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

Peptide nanoarchitectonics beyond long-range ordering

Long-range disordered structures are ubiquitous in biological organisms and hold crucial significance for their unique structure and function. Inspired by these natural architectures, much attention has been devoted to constructing long-range disordered materials based on biomolecules in vitro. Peptides, especially short peptides consisting of several to dozens of amino acids, have emerged as ideal building blocks due to their versatile structural and functional diversity, along with their notable biocompatibility and biodegradability. As a result, significant efforts have been made to develop short peptide nanoarchitectonics with long-range disorder (SPNLRD). Understanding the fundamental mechanisms underlying the formation of SPNLRD is crucial for the precise design and construction of these architectures with specific functionalities. This review summarizes the latest advancements in the construction and application of SPNLRD. We place particular emphasis on the design principles for SPNLRD construction and stabilization, based on a comprehensive discussion from the perspectives of thermodynamics, kinetics and intermolecular interactions. Finally, we assess the critical challenges currently facing SPNLRD and highlight the future directions in the field, proposing research strategies aimed at enhancing the stability and improving the precision of control over these materials.

Light-Responsive Mononucleotide Coacervates

Liquid-liquid phase separation (LLPS) is central to the formation of biomolecular condensates in modern cells and is also explored as a mechanism for assembling protocells. Phase-separated droplets provide dynamic micro-environments that concentrate reactants, enhance reactions, and allow molecular exchange, essential for both cellular regulation, and adaptive compartmentalization. While modern cells achieve dynamic LLPS through enzymatic and metabolic pathways, protocells may be designed to harness external stimuli such as pH, temperature, redox potential, or light. However, existing studies of light-responsive coacervates rely on complex biomolecules, limiting their use as minimal platforms of energy-driven phase separation. Here, we develop a minimal system of light-responsive coacervates composed of low-molecular-weight species: mononucleotides and azobenzene-based amphiphiles with varying charge valency. These coacervates undergo reversible phase transitions through azobenzene photoisomerization, with their behavior governed by charge valency and nucleotide structure. We demonstrate that coacervates formed with high-valency azobenzenes remain stable under UV irradiation but exhibit significant property changes, while those with low-valency azobenzenes dissolve, enabling light-controlled nucleotide release. Additionally, we achieved hierarchical droplet organization and light-actuated biomolecular localization within multiphase systems. Overall, these findings establish a minimal platform for designing light-responsive synthetic protocells, providing insights into dynamic compartmentalization in de novo life-like systems.

Adaptive ATP-induced molecular condensation in membranized protocells

Liquid-liquid phase separation (LLPS) has been achieved in various cytomimetic (protocell) models, but controlling molecular condensation using noninert crowders to systematically alter protocell function remains challenging. Intracellular ATP levels influence protein-protein interactions, and dysregulation of ATP can alter cellular crowding dynamics, thereby disrupting the normal formation or dissolution of condensates. Here, we develop a membranized protocell model capable of endogenous LLPS and liquid-gel-like phase separation through precise manipulation of intermolecular interactions within semipermeable polysaccharide-based microcapsules (polysaccharidosomes, P-somes), prepared using microtemplate-guided assembly. We demonstrate that intraprotocellular diffusion-mediated LLPS can be extended into the liquid-gel-like domain by the uptake of the biologically active crowder ATP, resulting in a range of modalities dependent on the fine-tuning of molecular condensation. Endogenous enzyme activity in these crowded polysaccharidosomes is enhanced compared to free enzymes in solution, though this enhancement diminishes at higher levels of intraprotocellular condensation. Additionally, increased molecular crowding inhibits intraprotocell DNA strand displacement reactions. Our findings introduce an expedient and optimized approach to the batch construction of membranized protocell models with controllable molecular crowding and functional diversity. Our mix-incubate-wash protocol for inducing endogenous LLPS in membranized protocells offers potential applications in microreactor technology, environmental sensing, and the delivery and sustained release of therapeutics.

Chemically Triggered Reactive Coacervates Show Life-Like Budding and Membrane Formation

Phase-separated coacervates can enhance reaction kinetics and guide multilevel self-assembly, mimicking early cellular evolution. In this work, we introduce "reactive" complex coacervates that undergo chemically triggered self-immolative transformations, directing the self-assembly of the reaction products within their matrix. These self-assemblies then evolve to show life-like properties such as budding and membrane formation. We find that the coacervate composition critically influences reaction rates and product distribution and guides the hierarchical self-assembly. This work showcases "reactive" coacervates as a versatile platform to influence reaction and self-assembly pathways for controlled supramolecular synthesis and hierarchical self-organization in confined spaces.

Construction of Somatostatin-Based Multiphase "Core-Shell" Coacervates as Photodynamic Biomimetic Organelles

Biomimetic coacervates have recently attracted great interest in biomedical fields, especially for drug delivery and as protocells. However, these membraneless structures are easily coalesced and poorly targetable, limiting their real biomedical applications. Here multiphase "core-shell" coacervate (CSC) constructed by dsDNA and somatostatin (SST), a 14-mer cyclopeptide is designed. The CSC shows enhanced tumor targetability through SST binding to SST receptors on the tumor cells' surface. G4 quadruplex-hemin complex can be embedded in the CSC by interaction with SST, as demonstrated by molecular simulation and isothermal titration calorimetry. The G4-hemin embedded CSC can further recruit photosensitizers such as tetracarboxyphenyl porphyrin to form the CSC-GHT composite for photodynamic therapy (PDT). As photodynamic biomimetic organelles, CSC-GHT can convert oxygen to singlet oxygen (catalyzed by the catalase-mimetic activity of G4-hemin), resulting in enhanced PDT effect, which allows the inhibition of cellular migration in vitro and tumor growth in vivo. Owing to high stability, targetability, and biosafety, the proposed CSC can recruit various cargos from small dyes to large biomacromolecules (up to 430 kDa), providing promising theranostic applications.

Coacervation for biomedical applications: innovations involving nucleic acids

Gene therapies, drug delivery systems, vaccines, and many other therapeutics, although seeing breakthroughs over the past few decades, still suffer from poor stability, biocompatibility, and targeting. Coacervation, a liquid-liquid phase separation phenomenon, is a pivotal technique increasingly employed to enhance the effectiveness of therapeutics. Through coacervation strategies, many current challenges in therapeutic formulations can be addressed due to the tunable nature of this technique. However, much remains to be explored to enhance these strategies further and scale them from the benchtop to industrial applications. In this review, we highlight the underlying mechanisms of coacervation, elucidating how factors such as pH, ionic strength, temperature, chirality, and charge patterning influence the formation of coacervates and the encapsulation of active ingredients. We then present a perspective on current strategies harnessing these systems, specifically for nucleic acid-based therapeutics. These include peptide-, protein-, and polymer-based approaches, nanocarriers, and hybrid methods, each offering unique advantages and challenges. Nucleic acid-based therapeutics are crucial for designing rapid responses to diseases, particularly in pandemics. While these exciting systems offer many advantages, they also present limitations and challenges which are explored in this work. Exploring coacervation in the biomedical frontier opens new avenues for innovative nucleic acid-based treatments, marking a significant stride towards advanced therapeutic solutions.

Random-Sequence DNA Oligomers Make Liquid Crystals: A Case of Collective Ordering in a Superdiverse Environment

The availability of synthetic, analytical, and predictive tools makes DNA an ideal platform, not yet considered, to investigate statistical and soft matter physics. Here we report and interpret the equilibrium collective ordering in solutions of random-sequence DNA (rsDNA) oligomers of lengths L = 8 and L = 12. Despite the extreme molecular diversity inherent in rsDNA solutions, which for L = 12 are composed of 20 million distinct molecular species, these systems develop long-range columnar liquid crystal (LC) ordering when equilibrated at high osmotic pressure. By a combination of experimental models and computed statistics, we demonstrate that the residual end-to-end attraction between rsDNA duplexes, which typically terminate with various forms of pairing errors, is indeed sufficient to drive LC ordering. The resulting narrow range of isotropic-LC phase coexistence, in seeming contrast with the variety of phase behaviors of the species composing rsDNA, demonstrates that the (nearly) continuum distribution of molecular interaction strengths effectively reduces the tendency for demixing instead of enhancing it, in line with theoretical modeling.

Coacervate Droplets as Biomimetic Models for Designing Cell-Like Microreactors

Coacervates are versatile compartments formed by liquid-liquid phase separation. Their dynamic behavior and molecularly crowded microenvironment make them ideal materials for creating cell-like systems such as synthetic cells and microreactors. Recently, combinations of synthetic and natural molecules have been exploited via simple or complex coacervation to create compartments that can be used to build hierarchical chemical systems with life-like properties. This review highlights recent advances in the design of coacervate compartments and their application as biomimetic compartments for the design of cell-like chemical reactors and cell mimicking systems. It first explores the variety of materials used for coacervation and the influence of their chemical structure on their controlled dynamic behavior. Then, the applications of coacervates as cell-like systems are reviewed, focusing on how they can be used as cell-like microreactors through their ability to sequester molecules and provide a distinct and regulatory microenvironment for chemical reactions in aqueous media.

Metal-phenolic network composites: from fundamentals to applications

Composites with tailored compositions and functions have attracted widespread scientific and industrial interest. Metal-phenolic networks (MPNs), which are composed of phenolic ligands and metal ions, are amorphous adhesive coordination polymers that have been combined with various functional components to create composites with potential in chemistry, biology, and materials science. This review aims to provide a comprehensive summary of both fundamental knowledge and advancements in the field of MPN composites. The advantages of amorphous MPNs, over crystalline metal-organic frameworks, for fabricating composites are highlighted, including their mild synthesis, diverse interactions, and numerous intrinsic functionalities. The formation mechanisms and state-of-the-art synthesis strategies of MPN composites are summarized to guide their rational design. Subsequently, a detailed overview of the chemical interactions and structure-property relationships of composites based on different functional components (e.g., small molecules, polymers, biomacromolecules) is provided. Finally, perspectives are offered on the current challenges and future directions of MPN composites. This tutorial review is expected to serve as a fundamental guide for researchers in the field of metal-organic materials and to provide insights and avenues to enhance the performance of existing functional materials in applications across diverse fields.

Nucleotide-mediated modulation of chemoselective protein functionalization in a liquid-like condensed phase

Liquid-like protein condensates are ubiquitous in cellular system and are increasingly recognized for their roles in physiological processes. Condensed phase harbors distinctive chemical microenvironment, markedly different than dilute aqueous phase. Herein, we demonstrate chemoselective modification pattern of nucleophilic canonical amino acid sidechains (namely - cysteine, tyrosine and lysine) of the protein towards 4-chloro-7-nitrobenzofurazan in the dilute and condensed phase. We also delineate how the effect of nucleotides and their in situ enzymatic dissociation temporally modulate the protein condensate's pH and the protein's corresponding chemoselective modification. We have shown that the pH of the condensate decreases in the presence of nucleoside triphosphate, whereas it increases in the presence of nucleoside monophosphates or phosphate ion. For instance, we find lysine-specific modification gets inhibited in the presence of adenosine triphosphate (ATP), but significantly enhanced in the presence of monophosphates. This feature enables us to gain temporal control over dynamic change in protein functionalization via enzymatic ATP hydrolysis. Overall, this work substantiates the alteration in pH-responsiveness of Brønsted basicity of a protein's ε-amine in the condensed phase. Furthermore, this environment sensitivity in chemoselective protein functionalization in condensed phase will be important in adaptable protein engineering to the chemical biology of protein phase separation.

A visible light-activated azo-fluorescent switch for imaging-guided and light-controlled release of antimycotics

Azo switches are widely employed as essential components in light-responsive systems. Here, we develop an azo-fluorescent switch that is visible light-responsive and its light-responsive processes can be monitored using fluorescence imaging. Visible light irradiation promotes isomerization, accompanied by changes in fluorescence that enable the process to be monitored through fluorescence imaging. Furthermore, we document that the nanocavity size of liposome encapsulated nanoparticles containing azo changes in the isomerization process and show that this change enables construction of a light-responsive nanoplatform for optically controlled release of antimycotics. Also, natural light activation of nanoparticles of the switch loaded with an antimycotic agent causes death of Rhizoctonia solani. The results show that these nanoparticles can double the holding period in comparison to small molecule antimycotics. The strategy used to design the imaging-guided light-controlled nano-antimycotic release system can be applicable to protocols for controlled delivery of a wide variety of drugs.

Optical Control over Liquid–Liquid Phase Separation

Liquid-liquid phase separation (LLPS) is responsible for the emergence of intracellular membrane-less organelles and the development of coacervate protocells. Benefitting from the advantages of simplicity, precision, programmability, and noninvasiveness, light has become an effective tool to regulate the assembly dynamics of LLPS, and mediate various biochemical processes associated with LLPS. In this review, recent advances in optically controlling membrane-less organelles within living organisms are summarized, thereby modulating a series of biological processes including irreversible protein aggregation pathologies, transcription activation, metabolic flux, genomic rearrangements, and enzymatic reactions. Among these, the intracellular systems (i.e., optoDroplet, Corelet, PixELL, CasDrop, and other optogenetic systems) that enable the photo-mediated control over biomolecular condensation are highlighted. The design of photoactive complex coacervate protocells in laboratory settings by utilizing photochromic molecules such as azobenzene and diarylethene is further discussed. This review is expected to provide in-depth insights into phase separation-associated biochemical processes, bio-metabolism, and diseases.

Spontaneous assembly of condensate networks during the demixing of structured fluids

Liquid-liquid phase separation, whereby two liquids spontaneously demix, is ubiquitous in industrial, environmental, and biological processes. While isotropic fluids are known to condense into spherical droplets in the binodal region, these dynamics are poorly understood for structured fluids. Here, we report the unique observation of condensate networks, which spontaneously assemble during the demixing of a mesogen from a solvent. Condensing mesogens form rapidly elongating filaments, rather than spheres, to relieve distortion of an internal smectic mesophase. As filaments densify, they collapse into bulged discs, lowering the elastic free energy. Additional distortion is relieved by retraction of filaments into the discs, which are straightened under tension to form a ramified network. Understanding and controlling these dynamics may provide different avenues to direct pattern formation or template materials.

Template-based copying in chemically fuelled dynamic combinatorial libraries

One of science's greatest challenges is determining how life can spontaneously emerge from a mixture of molecules. A complicating factor is that life and its molecules are inherently unstable-RNA and proteins are prone to hydrolysis and denaturation. For the de novo synthesis of life or to better understand its emergence at its origin, selection mechanisms are needed for unstable molecules. Here we present a chemically fuelled dynamic combinatorial library to model RNA oligomerization and deoligomerization and shine new light on selection and purification mechanisms under kinetic control. In the experiments, oligomers can only be sustained by continuous production. Hybridization is a powerful tool for selecting unstable molecules, offering feedback on oligomerization and deoligomerization rates. Moreover, we find that templation can be used to purify libraries of oligomers. In addition, template-assisted formation of oligomers within coacervate-based protocells changes its compartment's physical properties, such as their ability to fuse. Such reciprocal coupling between oligomer production and physical properties is a key step towards synthetic life.

How Droplets Can Accelerate Reactions─Coacervate Protocells as Catalytic Microcompartments

Coacervates are droplets formed by liquid-liquid phase separation (LLPS) and are often used as model protocells-primitive cell-like compartments that could have aided the emergence of life. Their continued presence as membraneless organelles in modern cells gives further credit to their relevance. The local physicochemical environment inside coacervates is distinctly different from the surrounding dilute solution and offers an interesting microenvironment for prebiotic reactions. Coacervates can selectively take up reactants and enhance their effective concentration, stabilize products, destabilize reactants and lower transition states, and can therefore play a similar role as micellar catalysts in providing rate enhancement and selectivity in reaction outcome. Rate enhancement and selectivity must have been essential for the origins of life by enabling chemical reactions to occur at appreciable rates and overcoming competition from hydrolysis. In this Accounts, we dissect the mechanisms by which coacervate protocells can accelerate reactions and provide selectivity. These mechanisms can similarly be exploited by membraneless organelles to control cellular processes. First, coacervates can affect the local concentration of reactants and accelerate reactions by copartitioning of reactants or exclusion of a product or inhibitor. Second, the local environment inside the coacervate can change the energy landscape for reactions taking place inside the droplets. The coacervate is more apolar than the surrounding solution and often rich in charged moieties, which can affect the stability of reactants, transition states and products. The crowded nature of the droplets can favor complexation of large molecules such as ribozymes. Their locally different proton and water activity can facilitate reactions involving a (de)protonation step, condensation reactions and reactions that are sensitive to hydrolysis. Not only the coacervate core, but also the surface can accelerate reactions and provides an interesting site for chemical reactions with gradients in pH, water activity and charge. The coacervate is often rich in catalytic amino acids and can localize catalysts like divalent metal ions, leading to further rate enhancement inside the droplets. Lastly, these coacervate properties can favor certain reaction pathways, and thereby give selectivity over the reaction outcome. These mechanisms are further illustrated with a case study on ribozyme reactions inside coacervates, for which there is a fine balance between concentration and reactivity that can be tuned by the coacervate composition. Furthermore, coacervates can both catalyze ribozyme reactions and provide product selectivity, demonstrating that coacervates could have functioned as enzyme-like catalytic microcompartments at the origins of life.

Simulating the Lyotropic Phase Behavior of a Partially Self-Complementary DNA Tetramer

DNA oligomers in solution have been found to develop liquid crystal phases via a hierarchical process that involves Watson-Crick base pairing, supramolecular assembly into columns of duplexes, and long-range ordering. The multiscale nature of this phenomenon makes it difficult to quantitatively describe and assess the importance of the various contributions, particularly for very short strands. We performed molecular dynamics simulations based on the coarse-grained oxDNA model, aiming to depict all of the assembly processes involved and the phase behavior of solutions of the DNA GCCG tetramers. We find good quantitative matching to experimental data at both levels of molecular association (thermal melting) and collective ordering (phase diagram). We characterize the isotropic state and the low-density nematic and high-density columnar liquid crystal phases in terms of molecular order, size of aggregates, and structure, together with their effects on diffusivity processes. We observe a cooperative aggregation mechanism in which the formation of dimers is less thermodynamically favored than the formation of longer aggregates.

Self-assembly of stabilized droplets from liquid-liquid phase separation for higher-order structures and functions

Dynamic microscale droplets produced by liquid-liquid phase separation (LLPS) have emerged as appealing biomaterials due to their remarkable features. However, the instability of droplets limits the construction of population-level structures with collective behaviors. Here we first provide a brief background of droplets in the context of materials properties. Subsequently, we discuss current strategies for stabilizing droplets including physical separation and chemical modulation. We also discuss the recent development of LLPS droplets for various applications such as synthetic cells and biomedical materials. Finally, we give insights on how stabilized droplets can self-assemble into higher-order structures displaying coordinated functions to fully exploit their potentials in bottom-up synthetic biology and biomedical applications.

Microfluidics-Based Drying-Wetting Cycles to Investigate Phase Transitions of Small Molecules Solutions

Drying-wetting cycles play a crucial role in the investigation of the origin of life as processes that both concentrate and induce the supramolecular assembly and polymerization of biomolecular building blocks, such as nucleotides and amino acids. Here, we test different microfluidic devices to study the dehydration-hydration cycles of the aqueous solutions of small molecules, and to observe, by optical microscopy, the insurgence of phase transitions driven by self-assembly, exploiting water pervaporation through polydimethylsiloxane (PDMS). As a testbed, we investigate solutions of the chromonic dye Sunset Yellow (SSY), which self-assembles into face-to-face columnar aggregates and produces nematic and columnar liquid crystal (LC) phases as a function of concentration. We show that the LC temperature-concentration phase diagram of SSY can be obtained with a fair agreement with previous reports, that droplet hydration-dehydration can be reversibly controlled and automated, and that the simultaneous incubation of samples with different final water contents, corresponding to different phases, can be implemented. These methods can be further extended to study the assembly of diverse prebiotically relevant small molecules and to characterize their phase transitions.

Emerging experimental methods to study the thermodynamics of biomolecular condensate formation

The formation of biomolecular condensates in vivo is increasingly recognized to underlie a multitude of crucial cellular functions. Furthermore, the evolution of highly dynamic protein condensates into progressively less reversible assemblies is thought to be involved in a variety of disorders, from cancer over neurodegeneration to rare genetic disorders. There is an increasing need for efficient experimental methods to characterize the thermodynamics of condensate formation and that can be used in screening campaigns to identify and rationally design condensate modifying compounds. Theoretical advances in the field are also identifying the key parameters that need to be measured in order to obtain a comprehensive understanding of the underlying interactions and driving forces. Here, we review recent progress in the development of efficient and quantitative experimental methods to study the driving forces behind and the temporal evolution of biomolecular condensates.

Primitive membraneless compartments as a window into the earliest cells

What did the first cells on Earth look like? This is an unanswered mystery investigated by researchers in the origins of life field. While at some point cells must have developed membranes, genetic components, and catalytic cycles and catalysts, when the earliest cells developed these is not clear. One system which could shed light into the structure and function of the first cells on Earth is membraneless compartments generated from phase separation, perhaps before or as a precursor to the advent of membrane-bound compartmentalization. Here, we briefly comment on two prebiotically relevant membraneless compartment systems: coacervates and polyester microdroplets. This discussion seeks to highlight the current understanding of these systems and to pose unanswered questions as a challenge to the field at large.

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.

Recent Progress in Azobenzene-Based Supramolecular Materials and Applications

Azobenzene-containing small molecules and polymers are functional photoswitchable molecules to form supramolecular nanomaterials for various applications. Recently, supramolecular nanomaterials have received enormous attention in material science because of their simple bottom-up synthesis approach, understandable mechanisms and structural features, and batch-to-batch reproducibility. Azobenzene is a light-responsive functional moiety in the molecular design of small molecules and polymers and is used to switch the photophysical properties of supramolecular nanomaterials. Herein, we review the latest literature on supramolecular nano- and micro-materials formed from azobenzene-containing small molecules and polymers through the combinatorial effect of weak molecular interactions. Different classes including complex coacervates, host-guest systems, co-assembled, and self-assembled supramolecular materials, where azobenzene is an essential moiety in small molecules, and photophysical properties are discussed. Afterward, azobenzene-containing polymers-based supramolecular photoresponsive materials formed through the host-guest approach, polymerization-induced self-assembly, and post-polymerization assembly techniques are highlighted. In addition to this, the applications of photoswitchable supramolecular materials in pH sensing, and CO2 capture are presented. In the end, the conclusion and future perspective of azobenzene-based supramolecular materials for molecular assembly design, and applications are given.