitro biocomputing methods, adding signal amplification and programmability, while avoiding common shortcomings of live cell-based biocomputing solutions. We have demonstrated the use of Trumpet to build all universal Boolean logic gates. We have also built a web-based platform for designing Trumpet gates and created a primitive processor by networking several gates as a proof-of-principle for future development. The Trumpet offers a change of paradigm in biocomputing, providing an efficient and easily programmable biological logic gate operating system.

A Theoretical Framework for Implementable Nucleic Acids Feedback Systems

Chemical reaction networks can be utilised as basic components for nucleic acid feedback control systems' design for Synthetic Biology application. DNA hybridisation and programmed strand-displacement reactions are effective primitives for implementation. However, the experimental validation and scale-up of nucleic acid control systems are still considerably falling behind their theoretical designs. To aid with the progress heading into experimental implementations, we provide here chemical reaction networks that represent two fundamental classes of linear controllers: integral and static negative state feedback. We reduced the complexity of the networks by finding designs with fewer reactions and chemical species, to take account of the limits of current experimental capabilities and mitigate issues pertaining to crosstalk and leakage, along with toehold sequence design. The supplied control circuits are quintessential candidates for the first experimental validations of nucleic acid controllers, since they have a number of parameters, species, and reactions small enough for viable experimentation with current technical capabilities, but still represent challenging feedback control systems. They are also well suited to further theoretical analysis to verify results on the stability, performance, and robustness of this important new class of control systems.

Transmembrane signaling by a synthetic receptor in artificial cells

Signal transduction across biological membranes is among the most important evolutionary achievements. Herein, for the design of artificial cells, we engineer fully synthetic receptors with the capacity of transmembrane signaling, using tools of chemistry. Our receptors exhibit similarity with their natural counterparts in having an exofacial ligand for signal capture, being membrane anchored, and featuring a releasable messenger molecule that performs enzyme activation as a downstream signaling event. The main difference from natural receptors is the mechanism of signal transduction, which is achieved using a self-immolative linker. The receptor scaffold is modular and can readily be re-designed to respond to diverse activation signals including biological or chemical stimuli. We demonstrate an artificial signaling cascade that achieves transmembrane enzyme activation, a hallmark of natural signaling receptors. Results of this work are relevant for engineering responsive artificial cells and interfacing them and/or biological counterparts in co-cultures.

Complex Coacervate Materials as Artificial Cells

Cells have evolved to be self-sustaining compartmentalized systems that consist of many thousands of biomolecules and metabolites interacting in complex cycles and reaction networks. Numerous subtle intricacies of these self-assembled structures are still largely unknown. The importance of liquid-liquid phase separation (both membraneless and membrane bound) is, however, recognized as playing an important role in achieving biological function that is controlled in time and space. Reconstituting biochemical reactions in vitro has been a success of the last decades, for example, establishment of the minimal set of enzymes and nutrients able to replicate cellular activities like the in vitro transcription translation of genes to proteins. Further than this though, artificial cell research has the aim of combining synthetic materials and nonliving macromolecules into ordered assemblies with the ability to carry out more complex and ambitious cell-like functions. These activities can provide insights into fundamental cell processes in simplified and idealized systems but could also have an applied impact in synthetic biology and biotechnology in the future. To date, strategies for the bottom-up fabrication of micrometer scale life-like artificial cells have included stabilized water-in-oil droplets, giant unilamellar vesicles (GUV's), hydrogels, and complex coacervates. Water-in-oil droplets are a valuable and easy to produce model system for studying cell-like processes; however, the lack of a crowded interior can limit these artificial cells in mimicking life more closely. Similarly membrane stabilized vesicles, such as GUV's, have the additional membrane feature of cells but still lack a macromolecularly crowded cytoplasm. Hydrogel-based artificial cells have a macromolecularly dense interior (although cross-linked) that better mimics cells, in addition to mechanical properties more similar to the viscoelasticity seen in cells but could be seen as being not dynamic in nature and limiting to the diffusion of biomolecules. On the other hand, liquid-liquid phase separated complex coacervates are an ideal platform for artificial cells as they can most accurately mimic the crowded, viscous, highly charged nature of the eukaryotic cytoplasm. Other important key features that researchers in the field target include stabilizing semipermeable membranes, compartmentalization, information transfer/communication, motility, and metabolism/growth. In this Account, we will briefly cover aspects of coacervation theory and then outline key cases of synthetic coacervate materials used as artificial cells (ranging from polypeptides, modified polysaccharides, polyacrylates, and polymethacrylates, and allyl polymers), finishing with envisioned opportunities and potential applications for coacervate artificial cells moving forward.

Bridging the Gap between Nonliving Matter and Cellular Life

A cell, the fundamental unit of life, contains the requisite blueprint information necessary to survive and to build tissues, organs, and systems, eventually forming a fully functional living creature. A slight structural alteration can result in data misprinting, throwing the entire life process off balance. Advances in synthetic biology and cell engineering enable the predictable redesign of biological systems to perform novel functions. Individual functions and fundamental processes at the core of the biology of cells can be investigated by employing a synthetically constrained micro or nanoreactor. However, constructing a life-like structure from nonliving building blocks remains a considerable challenge. Chemical compartments, cascade signaling, energy generation, growth, replication, and adaptation within micro or nanoreactors must be comparable with their biological counterparts. Although these reactors currently lack the power and behavioral sophistication of their biological equivalents, their interface with biological systems enables the development of hybrid solutions for real-world applications, such as therapeutic agents, biosensors, innovative materials, and biochemical microreactors. This review discusses the latest advances in cell membrane-engineered micro or nanoreactors, as well as the limitations associated with high-throughput preparation methods and biological applications for the real-time modulation of complex pathological states.

Artificial receptor-mediated phototransduction toward protocellular subcompartmentalization and signaling-encoded logic gates

Engineering artificial cellular systems capable of perceiving and transmitting external signals across membranes to activate downstream targets and coordinate protocellular responses is key to build cell-cell communications and protolife. Here, we report a synthetic photoreceptor-mediated signaling pathway with the integration of light harvesting, photo-to-chemical energy conversion, signal transmission, and amplification in synthetic cells, which ultimately resulted in protocell subcompartmentalization. Key to our design is a ruthenium-bipyridine complex that acts as a membrane-anchored photoreceptor to convert visible light into chemical information and transduce signals across the lipid membrane via flip-flop motion. By coupling receptor-mediated phototransduction with biological recognition and enzymatic cascade reactions, we further develop protocell signaling-encoded Boolean logic gates. Our results illustrate a minimal cell model to mimic the photoreceptor cells that can transduce the energy of light into intracellular responses and pave the way to modular control over the flow of information for complex metabolic and signaling pathways.

A Synthetic Protocell-Based Heparin Scavenger

Heparin is a commonly applied blood anticoagulant agent in clinical use. After treatment, excess heparin needs to be removed to circumvent side effects and recover the blood-clotting cascade. Most existing heparin antidotes rely on direct heparin binding and complexation, yet selective compartmentalization and sequestration of heparin would be beneficial for safety and efficiency. However, such systems have remained elusive. Herein, a semipermeable protein-based microcompartment (proteinosome) is loaded with a highly positively charged chitosan derivative, which can induce electrostatics-driven internalization of anionic guest molecules inside the compartment. Chitosan-loaded proteinosomes are subsequently employed to capture heparin, and an excellent heparin-scavenging performance is demonstrated under physiologically relevant conditions. Both the highly positive scavenger and the polyelectrolyte complex are confined and shielded by the protein compartment in a time-dependent manner. Moreover, selective heparin-scavenging behavior over serum albumin is realized through adjusting the localized scavenger or surrounding salt concentrations at application-relevant circumstances. In vitro studies reveal that the cytotoxicity of the cationic scavenger and the produced polyelectrolyte complex is reduced by protocell shielding. Therefore, the proteinosome-based systems may present a novel polyelectrolyte-scavenging method for biomedical applications.

Orthogonal Light-Dependent Membrane Adhesion Induces Social Self-Sorting and Member-Specific DNA Communication in Synthetic Cell Communities

Developing orthogonal chemical communication pathways in diverse synthetic cell communities is a considerable challenge due to the increased crosstalk and interference associated with large numbers of different types of sender-receiver pairs. Herein, the authors control which sender-receiver pairs communicate in a three-membered community of synthetic cells through red and blue light illumination. Semipermeable protein-polymer-based synthetic cells (proteinosomes) with complementary membrane-attached protein adhesion communicate through single-stranded DNA oligomers and synergistically process biochemical information within a community consisting of one sender and two different receiver populations. Different pairs of red and blue light-responsive protein-protein interactions act as membrane adhesion mediators between the sender and receivers such that they self-assemble and socially self-sort into different multicellular structures under red and blue light. Consequently, distinct sender-receiver pairs come into the signaling range depending on the light illumination and are able to communicate specifically without activation of the other receiver population. Overall, this work shows how photoswitchable membrane adhesion gives rise to different self-sorting protocell patterns that mediate member-specific DNA-based communication in ternary populations of synthetic cells and provides a step towards the design of orthogonal chemical communication networks in diverse communities of synthetic cells.

Self-Stacking Autocatalytic Molecular Circuit with Minimal Catalytic DNA Assembly

Isothermal autocatalytic DNA circuits have been proven to be versatile and powerful biocomputing platforms by virtue of their self-sustainable and self-accelerating reaction profiles, yet they are currently constrained by their complicated designs, severe signal leakages, and unclear reaction mechanisms. Herein, we developed a simpler-yet-efficient autocatalytic assembly circuit (AAC) for highly robust bioimaging in live cells and mice. The scalable and sustainable AAC system was composed of a mere catalytic DNA assembly reaction with minimal strand complexity and, upon specific stimulation, could reproduce numerous new triggers to expedite the whole reaction. Through in-depth theoretical simulations and systematic experimental demonstrations, the catalytic efficiency of these reproduced triggers was found to play a vital role in the autocatalytic profile and thus could be facilely improved to achieve more efficient and characteristic autocatalytic signal amplification. Due to its exponentially high signal amplification and minimal reaction components, our self-stacking AAC facilitated the efficient detection of trace biomolecules with low signal leakage, thus providing great clinical diagnosis and therapeutic assessment potential.

Extracting and characterizing protein-free megabase-pair DNA for in vitro experiments

Chromosome structure and function is studied using various cell-based methods as well as with a range of in vitro single-molecule techniques on short DNA substrates. Here, we present a method to obtain megabase-pair-length deproteinated DNA for in vitro studies. We isolated chromosomes from bacterial cells and enzymatically digested the native proteins. Mass spectrometry indicated that 97%-100% of DNA-binding proteins are removed from the sample. Fluorescence microscopy analysis showed an increase in the radius of gyration of the DNA polymers, while the DNA length remained megabase-pair sized. In proof-of-concept experiments using these deproteinated long DNA molecules, we observed DNA compaction upon adding the DNA-binding protein Fis or PEG crowding agents and showed that it is possible to track the motion of a fluorescently labeled DNA locus. These results indicate the practical feasibility of a "genome-in-a-box" approach to study chromosome organization from the bottom up.

Direct encapsulation of biomolecules in semi-permeable microcapsules produced with double-emulsions

Compartmentalization can serve different purposes such as the protection of biological active substances from the environment, or the creation of a unique combination of biomolecules for diagnostic, therapeutic, or other bioengineering applications. We present a method for direct encapsulation of molecules in biocompatible and semi-permeable microcapsules made from low-molecular weight poly(ethylene glycol) diacrylate (PEG-DA 258). Microcapsules are produced using a non-planar PDMS microfluidic chip allowing for one-step production of water-in-PEG-DA 258-in-water double-emulsions, which are polymerized with UV light into a poly-PEG-DA 258 shell. Semi-permeable microcapsules are obtained by adding an inert solvent to the PEG-DA 258. Due to the favorable hydrophilicity of poly-PEG-DA 258, proteins do not adsorb to the capsule shell, and we demonstrate the direct encapsulation of enzymes, which can also be dried in the capsules to preserve activity. Finally, we leverage capsule permeability for the implementation of a two-layer communication cascade using compartmentalized DNA strand displacement reactions. This work presents the direct encapsulation of active biomolecules in semi-permeable microcapsules, and we expect our platform to facilitate the development of artificial cells and generating encapsulated diagnostics or therapeutics.

Macrophage Reprogramming with Anti-miR223-Loaded Artificial Protocells Enhances In Vivo Cancer Therapeutic Potential

Several immune cell-expressed miRNAs (miRs) are associated with altered prognostic outcome in cancer patients, suggesting that they may be potential targets for development of cancer therapies. Here, translucent zebrafish (Danio rerio) is utilized to demonstrate that genetic knockout or knockdown of one such miR, microRNA-223 (miR223), globally or specifically in leukocytes, does indeed lead to reduced cancer progression. As a first step toward potential translation to a clinical therapy, a novel strategy is described for reprogramming neutrophils and macrophages utilizing miniature artificial protocells (PCs) to deliver anti-miRs against the anti-inflammatory miR223. Using genetic and live imaging approaches, it is shown that phagocytic uptake of anti-miR223-loaded PCs by leukocytes in zebrafish (and by human macrophages in vitro) effectively prolongs their pro-inflammatory state by blocking the suppression of pro-inflammatory cytokines, which, in turn, drives altered immune cell-cancer cell interactions and ultimately leads to a reduced cancer burden by driving reduced proliferation and increased cell death of tumor cells. This PC cargo delivery strategy for reprogramming leukocytes toward beneficial phenotypes has implications also for treating other systemic or local immune-mediated pathologies.

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.

Evolution of Transient Luminescent Assemblies Regulated by Trace Water in Organic Solvents

Trace water in organic solvents can play a crucial role in the construction of supramolecular assemblies, which has not gained enough attention until very recent years. Herein, we demonstrate that residual water in organic solvents plays a decisive role in the regulation of the evolution of assembled structures and their functionality. By adding Mg(ClO₄)₂ into a multi-component organic solution containing terpyridine-based ligand 3Tpy and monodentate imidazole-based ligand M2, the system underwent an unexpected kinetic evolution. Metallo-supramolecular polymers (MSP) formed first by the coordination of 3Tpy and Mg²⁺, but they subsequently decomposed due to the interference of M2, resulting in a transient MSP system. Further investigation revealed that this occurred because residual water in the solvent and M2 cooperatively coordinated with Mg²⁺. This allowed M2 to capture Mg²⁺ from MSP, which led to depolymerization. However, owing to the slow reaction between trace water/M2/Mg²⁺, the formation of MSP still occurred first. Therefore, water regulated both the thermodynamics and kinetics of the system and was the key factor for constructing the transient MSP. Fine-tuning the water content and other assembly motifs regulated the assembly evolution pathway, tuned the MSP lifetime, and made the luminescent color of the system undergo intriguing transition processes over time.