Dynamic Synthetic Cells Based on Liquid-Liquid Phase Separation

Constrained dynamics of DNA oligonucleotides in phase-separated droplets

Understanding the dynamics of biomolecules in complex environments is crucial for elucidating the effect of condensed and heterogeneous environments on their functional properties. A relevant environment-and one that can also be mimicked easily in vitro-is that of phase-separated droplets. While phase-separated droplet systems have been shown to compartmentalize a wide range of functional biomolecules, the effects of internal structuration of droplets on the dynamics and mobility of internalized molecules remain poorly understood. Here, we use fluorescence correlation spectroscopy to measure the dynamics of short oligonucleotides encapsulated within two representative kinds of uncharged and charged phase-separated droplets. We find that the internal structuration controls the oligonucleotide dynamics in these droplets, revealed by measuring physical parameters at high spatiotemporal resolution. By varying oligonucleotide length and salt concentrations (and thereby charge screening), we found that the dynamics are significantly affected in the noncharged droplets compared to the charged system. Our work lays the foundation for unraveling and quantifying the physical parameters governing biomolecular transport in the condensed environment.

Effect of trimethylamine-N-oxide on the phase separation of aqueous polyethylene glycol-600-Dextran-75 two-phase systems

The emergence of phase separation in both intracellular biomolecular condensates (membrane-less organelles) and in vitro aqueous two-phase systems (ATPS) relies on the formation of immiscible water-based phases/domains. The solvent properties and arrangement of hydrogen bonds within these domains have been shown to differ and can be modulated with the addition of various inorganic salts and osmolytes. The naturally occuring osmolyte, trimethylamine-N-oxide (TMAO), is well established as a biological condensate stabilizer whose presence results in enhanced phase separation of intracellular membrane-less compartments. Here, we show the unique effect of TMAO on the mechanism of phase separation in model PEG-600-Dextran-75 ATPS using dynamic and static light scattering in conjunction with ATR-FTIR and solvatochromic analysis. We observe that the presence of TMAO may enhance or destabilize phase separation depending on the concentration of phase forming components. Additionally, the behavior and density of mesoscopic polymer agglomerates, which arise prior to macroscopic phase separation, are altered by the presence and concentration of TMAO.

Interfacial Assembly of Bacterial Microcompartment Shell Proteins in Aqueous Multiphase Systems

Compartments are a fundamental feature of life, based variously on lipid membranes, protein shells, or biopolymer phase separation. Here, this combines self-assembling bacterial microcompartment (BMC) shell proteins and liquid-liquid phase separation (LLPS) to develop new forms of compartmentalization. It is found that BMC shell proteins assemble at the liquid-liquid interfaces between either 1) the dextran-rich droplets and PEG-rich continuous phase of a poly(ethyleneglycol)(PEG)/dextran aqueous two-phase system, or 2) the polypeptide-rich coacervate droplets and continuous dilute phase of a polylysine/polyaspartate complex coacervate system. Interfacial protein assemblies in the coacervate system are sensitive to the ratio of cationic to anionic polypeptides, consistent with electrostatically-driven assembly. In both systems, interfacial protein assembly competes with aggregation, with protein concentration and polycation availability impacting coating. These two LLPS systems are then combined to form a three-phase system wherein coacervate droplets are contained within dextran-rich phase droplets. Interfacial localization of BMC hexameric shell proteins is tunable in a three-phase system by changing the polyelectrolyte charge ratio. The tens-of-micron scale BMC shell protein-coated droplets introduced here can accommodate bioactive cargo such as enzymes or RNA and represent a new synthetic cell strategy for organizing biomimetic functionality.

Chapter 4: A Geological and Chemical Context for the Origins of Life on Early Earth

Within the first billion years of Earth's history, the planet transformed from a hot, barren, and inhospitable landscape to an environment conducive to the emergence and persistence of life. This chapter will review the state of knowledge concerning early Earth's (Hadean/Eoarchean) geochemical environment, including the origin and composition of the planet's moon, crust, oceans, atmosphere, and organic content. It will also discuss abiotic geochemical cycling of the CHONPS elements and how these species could have been converted to biologically relevant building blocks, polymers, and chemical networks. Proposed environments for abiogenesis events are also described and evaluated. An understanding of the geochemical processes under which life may have emerged can better inform our assessment of the habitability of other worlds, the potential complexity that abiotic chemistry can achieve (which has implications for putative biosignatures), and the possibility for biochemistries that are vastly different from those on Earth.

Chapter 1: The Astrobiology Primer 3.0

The Astrobiology Primer 3.0 (ABP3.0) is a concise introduction to the field of astrobiology for students and others who are new to the field of astrobiology. It provides an entry into the broader materials in this supplementary issue of Astrobiology and an overview of the investigations and driving hypotheses that make up this interdisciplinary field. The content of this chapter was adapted from the other 10 articles in this supplementary issue and thus represents the contribution of all the authors who worked on these introductory articles. The content of this chapter is not exhaustive and represents the topics that the authors found to be the most important and compelling in a dynamic and changing field.

Macromolecular Crowding, Phase Separation, and Homeostasis in the Orchestration of Bacterial Cellular Functions

Macromolecular crowding affects the activity of proteins and functional macromolecular complexes in all cells, including bacteria. Crowding, together with physicochemical parameters such as pH, ionic strength, and the energy status, influences the structure of the cytoplasm and thereby indirectly macromolecular function. Notably, crowding also promotes the formation of biomolecular condensates by phase separation, initially identified in eukaryotic cells but more recently discovered to play key functions in bacteria. Bacterial cells require a variety of mechanisms to maintain physicochemical homeostasis, in particular in environments with fluctuating conditions, and the formation of biomolecular condensates is emerging as one such mechanism. In this work, we connect physicochemical homeostasis and macromolecular crowding with the formation and function of biomolecular condensates in the bacterial cell and compare the supramolecular structures found in bacteria with those of eukaryotic cells. We focus on the effects of crowding and phase separation on the control of bacterial chromosome replication, segregation, and cell division, and we discuss the contribution of biomolecular condensates to bacterial cell fitness and adaptation to environmental stress.

Controlling the size and adhesion of DNA droplets using surface- enriched DNA molecules

Liquid droplets of biomolecules serve as organizers of the cellular interior and are of interest in biosensing and biomaterials applications. Here, we investigate means to tune the interfacial properties of a model biomolecular liquid consisting of multi-armed DNA 'nanostar' particles. We find that long DNA molecules that have binding affinity for the nanostars are preferentially enriched on the interface of nanostar droplets, thus acting as surfactants. Fluorescent measurements indicate that, in certain conditions, the interfacial density of the surfactant is around 20 per square micron, indicative of a sparse brush-like structure of the long, polymeric DNA. Increasing surfactant concentration leads to decreased droplet size, down to the sub-micron scale, consistent with droplet coalesence being impeded by the disjoining pressure created by the brush-like surfactant layer. Added DNA surfactant also keeps droplets from adhering to both hydrophobic and hydrophilic solid surfaces, apparently due to this same disjoining effect of the surfactant layer. We thus demonstrate control of the size and adhesive properties of droplets of a biomolecular liquid, with implications for basic biophysical understanding of such droplets, as well as for their applied use.

Tuning the bis-hydrophilic balance of microgels: A tool to control the stability of water-in-water emulsions

HYPOTHESIS

The stability of purely aqueous emulsions (W/W) formed by mixing incompatible polymers, can be achieved through the Pickering effect of particles adsorption at the interface. However, there is, as yet, no guideline regarding the chemical nature of the particles to predict whether they will stabilize a particular W/W emulsion. Bis-hydrophilic soft microgels, made of copolymerized poly(N-isopropylacrylamide) (pNIPAM) and dextran (Dex), act as very efficient stabilizers for PEO/Dextran emulsions, because the two polymers have an affinity for each polymer phase.

EXPERIMENTS

The ratio between both components of the microgels is varied in order to modulate the bis-hydrophilic balance, the content of Dex compared to pNIPAM varying from 0 to 60 wt%. The partition between the two aqueous phases and the adsorption of microgels at the W/W interface is measured by confocal microscopy. The stability of emulsions is assessed via turbidity measurements and microstructural investigations under sedimentation or compression.

FINDINGS

The adsorption of particles and their partitioning is found to evolve progressively as a function of bis-hydrophilic balance. At room temperature, the stability of the resulting W/W emulsions also depends on the bis-hydrophilic balance with a maximum of stability for the particles containing 50%wt of Dex, for the Dex-in-PEO emulsions, while the PEO-in-Dex become stable above this value. The thermo-responsiveness of the microgels translates into stability inversion of the emulsions below 50 wt% of Dex in the microgels, whereas above 50 wt%, no emulsion is stable. This work paves the way of a guideline to design efficient and responsive W/W stabilizers.

Enzyme-Mediated Temporal Control over the Conformational Disposition of a Condensed Protein in Macromolecular Crowded Media

Temporal regulation between input and output signals is one of the hallmarks of complex biological processes. Herein, we report that the conformational disposition of a protein in macromolecularly crowded media can be controlled with time using enzymes. First, we demonstrate the pH dependence of bovine serum albumin (BSA) condensation and conformational alteration in the presence of poly(ethylene glycol) as a crowder. However, by exploiting the strength of pH-modulatory enzymatic reactions (glucose oxidase and urease), the conversion time between the condensed and free forms can be tuned. Additionally, we demonstrate that the trapping of intermediate states with respect to the overall system at a particular α-helix or β-sheet composition and rotational mobility can be possible simply by altering the substrate concentration. Finally, we show that the intrinsic catalytic ability of BSA toward the Kemp elimination (KE) reaction is inhibited in the aggregated form but regained in the free form. In fact, the rate of KE reaction can also be actuated enzymatically in a temporal fashion, therefore demonstrating the programmability of a cascade of biochemical events in crowded media.

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.

Coacervate Droplets for Synthetic Cells

The design and construction of synthetic cells - human-made microcompartments that mimic features of living cells - have experienced a real boom in the past decade. While many efforts have been geared toward assembling membrane-bounded compartments, coacervate droplets produced by liquid-liquid phase separation have emerged as an alternative membrane-free compartmentalization paradigm. Here, the dual role of coacervate droplets in synthetic cell research is discussed: encapsulated within membrane-enclosed compartments, coacervates act as surrogates of membraneless organelles ubiquitously found in living cells; alternatively, they can be viewed as crowded cytosol-like chassis for constructing integrated synthetic cells. After introducing key concepts of coacervation and illustrating the chemical diversity of coacervate systems, their physicochemical properties and resulting bioinspired functions are emphasized. Moving from suspensions of free floating coacervates, the two nascent roles of these droplets in synthetic cell research are highlighted: organelle-like modules and cytosol-like templates. Building the discussion on recent studies from the literature, the potential of coacervate droplets to assemble integrated synthetic cells capable of multiple life-inspired functions is showcased. Future challenges that are still to be tackled in the field are finally discussed.

The Role of Chemically Innocent Polyanions in Active, Chemically Fueled Complex Coacervate Droplets

Complex coacervation describes the liquid-liquid phase separation of oppositely charged polymers. Active coacervates are droplets in which one of the electrolyte's affinity is regulated by chemical reactions. These droplets are particularly interesting because they are tightly regulated by reaction kinetics. For example, they serve as a model for membraneless organelles that are also often regulated by biochemical transformations such as post-translational modifications. They are also a great protocell model or could be used to synthesize life-they spontaneously emerge in response to reagents, compete, and decay when all nutrients have been consumed. However, the role of the unreactive building blocks, e.g., the polymeric compounds, is poorly understood. Here, we show the important role of the chemically innocent, unreactive polyanion of our chemically fueled coacervation droplets. We show that the polyanion drastically influences the resulting droplets' life cycle without influencing the chemical reaction cycle-either they are very dynamic or have a delayed dissolution. Additionally, we derive a mechanistic understanding of our observations and show how additives and rational polymer design help to create the desired coacervate emulsion life cycles.

pH-Responsive Elastin-Like Polypeptide Designer Condensates

Biomolecular condensates are macromolecular complexes formed by liquid-liquid phase separation. They regulate key biological functions by reversibly compartmentalizing molecules in cells, in a stimulus-dependent manner. Designing stimuli-responsive synthetic condensates is crucial for engineering compartmentalized synthetic cells that are able to mimic spatiotemporal control over the biochemical reactions. Here, we design and test a family of condensate-forming, pH-responsive elastin-like polypeptides (ELPs) that form condensates above critical pH values ranging between 4 and 7, for temperatures between 20 and at 37 °C. We show that the condensation occurs rapidly, in sharp pH intervals (ΔpH < 0.3). For eventual applications in engineering synthetic cell compartments, we demonstrate that multiple types of pH-responsive ELPs can form mixed condensates inside micron-sized vesicles. When genetically fused with enzymes, receptors, and signaling molecules, these pH-responsive ELPs could be potentially used as pH-switchable functional condensates for spatially controlling biochemistry in engineered synthetic cells.

Thermodynamically controlled multiphase separation of heterogeneous liquid crystal colloids

Phase separation is a universal physical transition process whereby a homogeneous mixture splits into two distinct compartments that are driven by the component activity, elasticity, or compositions. In the current work, we develop a series of heterogeneous colloidal suspensions that exhibit both liquid-liquid phase separation of semiflexible binary polymers and liquid crystal phase separation of rigid, rod-like nanocellulose particles. The phase behavior of the multicomponent mixture is controlled by the trade-off between thermodynamics and kinetics during the two transition processes, displaying cholesteric self-assembly of nanocellulose within or across the compartmented aqueous phases. Upon thermodynamic control, two-, three-, and four-phase coexistence behaviors with rich liquid crystal stackings are realized. Among which, each relevant multiphase separation kinetics shows fundamentally different paths governed by nucleation and growth of polymer droplets and nanocellulose tactoids. Furthermore, a coupled multiphase transition can be realized by tuning the composition and the equilibrium temperature, which results in thermotropic behavior of polymers within a lyotropic liquid crystal matrix. Finally, upon drying, the multicomponent mixture undergoes a hierarchical self-assembly of nanocellulose and polymers into stratified cholesteric films, exhibiting compartmentalized polymer distribution and anisotropic microporous structure.

Effect of charge on the stabilization of water-in-water emulsions by thermosensitive bis-hydrophilic microgels

HYPOTHESIS

Molecular surfactants are not able to stabilize water-in-water (W/W) emulsions, unlike nano or micro-particles, which can achieve this in some cases. However, the effect of electrostatic interactions between particles on the emulsion stability has rarely been investigated. We hypothesize that introducing charges modifies the stabilization capacity of particles and renders it both pH- and ionic strength-dependent.

EXPERIMENTS

Charge was introduced into bis-hydrophilic and thermoresponsive dextran/polyN-isopropylacrylamide microgels by replacing a small fraction of polyN-isopropylacrylamide with acrylic acid groups. The size of the microgels was obtained by dynamic light scattering. The stability and microstructure of dextran/poly(ethyleneoxide)-based W/W emulsions, was studied as a function of pH, NaCl concentration and temperature using confocal microscopy and by analytical centrifugation.

FINDINGS

The swelling degree of charged microgels depends on the pH, ionic strength and the temperature. In the absence of salt, charged microgels do not adsorb at the interface and have little stabilizing effect even after neutralization. However, the interfacial coverage and the stability increase with rising concentration of NaCl. Saltinduced stabilization of these emulsions was also observed at 50 °C. Increasing the temperature strongly influences the emulsion stability at low pH.

Non-enzymatic oligonucleotide ligation in coacervate protocells sustains compartment-content coupling

Modern cells are complex chemical compartments tightly regulated by an underlying DNA-encoded program. Achieving a form of coupling between molecular content, chemical reactions, and chassis in synthetic compartments represents a key step to the assembly of evolvable protocells but remains challenging. Here, we design coacervate droplets that promote non-enzymatic oligonucleotide polymerization and that restructure as a result of the reaction dynamics. More specifically, we rationally exploit complexation between end-reactive oligonucleotides able to stack into long physical polymers and a cationic azobenzene photoswitch to produce three different phases-soft solids, liquid crystalline or isotropic coacervates droplets-each of them having a different impact on the reaction efficiency. Dynamical modulation of coacervate assembly and dissolution via trans-cis azobenzene photo-isomerization is used to demonstrate cycles of light-actuated oligonucleotide ligation. Remarkably, changes in the population of polynucleotides during polymerization induce phase transitions due to length-based DNA self-sorting to produce multiphase coacervates. Overall, by combining a tight reaction-structure coupling and environmental responsiveness, our reactive coacervates provide a general route to the non-enzymatic synthesis of polynucleotides and pave the way to the emergence of a primitive compartment-content coupling in membrane-free protocells.

Multispecies autocatalytic RNA reaction networks in coacervates

Robust localization of self-reproducing autocatalytic chemistries is a key step in the realization of heritable and evolvable chemical systems. While autocatalytic chemical reaction networks already possess attributes such as heritable self-reproduction and evolvability, localizing functional multispecies networks within complex primitive phases, such as coacervates, has remained unexplored. Here, we show the self-reproduction of the Azoarcus ribozyme system within charge-rich coacervates where catalytic ribozymes are produced by the autocatalytic assembly of constituent smaller RNA fragments. We systematically demonstrate the catalytic assembly of active ribozymes within phase-separated coacervates-both in micron-sized droplets as well as in a coalesced macrophase, underscoring the facility of the complex, charge-rich phase to support these reactions in multiple configurations. By constructing multispecies reaction networks, we show that these newly assembled molecules are active, participating both in self- and cross-catalysis within the coacervates. Finally, due to differential molecular transport, these phase-separated compartments endow robustness to the composition of the collectively autocatalytic networks against external perturbations. Altogether, our results establish the formation of multispecies self-reproducing reaction networks in phase-separated compartments which in turn render transient robustness to the network composition.

DNA Droplets: Intelligent, Dynamic Fluid

Breathtaking advances in DNA nanotechnology have established DNA as a promising biomaterial for the fabrication of programmable higher-order nano/microstructures. In the context of developing artificial cells and tissues, DNA droplets have emerged as a powerful platform for creating intelligent, dynamic cell-like machinery. DNA droplets are a microscale membrane-free coacervate of DNA formed through phase separation. This new type of DNA system couples dynamic fluid-like property with long-established DNA programmability. This hybrid nature offers an advantageous route to facile and robust control over the structures, functions, and behaviors of DNA droplets. This review begins by describing programmable DNA condensation, commenting on the physical properties and fabrication strategies of DNA hydrogels and droplets. By presenting an overview of the development pathways leading to DNA droplets, it is shown that DNA technology has evolved from static, rigid systems to soft, dynamic systems. Next, the basic characteristics of DNA droplets are described as intelligent, dynamic fluid by showcasing the latest examples highlighting their distinctive features related to sequence-specific interactions and programmable mechanical properties. Finally, this review discusses the potential and challenges of numerical modeling able to connect a robust link between individual sequences and macroscopic mechanical properties of DNA droplets.

Assembly of biomimetic microreactors using caged-coacervate droplets

Complex coacervates are liquid-like droplets that can be used to create adaptive cell-like compartments. These compartments offer a versatile platform for the construction of bioreactors inspired by living cells. However, the lack of a membrane significantly reduces the colloidal stability of coacervates in terms of fusion and surface wetting, which limits their suitability as compartments. Here, we describe the formation of caged-coacervates surrounded by a semipermeable shell of silica nanocapsules. We demonstrate that the silica nanocapsules create a protective shell that also regulates the molecular transport of water-soluble compounds as a function of nanocapasule size. The adjustable semipermeability and intrinsic affinity of enzymes for the interior of the caged-coacervates allowed us to assemble biomimetic microreactors with enhanced colloidal stability.

Membranized Coacervate Microdroplets: from Versatile Protocell Models to Cytomimetic Materials

Although complex coacervate microdroplets derived from associative phase separation of counter-charged electrolytes have emerged as a broad platform for the bottom-up construction of membraneless, molecularly crowded protocells, the absence of an enclosing membrane limits the construction of more sophisticated artificial cells and their use as functional cytomimetic materials. To address this problem, we and others have recently developed chemical-based strategies for the membranization of preformed coacervate microdroplets. In this Account, we review our recent work on diverse coacervate systems using a range of membrane building blocks and assembly processes. First, we briefly introduce the unusual nature of the coacervate/water interface, emphasizing the ultralow interfacial tension and broad interfacial width as physiochemical properties that require special attention in the judicious design of membranized coacervate microdroplets. Second, we classify membrane assembly into two different approaches: (i) interfacial self-assembly by using diverse surface-active building blocks such as molecular amphiphiles (fatty acids, phospholipids, block copolymers, protein-polymer conjugates) or nano- and microscale objects (liposomes, nanoparticle surfactants, cell fragments, living cells) with appropriate wettability; and (ii) coacervate droplet-to-vesicle reconfiguration by employing auxiliary surface reconstruction agents or triggering endogenous transitions (self-membranization) under nonstoichiometric (charge mismatched) conditions. We then discuss the key cytomimetic behaviors of membranized coacervate-based model protocells. Customizable permeability is achieved by synergistic effects operating between the molecularly crowded coacervate interior and surrounding membrane. In contrast, metabolic-like endogenous reactivity, diffusive chemical signaling, and collective chemical operations occur specifically in protocell networks comprising diverse populations of membranized coacervate microdroplets. In each case, these cytomimetic behaviors can give rise to functional microscale materials capable of promising cell-like applications. For example, immobilizing spatially segregated enzyme-loaded phospholipid-coated coacervate protocells in concentrically tubular hydrogels delivers prototissue-like bulk materials that generate nitric oxide in vitro, enabling platelet deactivation and inhibition of blood clot formation. Alternatively, therapeutic protocells with in vivo vasoactivity, high hemocompatibility, and increased blood circulation times are constructed by spontaneous assembly of hemoglobin-containing cell-membrane fragments on the surface of enzyme-loaded coacervate microdroplets. Higher-order properties such as artificial endocytosis are achieved by using nanoparticle-caged coacervate protocell hosts that selectively and actively capture guest nano- and microscale objects by responses to exogenous stimuli or via endogenous enzyme-mediated reactions. Finally, we discuss the current limitations in the design and programming of membranized coacervate microdroplets, which may help to guide future directions in this emerging research area. Taken together, we hope that this Account will inspire new advances in membranized coacervate microdroplets and promote their application in the development of integrated protocell models and functional cytomimetic materials.

Mechanism of Phase Separation in Aqueous Two-Phase Systems

Liquid-liquid phase separation underlies the formation of membrane-less organelles inside living cells. The mechanism of this process can be examined using simple aqueous mixtures of two or more solutes, which are able to phase separate at specific concentration thresholds. This work presents the first experimental evidence that mesoscopic changes precede visually detected macroscopic phase separation in aqueous mixtures of two polymers and a single polymer and salt. Dynamic light scattering (DLS) analysis indicates the formation of mesoscopic polymer agglomerates in these systems. These agglomerates increase in size with increasing polymer concentrations prior to visual phase separation. Such mesoscopic changes are paralleled by changes in water structure as evidenced by Attenuated Total Reflection-Fourier Transform Infrared (ATR-FTIR) spectroscopic analysis of OH-stretch bands. Through OH-stretch band analysis, we obtain quantitative estimates of the relative fractions of four subpopulations of water structures coexisting in aqueous solutions. These estimates indicate that abrupt changes in hydrogen bond arrangement take place at concentrations below the threshold of macroscopic phase separation. We used these experimental observations to develop a model of phase separation in aqueous media.

Mechanistic Insights into the Phase Separation Behavior and Pathway-Directed Information Exchange in all-DNA Droplets

Liquid-liquid phase separation provides a versatile approach to fabricating cell-mimicking coacervates. Recently, it was discovered that phase separation of single-stranded DNA (ssDNA) allows for forming protocells and microgels in multicomponent systems. However, the mechanism of the ssDNA phase separation is not comprehensively understood. Here, we present mechanistic insights into the metal-dependent phase separation of ssDNA and leverage this understanding for a straightforward formation of all-DNA droplets. Two phase separation temperatures are found that correspond to the formation of primary nuclei and a growth process. Ca²⁺ allows for irreversible, whereas Mg²⁺ leads to reversible phase separation. Capitalizing on these differences makes it possible to control the information transfer of one-component DNA droplets and two-component core-shell protocells. This study introduces new kinetic traps of phase separating ssDNA that lead to new phenomena in cell-mimicking systems.

Leveraging ultra-low interfacial tension and liquid-liquid phase separation in embedded 3D bioprinting

Many recently developed 3D bioprinting strategies operate by extruding aqueous biopolymer solutions directly into a variety of different support materials constituted from swollen, solvated, aqueous, polymer assemblies. In developing these 3D printing methods and materials, great care is often taken to tune the rheological behaviors of both inks and 3D support media. By contrast, much less attention has been given to the physics of the interfaces created when structuring one polymer phase into another in embedded 3D printing applications. For example, it is currently unclear whether a dynamic interfacial tension between miscible phases stabilizes embedded 3D bioprinted structures as they are shaped while in a liquid state. Interest in the physics of interfaces between complex fluids has grown dramatically since the discovery of liquid-liquid phase separation (LLPS) in living cells. We believe that many new insights coming from this burst of investigation into LLPS within biological contexts can be leveraged to develop new materials and methods for improved 3D bioprinting that leverage LLPS in mixtures of biopolymers, biocompatible synthetic polymers, and proteins. Thus, in this review article, we highlight work at the interface between recent LLPS research and embedded 3D bioprinting methods and materials, and we introduce a 3D bioprinting method that leverages LLPS to stabilize printed biopolymer inks embedded in a bioprinting support material.

Dynamic Compartmentalization of Peptide-Oligonucleotide Conjugates with Reversible Nanovesicle-Microdroplet Phase Transition Behaviors

Developing artificial microsystems based on liquid-liquid phase separation (LLPS) to mimic cellular dynamic compartmentalization has gained increasing attention. However, limitations including complicated components and laborious fabrication techniques have hindered their development. Herein, we describe a new single-component dynamic compartmentalization system using peptide-oligonucleotide conjugates (POCs) produced from short elastin-like polypeptides (sELPs) and oligonucleotides (ONs), which can perform thermoreversible phase transition between a nanovesicle and a microdroplet. The phase transition of sELP-ONs is thoroughly investigated, of which the transition temperature can be controlled by concentration, length of sELPs and ONs, base sequences, and salt. Moreover, the sELP-ON microcompartment can enrich a variety of functional molecules including small molecules, polysaccharides, proteins, and nucleic acids. Two sELP-ON compartments are used as nano- and microreactors for enzymatic reactions, separately, in which chemical activities are successfully regulated under different-scaled confinement effects, demonstrating their broad potential application in matter exchange and artificial cells.

Application of Super Photoacids in Controlling Dynamic Processes: Light-Triggering the Self-Propulsion of Oil Droplets

The dynamic control of pH-responsive systems is at the heart of many natural and artificial processes. Here, we use photoacids, molecules that dissociate only in their excited state and transfer their proton to nearby proton acceptors, for the dynamic control of processes. A problem arises when there is a need to protonate highly acidic acceptors. We solve this problem using super photoacids that have an excited-state pK_a of -8, thus enabling them to protonate very weak proton acceptors. The process that we target is the light-triggered self-propulsion of droplets, initiated by an excited-state proton transfer (ESPT) from a super photoacid donor to a surfactant acceptor situated on the surface of the droplet with a pK_a of ∼0. We first confirm using steady-state and time-resolved spectroscopy that a super photoacid can undergo ESPT to the acidic surfactant, whereas a "regular" photoacid cannot. Next, we show self-propulsion of the droplet upon irradiating the solvated super photoacid. We further confirm the protonation of the surfactant on the surface of the droplet using transient surface tension measurements. Our system is the first example of the application of super photoacids to control dynamic processes and opens new possibilities in the field of light-triggered dynamic systems.

Signal-processing and adaptive prototissue formation in metabolic DNA protocells

The fundamental life-defining processes in living cells, such as replication, division, adaptation, and tissue formation, occur via intertwined metabolic reaction networks that process signals for downstream effects with high precision in a confined, crowded environment. Hence, it is crucial to understand and reenact some of these functions in wholly synthetic cell-like entities (protocells) to envision designing soft materials with life-like traits. Herein, we report on all-DNA protocells composed of a liquid DNA interior and a hydrogel-like shell, harboring a catalytically active DNAzyme, that converts DNA signals into functional metabolites that lead to downstream adaptation processes via site-selective strand displacement reactions. The downstream processes include intra-protocellular phenotype-like changes, prototissue formation via multivalent interactions, and chemical messenger communication between active sender and dormant receiver cell populations for sorted heteroprototissue formation. The approach integrates several tools of DNA-nanoscience in a synchronized way to mimic life-like behavior in artificial systems for future interactive materials.

Chemical Communication in Artificial Cells: Basic Concepts, Design and Challenges

In the past decade, the focus of bottom-up synthetic biology has shifted from the design of complex artificial cell architectures to the design of interactions between artificial cells mediated by physical and chemical cues. Engineering communication between artificial cells is crucial for the realization of coordinated dynamic behaviours in artificial cell populations, which would have implications for biotechnology, advanced colloidal materials and regenerative medicine. In this review, we focus our discussion on molecular communication between artificial cells. We cover basic concepts such as the importance of compartmentalization, the metabolic machinery driving signaling across cell boundaries and the different modes of communication used. The various studies in artificial cell signaling have been classified based on the distance between sender and receiver cells, just like in biology into autocrine, juxtacrine, paracrine and endocrine signaling. Emerging tools available for the design of dynamic and adaptive signaling are highlighted and some recent advances of signaling-enabled collective behaviours, such as quorum sensing, travelling pulses and predator-prey behaviour, are also discussed.

Thermo-induced inversion of water-in-water emulsion stability by bis-hydrophilic microgels

HYPOTHESIS

Stabilization of water-in-water (W/W) emulsions resulting from the separation of polymeric phases such as dextran (DEX) and poly(ethyleneoxide) (PEO) is highly challenging, because of the very low interfacial tensions between the two phases and because of the interface thickness extending over several nanometers. In the present work, we present a new type of stabilizers, based on bis-hydrophilic, thermoresponsive microgels, incorporating in the same structure poly(N-isopropylacrylamide) (pNIPAM) chains having an affinity for the PEO phase and dextran moieties. We hypothesize that these particles allow better control of the stability of the W/W emulsions.

EXPERIMENTS

The microgels were synthesized by copolymerizing the NIPAM monomer with a multifunctional methacrylated dextran. They were characterized by dynamic light scattering, zeta potential measurements and nuclear magnetic resonance as a function of temperature. Microgels with different compositions were tested as stabilizers of droplets of the PEO phase dispersed in the DEX phase (P/D) or vice-versa (D/P), at different concentrations and temperatures.

FINDINGS

Only microgels with the highest DEX content revealed excellent stabilizing properties for the emulsions by adsorbing at the droplet surface, thus demonstrating the fundamental role of bis-hydrophilicity. At room temperature, both pNIPAM and DEX chains were swollen by water and stabilized better D/P emulsions. However, above the volume phase transition temperature (VPTT ≈ 32 °C) of pNIPAM the microgels shrunk and stabilized better P/D emulsions. At all temperatures, excess microgels partitioned more to the PEO phase. The change in structure and interparticle interaction induced by heating can be exploited to control the W/W emulsion stability.

Fatty Acid-Based Coacervates as a Membrane-free Protocell Model

Membrane-less scenarios that involve liquid-liquid phase separation (coacervation) provide clues for how protocells might emerge. Here, we report a versatile approach to construct coacervates by mixing fatty acid with biomolecule dopamine as the protocell model. The coacervate droplets are easily formed over a wide range of concentrations. The solutes with different interaction characteristics, including cationic, anionic, and hydrophobic dyes, can be well concentrated within the coacervates. In addition, reversible self-assemblies of the coacervates can be controlled by concentration, pH, temperature, salinity, and bioreaction realizing cycles between compartmentalization and noncompartmentalization. Through in situ dopamine polymerization, the stability of coacervate droplets is significantly improved, leading to higher resistance toward external factors. Therefore, the coacervates based on fatty acid and dopamine could serve as a bottom-up membrane-less protocell model that provides the links between the simple (small molecule) and complex (macromolecule) systems in the process of cell evolution.

Microfluidic Control of Coexisting Chemical Microenvironments within Multiphase Water-in-Fluorocarbon Droplets

The use of aqueous polymer-based phase separation within water-in-oil emulsion droplets provides a powerful platform for exploring the impact of compartmentalization and preferential partitioning on biologically relevant solutes. By forming an emulsion, a bulk solution is converted into a large number of chemically isolated microscale droplets. Microfluidic techniques provide an additional level of control over the formation of such systems. This enables the selective production of multiphase droplets with desired solution compositions and specific characteristics, such as solute partitioning. Here, we demonstrate control over the chemical microenvironment by adjusting the composition to increase tie line length for poly(ethylene glycol) (PEG)-dextran aqueous two-phase systems (ATPS) encapsulated within multiphase water-in-fluorocarbon oil emulsion droplets. Through rational adjustment of microfluidic parameters alone, ATPS droplets containing differing compositions could be produced during the course of a single experiment, with the produced droplets demonstrating a controllable range of tie line lengths. This provided control over partitioning behavior for biologically relevant macromolecules such that the difference in local protein concentration between adjacent phases could be rationally tuned. This work illustrates a broadly applicable technique to rationally create emulsified multiphase aqueous systems of desired compositions through the adjustment of microfluidic parameters alone, allowing for easy and rapid screening of various chemical microenvironments.

Programmable Zwitterionic Droplets as Biomolecular Sorters and Model of Membraneless Organelles

Increasing evidence indicates that cells can regulate biochemical functions in time and space by generating membraneless compartments with well-defined mesoscopic properties. One important mechanism underlying this control is simple coacervation driven by associative disordered proteins that encode multivalent interactions. Inspired by these observations, programmable droplets based on simple coacervation of responsive synthetic polymers that mimic the "stickers-and-spacers" architecture of biological disordered proteins are developed. Zwitterionic polymers that undergo an enthalpy-driven liquid-liquid phase separation process and form liquid droplets that remarkably exclude most molecules are developed. Starting from this reference material, different functional groups in the zwitterionic polymer are progressively added to encode an increasing number of different intermolecular interactions. This strategy allowed the multiple emerging properties of the droplets to be controlled independently, such as stimulus-responsiveness, polarity, selective uptake of client molecules, fusion times, and miscibility. By exploiting this high programmability, a model of cellular compartmentalization is reproduced and droplets capable of confining different molecules in space without physical barriers are generated. Moreover, these biomolecular sorters are demonstrated to be able to localize, separate, and enable the detection of target molecules even within complex mixtures, opening attractive applications in bioseparation, and diagnostics.

Coacervate microdroplet protocell-mediated gene transfection for nitric oxide production and induction of cell apoptosis

Liquid coacervate microdroplets have been widely explored as membrane-free compartment protocells for cargo delivery in therapeutic applications. In this study, coacervate protocells were developed as gene carriers for transfection of nitric oxide synthase (NOS) and overproduction of nitric oxide (NO) for killing of cancer cells. The coacervate microdroplet protocells were formed via the liquid-liquid phase separation of oppositely charged diethylaminoethyl-dextran/polyacrylic acids. The coacervate microdroplet protocells were found to facilitate gene transfection, which was demonstrated by cell imaging of the internalized coacervate microdroplets containing plasmids of enhanced green fluorescent protein. Due to their high transfection capability, the coacervate protocells were subsequently utilized for the delivery of NOS plasmids (pNOS). The cellular internalization of pNOS-containing coacervate carriers was found to result in high NOS expression coupled with NO overproduction, which then induced cell apoptosis and decreased cell viability. The cell apoptosis is associated with NO-mediated mitochondrial damage. The enhanced gene transfection was attributed to coacervate microdroplets' unique high sequestration capability and liquid-like fluidity. Overall, the incorporation of genes in coacervate microdroplets was demonstrated as a viable and novel strategy for the development of cargo biocarriers for biomedical applications.

Hydrogen Bond Arrangement Is Shown to Differ in Coexisting Phases of Aqueous Two-Phase Systems

Analysis by attenuated total reflection–Fourier transform infrared spectroscopy shows that each coexisting phase in aqueous two-phase systems has a different arrangement of hydrogen bonds. Specific arrangements vary for systems formed by different solutes. The hydrogen bond arrangement is shown to correlate with differences in hydrophobic and electrostatic properties of the different phases of five specific systems, four formed by two polymers and one by a single polymer and salt. The results presented here suggest that the arrangement of hydrogen bonds may be an important factor in phase separation.

Chemical communication at the synthetic cell/living cell interface

Although the complexity of synthetic cells has continued to increase in recent years, chemical communication between protocell models and living organisms remains a key challenge in bottom-up synthetic biology and bioengineering. In this Review, we discuss how communication channels and modes of signal processing can be established between living cells and cytomimetic agents such as giant unilamellar lipid vesicles, proteinosomes, polysaccharidosomes, polymer-based giant vesicles and membrane-less coacervate micro-droplets. We describe three potential modes of chemical communication in consortia of synthetic and living cells based on mechanisms of distributed communication and signal processing, physical embodiment and nested communication, and network-based contact-dependent communication. We survey the potential for applying synthetic cell/living cell communication systems in biomedicine, including the in situ production of therapeutics and development of new bioreactors. Finally, we present a short summary of our findings.

Proliferating coacervate droplets as the missing link between chemistry and biology in the origins of life

The hypothesis that prebiotic molecules were transformed into polymers that evolved into proliferating molecular assemblages and eventually a primitive cell was first proposed about 100 years ago. To the best of our knowledge, however, no model of a proliferating prebiotic system has yet been realised because different conditions are required for polymer generation and self-assembly. In this study, we identify conditions suitable for concurrent peptide generation and self-assembly, and we show how a proliferating peptide-based droplet could be created by using synthesised amino acid thioesters as prebiotic monomers. Oligopeptides generated from the monomers spontaneously formed droplets through liquid-liquid phase separation in water. The droplets underwent a steady growth-division cycle by periodic addition of monomers through autocatalytic self-reproduction. Heterogeneous enrichment of RNA and lipids within droplets enabled RNA to protect the droplet from dissolution by lipids. These results provide experimental constructs for origins-of-life research and open up directions in the development of peptide-based materials.

Directing Transition of Synthetic Protocell Models via Physicochemical Cues-Triggered Interfacial Dynamic Covalent Chemistry

As the preliminary synthetic analogs of living cells, protocells with life-like features serve as a versatile platform to explore the origin of life. Although protocells constructed from multiple components have been developed, the transition of primitive cellular compartments toward structural complexity and advanced function remains a scientific challenge. Herein, a programmable pathway is established to exploit a simple chemistry to construct structural transition of protocell models from emulsion droplets, nanocapsules to molecularly crowded droplets. The transitional process toward distinct cell-like compartments is driven by interfacial self-assembly of simple components and regulated by physicochemical cues (e.g., mechanical force, solvent evaporation, acid/base equilibrium) triggered dynamic covalent chemistry. These protocell models are further studied by comparing their compartmentalization behavior, sequestration efficiency, and the ability to enrich biomolecules (e.g., enzyme and substrate) toward catalytic reaction or biological activity within the compartments. The results showcase physiochemical cues-driven programmable transition of life-like compartments toward functionalization, and offer a new step toward the design of living soft materials.

Phase Separation and Protein Partitioning in Compartmentalized Cell-Free Expression Reactions

Liquid-liquid phase separation (LLPS) is important to control a wide range of reactions from gene expression to protein degradation in a cell-sized space. To bring a better understanding of the compatibility of such phase-separated structures with protein synthesis, we study emergent LLPS in a cell-free transcription-translation (TXTL) reaction. When the TXTL reaction composed of many proteins is concentrated, the uniformly mixed state becomes unstable, and membrane-less phases form spontaneously. This LLPS droplet formation is induced when the TXTL reaction is enclosed in water-in-oil emulsion droplets, in which water evaporates from the surface. As the emulsion droplets shrink, smaller LLPS droplets appear inside the emulsion droplets and coalesce into large phase-separated domains that partition the localization of synthesized reporter proteins. The presence of PEG in the TXTL reaction is important not only for versatile cell-free protein synthesis but also for the formation of two large domains capable of protein partitioning. Our results may shed light on the dynamic interplay of LLPS formation and cell-free protein synthesis toward the construction of synthetic organelles.

Translation-coupled RNA replication and parasitic replicators in membrane-free compartments

We report RNA self-replication through the translation of its encoded protein within membrane-free compartments generated by liquid-liquid phase separation. The aqueous droplets support RNA self-replication by concentrating a genomic RNA and translation proteins, facilitating the uptake of small substrates, and preventing the replication of parasitic RNAs through compartmentalization.

Membrane-confined liquid-liquid phase separation toward artificial organelles

As the basic unit of life, cells are compartmentalized microreactors with molecularly crowded microenvironments. The quest to understand the cell origin inspires the design of synthetic analogs to mimic their functionality and structural complexity. In this work, we integrate membraneless coacervate microdroplets, a prototype of artificial organelles, into a proteinosome to build hierarchical protocells that may serve as a more realistic model of cellular organization. The protocell subcompartments can sense extracellular signals, take actions in response to these stimuli, and adapt their physicochemical behaviors. The tiered protocells are also capable of enriching biomolecular reactants within the confined organelles, thereby accelerating enzymatic reactions. The ability of signal processing inside protocells allows us to design the Boolean logic gates (NOR and NAND) using biochemical inputs. Our results highlight possible exploration of protocell-community signaling and render a flexible synthetic platform to study complex metabolic reaction networks and embodied chemical computation.

Exploring New Horizons in Liquid Compartmentalization via Microfluidics

Spatial organization of cellular processes is crucial to efficiently regulate life's essential reactions. Nature does this by compartmentalization, either using membranes, such as the cell and nuclear membrane, or by liquid-like droplets formed by aqueous liquid-liquid phase separation. Aqueous liquid-liquid phase separation can be divided in two different phenomena, associative and segregative phase separation, of which both are studied for their membraneless compartmentalization abilities. For centuries, segregative phase separation has been used for the extraction and purification of biomolecules. With the emergence of microfluidic techniques, further exciting possibilities were explored because of their ability to fine-tune phase separation within emulsions of various compositions and morphologies and achieve one of the simplest forms of compartmentalization. Lately, interest in aqueous liquid-liquid phase separation has been revived due to the discovery of membraneless phases within the cell. In this Perspective we focus on segregative aqueous phase separation, discuss the theory of this interesting phenomenon, and give an overview of the evolution of aqueous phase separation in microfluidics.