Colloidal ionogels: Controlled assembly and self-propulsion upon tunable swelling

Active colloids driven out of thermal equilibrium serve as building blocks for smart materials with tunable structures and functions. Using chemical energy to drive colloids is advantageous but requires precise control over chemical release. To address this, we developed colloidal ionogels-polymer microspheres infused with ionic liquids-that show controlled assembly and self-propulsion upon tunable swelling. For example, we synthesized microspheres of polymethylmethacrylate loaded with ionic liquid [Bmim][PF6], which were released from the colloidal ionogel upon swelling in alcohol-water mixtures and dissociated into cations and anions of different diffusivities. The resulting electric field leads to four types of pair-wise colloidal interactions via ionic diffusiophoresis and diffusioosmosis, giving rise to four types of self-assembled superstructures. These interactions were precisely modulated by altering the swelling conditions and the ionic liquids used. Additionally, partially blocking the ionogel's surface induces anisotropic swelling and asymmetric ion release, turning the colloidal ionogel into a self-propelled Janus colloidal motor powered by ionic self-diffusiophoresis, reaching speeds of several µm/s and lasting about 100 s. These findings indicate that colloidal ionogels are smart colloidal building blocks with highly tunable pair-wise interactions, self-assembled structures, and self-propulsion, offering potential applications in biomedical sensing, environmental monitoring, and photonics.

Metabolite-Responsive Control of Transcription by Phase Separation-Based Synthetic Organelles

Living natural materials have remarkable sensing abilities that translate external cues into functional changes of the material. The reconstruction of such sensing materials in bottom-up synthetic biology provides the opportunity to develop synthetic materials with life-like sensing and adaptation ability. Key to such functions are material modules that translate specific input signals into a biomolecular response. Here, we engineer a synthetic organelle based on liquid-liquid phase separation that translates a metabolic signal into the regulation of gene transcription. To this aim, we engineer the pyruvate-dependent repressor PdhR to undergo liquid-liquid phase separation in vitro by fusion to intrinsically disordered regions. We demonstrate that the resulting coacervates bind DNA harboring PdhR-responsive operator sites in a pyruvate dose-dependent and reversible manner. We observed that the activity of transcription units on the DNA was strongly attenuated following recruitment to the coacervates. However, the addition of pyruvate resulted in a reversible and dose-dependent reconstitution of transcriptional activity. The coacervate-based synthetic organelles linking metabolic cues to transcriptional signals represent a materials approach to confer stimulus responsiveness to minimal bottom-up synthetic biological systems and open opportunities in materials for sensor applications.

Imine-Based Transient Supramolecular Polymers

Systems that change properties upon exposure to chemical stimuli offer the interesting prospect of (partially) mimicking the functions of living systems. Over the past decade, numerous supramolecular systems whose chemical composition and properties are regulated by the dissipation of chemical fuels have been reported. These systems are typically based on the transient transformation of a "dormant" species into an active, self-assembling supramolecular monomer. The process is powered by fuel consumption and terminates upon fuel depletion, restoring the initial dormant state. Previously reported out-of-equilibrium supramolecular polymerizations relied on the activation of the dormant species by adding or removing small structural units to enable supramolecular polymerization. Here, we present an approach that combines the reversibility of dynamic covalent chemistry and supramolecular chemistry to trigger transient supramolecular polymerizations by "recycling" the components of a dynamic combinatorial library (DCL). Treatment of an equilibrated DCL of aliphatic imines and aromatic amines with an activated carboxylic acid (ACA) generates a dissipative dynamic combinatorial library of aromatic imines and protonated aliphatic amines. The transient acidic conditions enable the creation of a supramolecular polymer held together by interactions between the protonated aliphatic amines and the crown ether moieties embedded in the scaffold of the aromatic imines. Thus, fuel dissipation reshuffles the chemical connectivity and enables the temporary transformation of a purely covalent (polymeric) system into a supramolecular polymer. We demonstrate the strategy using two different covalent dormant feedstocks consisting of a diimine macrocycle involving a calix[4]arene scaffold and a distribution of imine (cyclo)oligomers derived from an isophthalaldehyde skeleton.

Heterometallic CuCd and Cu2Zn complexes with o-vanillin and its Schiff-base derivative: slow magnetic relaxation and catalytic activity associated with Cu(II) centres

In this work, two novel heterometallic mixed-ligand mixed-anion complexes [CuIICdIIClL(o-Van)(OAc)]·3H2O (1) and [CuII2ZnIICl2L2(o-Van)(OAc)] (2) were prepared by reacting fine copper powder and Cd(II) or Zn(II) acetate with an ethanol solution of the Schiff-base ligand HL formed in situ in the condensation reaction of 2-hydroxy-3-methoxy-benzaldehyde (o-VanH) and CH3NH2·HCl. The compounds were thoroughly characterized by elemental analysis, FT-IR, UV/Vis and EPR spectroscopy, cyclic voltammetry, and single-crystal X-ray diffraction, revealing the neutral molecular nature of both the compounds. Catalytic properties of 1 and 2 were studied in the oxidation of hydrocarbons with H2O2 under mild conditions, showing the maximum reaction rate of 4 × 10-5 M s-1 and TOF up to 640 h-1. Both compounds undergo complex transformations in solution as evidenced by kinetic analysis and time-dependent UV/Vis spectroscopy, indicating that the reduced Cu(I) form of 1 is unexpectedly unfavorable. Complex 1 demonstrates slow magnetic relaxation dominated by the direct relaxation process between T = 1.8 and 7 K under an external DC field of 0.2 and 0.4 T, a very rarely observable effect in the coordination compounds of Cu(II). Complex 2 possesses weak ferromagnetism (J = 4.50 cm-1, zJ' = -0.201 cm-1 for H = -JS1S2 formalism) occurring through the Cu-O-Cu pathways. Theoretical CASSCF, DFT and TDDFT calculations were applied to investigate the electronic structures of 1 and 2 and rationalize their behavior in solution.

Coacervates as enzymatic microreactors

Compartmentalization, a key aspect of biochemical regulation, naturally occurs in cellular organelles, including biomolecular condensates formed through liquid-liquid phase separation (LLPS). Inspired by biological compartments, synthetic coacervates have emerged as versatile microreactors, which can provide customed environments for enzymatic reactions. In this review, we explore recent advances in coacervate-based microreactors, while emphasizing the mechanisms by which coacervates accelerate enzymatic reactions, namely by enhancing substrate and enzyme concentrations, stabilizing intermediates, and providing molecular crowding. We discuss diverse coacervate systems, including those based on synthetic polymers, peptides, and nucleic acids, and describe the selection of enzymatic model systems, as well as strategies for enzyme recruitment and their impact on reaction kinetics. Furthermore, we discuss the challenges in monitoring reactions within coacervates and review the currently available techniques including fluorescence techniques, chromatography, and NMR spectroscopy. Altogether, this review offers a comprehensive perspective on recent progress and challenges in the design of coacervate microreactors, and addresses their potential in biocatalysis, synthetic biology, and nanotechnology.

Gravity-Induced Symmetry Breaking in Chemical Gardens

Chemical gardens are hollow precipitates with a plant-like appearance formed when a metal salt seed is immersed in an alkaline aqueous solution containing silicate, phosphate, or carbonate ions. Due to their potential to mimic biological and geological structures relevant to the understanding of life's emergence on Earth and Mars, the study of the nonequilibrium properties of chemical gardens has become increasingly important. Hence, in this article, the influence of gravity on the formation and growth of chemical gardens is investigated. To this end, experimental evidence of the influence of gravity on the formation and growth of chemical gardens is analyzed according to nonequilibrium sensitivity theory. The results obtained from the nonequilibrium sensitivity analysis show that the upward-growing pattern observed in chemical gardens, usually formed under Earth's gravity, is a consequence of symmetry breaking in the system's bifurcating solutions. Under these circumstances, the thermal fluctuations within the system become negligible, favoring the vertical growth of the chemical garden. Moreover, by exploiting the definition of nonequilibrium sensitivity, the minimum magnitude of the gravitational field necessary for the vertical growth of a chemical garden was estimated. The results indicate that the upward growth pattern emerges as the dominant dissipative structure for gravitational field magnitudes larger than 10-5 m s-2, provided fluctuations remain negligible.

Stimuli-Responsive Self-Healing Ionic Gels: A Promising Approach for Dermal and Tissue Engineering Applications

The rapid increase in the number of stimuli-responsive polymers, also known as smart polymers, has significantly advanced their applications in various fields. These polymers can respond to multiple stimuli, such as temperature, pH, solvent, ionic strength, light, and electrical and magnetic fields, making them highly valuable in both the academic and industrial sectors. Recent studies have focused on developing hydrogels with self-healing properties that can autonomously recover their structural integrity and mechanical properties after damage. These hydrogels, formed through dynamic covalent reactions, exhibit superior biocompatibility, mechanical strength, and responsiveness to stimuli, particularly pH changes. However, conventional hydrogels are limited by their weak and brittle nature. To address this, ionizable moieties within polyelectrolytes can be tuned to create ionically cross-linked hydrogels, leveraging natural polymers such as alginate, chitosan, hyaluronic acid, and cellulose. The integration of ionic liquids into these hydrogels enhances their mechanical properties and conductivity, positioning them as significant self-healing agents. This review focuses on the emerging field of stimuli-responsive ionic-based hydrogels and explores their potential in dermal applications and tissue engineering.

Understanding multicomponent low molecular weight gels from gelators to networks

BACKGROUND

The construction of gels from low molecular weight gelators (LMWG) has been extensively studied in the fields of bio-nanotechnology and other fields. However, the understanding gaps still prevent the prediction of LMWG from the full design of those gel systems. Gels with multicomponent become even more complicated because of the multiple interference effects coexist in the composite gel systems.

AIM OF REVIEW

This review emphasizes systems view on the understanding of multicomponent low molecular weight gels (MLMWGs), and summarizes recent progress on the construction of desired networks of MLMWGs, including self-sorting and co-assembly, as well as the challenges and approaches to understanding MLMWGs, with the hope that the opportunities from natural products and peptides can speed up the understanding process and close the gaps between the design and prediction of structures.

KEY SCIENTIFIC CONCEPTS OF REVIEW

This review is focused on three key concepts. Firstly, understanding the complicated multicomponent gels systems requires a systems perspective on MLMWGs. Secondly, several protocols can be applied to control self-sorting and co-assembly behaviors in those multicomponent gels system, including the certain complementary structures, chirality inducing and dynamic control. Thirdly, the discussion is anchored in challenges and strategies of understanding MLMWGs, and some examples are provided for the understanding of multicomponent gels constructed from small natural products and subtle designed short peptides.

Transient colloidal crystals fueled by electrochemical reaction products

Conventional electric field directed colloidal assembly enables fabricating ordered structures but lacks temporal control over assembly state. Chemical reaction networks have been discovered that transiently assemble colloids; however, they have slow dynamics (hrs - days) and poor temporal tunability, utilize complex reagents, and produce kinetically trapped states. Here we demonstrate transient colloidal crystals that autonomously form, breakup, and reconstitute in response to an electrochemical reaction network driven by a time invariant electrical stimulus. Aqueous mixtures of micron sized colloids and para-benzoquinone (BQ) were subjected to superimposed oscillatory and steady electric potentials, i.e., multimode potentials, that induce electrokinetic flows around colloids and proton-coupled BQ redox reactions. Transient assembly states coincided with electrochemically generated pH spikes near the cathode. We demonstrate wide tunability of transient assembly state lifetimes over two orders of magnitude by modifying the electric potential and electrode separation. An electrochemical transport model showed that interaction of advancing acidic and alkaline pH fronts from anodic BQ oxidation and cathodic BQ reduction caused pH transients. We present theoretical and experimental evidence that indicates transient colloidal crystals were mediated by competition between opposing colloidal scale electrohydrodynamic and electroosmotic flows, the latter of which is pH dependent.

The usage of color coordinates preserved in microscopic image for elucidation on chemical behavior in confined micro-/nano-spaces

Characterizing the properties of micro-/nanomaterials and micro-/nanospaces is crucial due to their widespread use in diverse applications, including analytical methods. While microspectroscopy offers a powerful characterization technique, limitations in acquisition speed and instrument accessibility persist. This study comprehensively explores the use of color coordinates to elucidate the chemical phenomena within confined micro-/nanospaces. Encoding spectral information directly as color coordinates within digital images enables rapid data acquisition. In addition, simple instrumentation that requires only a camera as a detector expands the versatility of solving tasks that occur in microspectroscopy. This work details the fundamental principles of color coordinates and presents illustrative research examples demonstrating their utility in characterizing chemical reactions and physicochemical properties within confined spaces. Herein, the evaluation of the chemical reactions occurring in the confined microspace is explained, including the steel corrosion occurring in the freeze concentration of the salt solutions (FCS) formed in the frozen salt solutions, proton-involved reactions in the FCS, liquid/liquid and solid/gel interface. This work aims to promote the adoption of image processing for colorimetric analysis as a complementary or alternative approach to conventional microspectroscopy.

Covalent Dynamic DNA Networks to Translate Multiple Inputs into Programmable Outputs

Inspired by naturally occurring protein dimerization networks, in which a set of proteins interact with each other to achieve highly complex input-output behaviors, we demonstrate here a fully synthetic DNA-based dimerization network that enables highly programmable input-output computations. Our DNA-based dimerization network consists of DNA oligonucleotide monomers modified with reactive moieties that can covalently bond with each other to form dimer outputs in an all-to-all or many-to-many fashion. By designing DNA-based input strands that can specifically sequester DNA monomers, we can control the size of the reaction network and thus fine-tune the yield of each DNA dimer output in a predictable manner. Thanks to the programmability and specificity of DNA-DNA interactions, we show that this approach can be used to control the yield of different dimer outputs using different inputs. The approach is also versatile and we demonstrate dimerization networks based on two distinct covalent reactions: thiol-disulfide and strain-promoted azide-alkyne cycloaddition (SPAAC) reactions. Finally, we show here that the DNA-based dimerization network can be used to control the yield of a functional dimer output, ultimately controlling the assembly and disassembly of DNA nanostructures. The covalent dynamic DNA networks shown here provide a way to convert multiple inputs into programmable outputs that can control a broader range of functions, including ones that mimic those of living cells.

Growth of Hexagonal Boron Nitride from Molten Nickel Solutions: A Reactive Molecular Dynamics Study

Metal flux methods are excellent for synthesizing high-quality hexagonal boron nitride (hBN) crystals, but the atomic mechanisms of hBN nucleation and growth in these systems are poorly understood and difficult to probe experimentally. Here, we harness classical reactive molecular dynamics (ReaxFF) to unravel the mechanisms of hBN synthesis from liquid nickel solvent over time scales up to 30 ns. These simulations mimic experimental conditions by including relatively large liquid nickel slabs containing dissolved boron and a molecular nitrogen gas phase. Overall, the reaction takes place almost exclusively on the surface of the liquid nickel, owing to the low solubility of nitrogen in bulk nickel and the intermediate species' preference for the metal-gas interface. The formation of hBN invariably begins by reaction of dinitrogen with nickel-solvated boron atoms at the surface, forming intermediate N-N-B species, which typically evolve into B-N-B units through a short-lived intermediate where a single nitrogen atom is coordinated by one nitrogen and two boron atoms. The resulting B-N-B units, in turn, coalesce with growing hBN nuclei and carry nitrogen between hBN nanocrystals in an Ostwald ripening process. The amount of hBN produced on the tens of nanosecond time scale depends critically on the boron concentration, while having a much weaker dependence on the N2 pressure for the regime considered (N2 pressures of 2.5-10 MPa, Ni-B solutions with 6-12% boron by atom fraction). The highest rate of hBN formation occurs at the lowest temperature considered (1750 K, just above the melting point of nickel), while no hBN sheets are formed at 2000 K or above. An analysis of the transition pathways for nitrogen atoms shows that the final step, incorporation of small B-N motifs into larger hBN sheets, is the rate-limiting step in the regimes considered. While raising the temperature from 1750 to 2000 K has little effect on the formation of intermediates (N-N-B, B-N-B, etc.), the lack of large hBN sheets at temperatures >1900 K is explained by decreased probability of the final step and increased probability of breakup of hBN into B-N motifs.

Regulating Protein Immobilization During Cell-Free Protein Synthesis in Hyaluronan Microgels

Cell-like platforms are being studied intensively for their application in synthetic biology to mimic aspects of life in an artificial environment. Here, micrometer-sized, bifunctional microgels are used as an experimental platform to investigate the interplay of cell-free protein synthesis (CFPS) and in situ protein accumulation inside the microgel volume. In detail, microgels made of hyaluronic acid (HA) are first modified with different amounts of nitrilotriacetic acid (NTA) moieties to characterize the capability and maximum capacity of binding His-tag modified GFP. CFPS is optimized for the system used here, particularly when using a linear DNA template. Afterward, HA-microgels are functionalized with the linear DNA template and Ni2+-activated NTA moieties to bind in situ synthesized GFP-His. CFPS and parallel protein accumulation within the microgels are observed over time to determine the GFP-His binding to the microgel platform. With this approach, the study presents the first steps for a platform to study the temporal-spatial regulation of protein synthesis by tailored protein binding or release from the microgel matrix-based reaction environment.

A Comprehensive Review of Current Approaches in Bladder Cancer Treatment

Bladder cancer is one of the most common malignant tumors of the urinary system globally. It is also one of the most expensive cancers to manage, due to the need for extensive treatment and follow-ups that often involve invasive and costly procedures. Although there have been some improvements in treatment options, the quality of life they offer has not improved at the same rate as other cancers. Therefore, there is an urgent need to find new alternatives to ease the burden of bladder cancer on patients. Recent discoveries have opened new avenues for the diagnosis and management of bladder cancer even though the clinical approach has largely remained the same for years. The decline in bladder cancer-specific mortality in regions that promote social awareness of risk factors and reduction of carcinogenic exposure demonstrates the effectiveness of such measures. New agents have been approved for patients who have undergone radical cystectomy after Bacillus Calmette-Guérin failure. Current best practices for diagnosing and treating bladder cancer are presented in this review. The review discusses radiation therapy, photodynamic therapy, gene therapy, chemotherapy, and nanomedicine in relation to non muscle-invasive cancers and muscle-invasive bladder cancers, as well as systemic treatments.

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.

Evolution of complex chemical mixtures reveals combinatorial compression and population synchronicity

Many open questions about the origins of life are centred on the generation of complex chemical species. Past work has characterized specific chemical reactions that might lead to biological molecules. Here we establish an experimental model of chemical evolution to investigate general processes by which chemical systems continuously change. We used water as a chemical reactant, product and medium. We leveraged oscillating water activity at near-ambient temperatures to cause ratcheting of near-equilibrium reactions in mixtures of organic molecules containing carboxylic acids, amines, thiols and hydroxyl groups. Our system (1) undergoes continuous change with transitions to new chemical spaces while not converging throughout the experiment; (2) demonstrates combinatorial compression with stringent chemical selection; and (3) displays synchronicity of molecular populations. Our results suggest that chemical evolution and selection can be observed in organic mixtures and might ultimately be adapted to produce a broad array of molecules with novel structures and functions.

Coacervates Composed of Low-Molecular-Weight Compounds- Molecular Design, Stimuli Responsiveness, Confined Reaction

The discovery of coacervation within living cells through liquid-liquid phase separation has inspired scientists to investigate its fundamental principles and significance. Indeed, coacervates composed of low-molecular-weight compounds based on supramolecular strategy can offer valuable models for biomolecular condensates and useful tools. This mini-review highlights recent findings and advances in coacervates (artificial condensates), primarily composed of low-molecular-weight compounds, with focuses on their molecular design, stimuli responsiveness, and controlled reactions within or leading to the coacervates.

Insights into the Mechanism of Protein Loading by Chain-Length Asymmetric Complex Coacervates

The study of the phase behavior of polyelectrolyte complex coacervates has attracted significant attention in recent years due to their potential use as membrane-less organelles, microreactors, and drug delivery platforms. In this work, we investigate the mechanism of protein loading in chain-length asymmetric complex coacervates composed of a polyelectrolyte and an oppositely charged multivalent ion. Unlike the symmetric case (polycation + polyanion), we show that protein loading is highly selective based on the protein's net charge: only proteins with charges opposite to the polyelectrolyte can be loaded. Through a series of systematic experiments, we identified that the protein loading process relies on the formation of a neutral three-component coacervate in which both the protein and the multivalent ion serve as complexing agents for the polyelectrolyte. Lastly, we demonstrated that this mechanism extends to the sequestration of other charged small molecules, offering valuable insights into designing functional multicomponent coacervates.

Controlled Lipid Domain Positioning and Polarization in Confined Minimal Cell Models

Giant unilamellar vesicles (GUVs) are widely used minimal cell models where essential biological features can be reproduced, isolated and studied. Although precise spatio-temporal distribution of membrane domains is a process of crucial importance in living cells, it is still highly challenging to generate anisotropic GUVs with domains at user-defined positions. Here we describe a novel and robust method to control the spatial position of lipid domains of liquid-ordered (Lo)/liquid-disordered (Ld) phase in giant unilamellar vesicles. Our strategy consists in confining Lo/Ld phase-separating GUVs in microfluidic channels to define free curved regions where the minority-phase domains localize and coalesce by decreasing the line energy through domain fusion. We show that this process is governed by the respective fraction of the two phases, and not by the chemical nature of the lipids involved. The spatial position and number of domains are controlled by the design of the confining microchannel and could result in polarized GUVs with a controllable number of poles. The developed method is versatile and user-friendly, while allowing multiple single-vesicle experiments in parallel.

A Tetrazine Amplification System for Visual Detection of Trace Analytes via Click-Release Reactions

Achieving visual detection of analytes at ultra-low concentrations in complex mixtures remains a persistent challenge. While sophisticated techniques offer single-molecule sensitivity, practical hurdles remain, necessitating tailored signal amplification systems for direct visual detection. In this study, we develop a strategy for the visualized detection of tetrazine through a "click-release-oxidation-cycle" (CROC) cascade amplification process. We systematically describe the construction and synthesis of this system, the kinetic process of click release, the kinetics of oxidation to tetrazine and its cascade amplification effect in trace amounts of tetrazine. This system is capable of amplifying the signal of tetrazine at a concentration as low as 2 nM by 105-fold, thereby providing a clearly visible purple signal. Finally, as proof of concept, we successfully apply this method to visually detect trace β-galactosidase (β-gal) and Pd2+.

Programmed Fabrication of Vesicle-Based Prototissue Fibers with Modular Functionalities

Multicellular organisms have hierarchical structures where multiple cells collectively form tissues with complex 3D architectures and exhibit higher-order functions. Inspired by this, to date, multiple protocell models have been assembled to form tissue-like structures termed prototissues. Despite recent advances in this research area, the programmed assembly of protocells into prototissue fibers with emergent functions still represents a significant challenge. The possibility of assembling prototissue fibers will open up a way to a novel type of prototissue subunit capable of hierarchical assembly into unprecedented soft functional materials with tunable architectures, modular and distributed functionalities. Herein, the first method to fabricate freestanding vesicle-based prototissue fibers with controlled lengths and diameters is devised. Importantly, it is also shown that the fibers can be composed of different specialized modules that, for example, can endow the fiber with magnetotaxis capabilities, or that can work synergistically to take an input diffusible chemical signals and transduce it into a readable fluorescent output through a hosted enzyme cascade reaction. Overall, this research addresses an important challenge of prototissue engineering and will find important applications in 3D bio-printing, tissue engineering, and soft robotics as next-generation bioinspired materials.

A Single Amino Acid Model for Hydrophobically Driven Liquid-Liquid Phase Separation

This study proposes fluorenylmethoxycarbonyl (Fmoc)-protected single amino acids (Fmoc-AAs) as a minimalistic model system to investigate liquid-liquid phase separation (LLPS) and the elusive liquid-to-solid transition of condensates. We demonstrated that Fmoc-AAs exhibit LLPS depending on the pH and ionic strength, primarily driven by hydrophobic interactions. Systematic examination of the conditions under which each Fmoc-AA undergoes LLPS revealed distinct residue-dependent trends in the critical concentrations and phase behavior. Importantly, we elucidated the liquid-to-solid transition process, suggesting that it may be driven by a molecular mechanism different from that of LLPS. Fmoc-AA condensates showed promise for biomolecular enrichment and catalytic applications. This work provides significant insights into the molecular mechanisms of LLPS and the subsequent liquid-to-solid transition, offering a robust platform for future studies related to protocells and protein aggregation diseases.

Bistable Functions and Signaling Motifs in Systems Chemistry: Taking the Next Step Toward Synthetic Cells

ConspectusA key challenge in modern chemistry research is to mimic life-like functions using simple molecular networks and the integration of such networks into the first functional artificial cell. Central to this endeavor is the development of signaling elements that can regulate the cell function in time and space by producing entities of code with specific information to induce downstream activity. Such artificial signaling motifs can emerge in nonequilibrium systems, exhibiting complex dynamic behavior like bistability, multistability, oscillations, and chaos. However, the de novo, bottom-up design of such systems remains challenging, primarily because the kinetic characteristics and energy aspects yielding bifurcation have not yet been globally defined. We herein review our recent work that focuses on the design and functional analysis of peptide-based networks, propelled by replication reactions and exhibiting bistable behavior. Furthermore, we rationalize and discuss their exploitation and implementation as variable signaling motifs in homogeneous and heterogeneous environments.The bistable reactions constitute reversible second-order autocatalysis as positive feedback to generate two distinct product distributions at steady state (SS), the low-SS and high-SS. Quantitative analyses reveal that a phase transition from simple reversible equilibration dynamics into bistability takes place when the system is continuously fueled, using a reducing agent, to keep it far from equilibrium. In addition, an extensive set of experimental, theoretical, and simulation studies highlight a defined parameter space where bistability operates.Analogous to the arrangement of protein-based bistable motifs in intracellular signaling pathways, sequential concatenation of the synthetic bistable networks is used for signal processing in homogeneous media. The cascaded network output signals are switched and erased or transduced by manipulating the order of addition of the components, allowing it to reach "on demand" either the low-SS or high-SS. The pre-encoded bistable networks are also useful as a programming tool for the downstream regulation of nanoscale materials properties, bridging together the Systems Chemistry and Nanotechnology fields. In such heterogeneous cascade pathways, the outputs of the bistable network serve as input signals for consecutive nanoparticle formation reaction and growth processes, which-depending on the applied conditions-regulate various features of (Au) nanoparticle shape and assembly.Our work enables the design and production of various signaling apparatus that feature higher complexity than previously observed in chemical networks. Future studies, briefly discussed at the end of the Account, will be directed at the design and analysis of more elaborate functionality, such as bistability under flow conditions, multistability, and oscillations. We propose that a profound understanding of the design principles facilitating the replication-based bistability and related functions bear implications for exploring the origin of protein functionality prior to the highly evolved replication-translation-transcription machinery. The integration of our peptide-based signaling motifs within future synthetic cells seems to be a straightforward development of the two alternating states as memory and switch elements for controlling cell growth and division and even communication among different cells. We furthermore suggest that such systems can be introduced into living cells for various biotechnology applications, such as switches for cell temporal and spatial manipulations.

Selective peptide bond formation via side chain reactivity and self-assembly of abiotic phosphates

In the realm of biology, peptide bonds are formed via reactive phosphate-containing intermediates, facilitated by compartmentalized environments that ensure precise coupling and folding. Herein, we use aminoacyl phosphate esters, synthetic counterparts of biological aminoacyl adenylates, that drive selective peptide bond formation through side chain-controlled reactivity and self-assembly. This strategy results in the preferential incorporation of positively charged amino acids from mixtures containing natural and non-natural amino acids during the spontaneous formation of amide bonds in water. Conversely, aminoacyl phosphate esters that lack assembly and exhibit fast reactivity result in random peptide coupling. By introducing structural modifications to the phosphate esters (ethyl vs. phenyl) while retaining aggregation, we are able to tune the selectivity by incorporating aromatic amino acid residues. This approach enables the synthesis of sequences tailored to the specific phosphate esters, overcoming limitations posed by certain amino acid combinations. Furthermore, we demonstrate that a balance between electrostatic and aromatic stacking interactions facilitates covalent self-sorting or co-assembly during oligomerization reactions using unprotected N-terminus aminoacyl phosphate esters. These findings suggest that self-assembly of abiotic aminoacyl phosphate esters can activate a selection mechanism enabling the departure from randomness during the autonomous formation of amide bonds in water.

Protein quality control machinery: regulators of condensate architecture and functionality

Protein quality control (PQC) mechanisms including the ubiquitin (Ub)-proteasome system (UPS), autophagy, and chaperone-mediated refolding are essential to maintain protein homeostasis in cells. Recent studies show that these PQC mechanisms are further modulated by biomolecular condensates that sequester PQC components and compartmentalize reactions. Accumulating evidence points towards the PQC machinery playing a pivotal role in regulating the assembly, disassembly, and viscoelastic properties of several condensates. Here, we discuss how the PQC machinery can form their own condensates and also be recruited to known condensates under physiological or stress-induced conditions. We present molecular insights into how the multivalent architecture of polyUb chains, Ub-binding adaptor proteins, and other PQC machinery contribute to condensate assembly, leading to the regulation of downstream PQC outcomes and therapeutic potential.

The non-canonical nucleotides and prebiotic evolution

The mystery of the origin of life has been puzzling mankind for several millenia. Starting from the second half of the 20th century, when the crucial role of nucleic acids in biological heredity became apparent, the emphasis in the field has shifted to the explanation of the origin of nucleic acids and the mechanisms of copying of macromolecules. In the 1960s, the hypothesis of the RNA World was proposed, according to which the first stages of the origin of life on Earth were associated with the appearance of self-replicating complexes based on RNA, that were akin to RNA-enzymes that catalyze critical for life chemical reactions. Currently, it has been shown that different forms of RNA include not only canonical (adenine, uracil, guanine, cytosine), but also about 170 non-canonical nucleotides. In this review, we discuss potential roles of these non-canonical nucleotides in the processes of molecular prebiotic evolution, such as the emergence of canonical RNA nucleotides and catalytic RNAs, as well as the origin of template synthesis of RNA and proteins.

Excited-State Carrier Dynamics in Semiconducting Heterostructures from Self-Sorted NIR Active Dyes

Heterostructures comprise two or more different semiconducting materials stacked either as co-assemblies or self-sorted based on their dynamics of aggregates. However, self-sorting in heterostructures is rather significant in improving the short exciton diffusion length and charge separation. Despite small organic molecules being known for their self-sorting nature, macrocyclic are hitherto unknown owing to unrestrained assemblies from extended π-conjugated systems. Herein, two near infrared region (NIR) active molecules comprised of porphyrin appended D-π-D (1) and A-π-A (2) have been reported to show the self-assembled 0D and 2D nanostructures via J-aggregates. Interestingly, the mixture of 1 and 2 reveals self-sorting at the molecular level promoting nanosphere and sheet structures which further rolled over to spheres through π-π stacking leading to core-shell type heterostructure. Consequently, electrical conductivity is 10 times higher than the individual assemblies due to excited state electron transfer from 1 to 2 in a mixture, confirmed by femto second-transient absorption spectroscopy and electrochemical impedance spectroscopy. These results suggest that controlling the self-sorted heterostructures fosters refining the electronic properties which pave the way for designing novel NIR-absorbed molecules for organic solar cells (OSCs).

Synthetic ion channels made of DNA

Natural ion channels have long inspired the design of synthetic nanopores with protein-like features. A significant leap towards this endeavor has been made possible using DNA origami. The exploitation of DNA as a building material has enabled the construction of biomimetic DNA nanopores with a range of pore dimensions and stimuli-responsive capabilities. However, structural fluctuations and ion leakage across the walls of DNA nanopores greatly limit their use in various applications like label-free sensing and as a research tool in functional studies of ion channels. This review outlines some of the guiding principles for biomimetic engineering of DNA-based ion channels, discusses the weaknesses of current DNA nanopore designs, and presents recent efforts to alleviate these limitations.

Biphasic Coacervation Controlled by Kinetics as Studied by De Novo-Designed Peptides

Coacervation is generally treated as a liquid-liquid phase separation process and is controlled mainly by thermodynamics. However, kinetics could make a dominant contribution, especially in systems containing multiple interactions. In this work, using peptides of (XXLY)6SSSGSS to tune the charge density and the degree of hydrophobicity, as well as to introduce secondary structures, we evaluated the effect of kinetics on biphasic coacervates formed by peptides with single-stranded oligonucleotides and quaternized dextran at varying pH values. Only in the case where the charge density is constant and the electrostatic interaction is the major driving force for Coacervation is the effect of kinetics negligible. When pH-dependent electrostatic interaction and hydrophobic interaction are involved or the peptides form secondary structures, the Coacervation process is then path-dependent, indicating that the kinetics controls the phase separation process. The Coacervation by combining two different peptides suggests that the peptide with a higher charge density plays a leading role in the early stage, while the cooperation of both peptides takes over afterward. Our work demonstrates that it is normal to observe coacervates with different morphologies and functions due to kinetic control, especially in living cells. Peptides with minimized sequences are a practical approach to reveal the mechanism of Coacervation processes controlled by kinetics.

Spontaneous Emergence of Lipid Vesicles in a Coacervate-Based Compartmentalized System

The spontaneous emergence of lipid vesicles in the absence of evolved biological machinery represents a major challenge for bottom-up synthetic biology. We show that coacervate microdroplets could create a compartmentalized environment that enriches lipid molecules and facilitates their spontaneous assembly into lipid vesicles. These vesicles can escape from the coacervate microdroplets in a continuous process under non-equilibrium conditions, resembling a constant production process akin to a "primitive enzyme" factory assembly line. These findings significantly extend our understanding of the intricate interaction between lipid molecules and coacervate microdroplets, shedding light on the emergence of cellular systems and offering a new perspective on the conditions necessary for the development of life on Earth.

Selective Nonenzymatic Formation of Biologically Common RNA Hairpins

The prebiotic formation of RNA building blocks is well-supported experimentally, yet the emergence of sequence- and structure-specific RNA oligomers is generally attributed to biological selection via Darwinian evolution rather than prebiotic chemical selectivity. In this study, we used deep sequencing to investigate the partitioning of randomized RNA overhangs into ligated products by either splinted ligation or loop-closing ligation. Comprehensive sequence-reactivity profiles revealed that loop-closing ligation preferentially yields hairpin structures with loop sequences UNNG, CNNG, and GNNA (where N represents A, C, G, or U) under competing conditions. In contrast, splinted ligation products tended to be GC rich. Notably, the overhang sequences that preferentially partition to loop-closing ligation significantly overlap with the most common biological tetraloops, whereas the overhangs favoring splinted ligation exhibit an inverse correlation with biological tetraloops. Applying these sequence rules enables the high-efficiency assembly of functional ribozymes from short RNAs without template inhibition. Our findings suggest that the RNA tetraloop structures that are common in biology may have been predisposed and prevalent in the prebiotic pool of RNAs, prior to the advent of Darwinian evolution. We suggest that the one-step prebiotic chemical process of loop-closing ligation could have favored the emergence of the first RNA functions.

Fuel-Driven π-Conjugated Superstructures to Form Transient Conductive Hydrogels

Despite advances in creating dissipative materials with transient properties, such as hydrogels and active droplets, their application remains confined to temporal changes in structural properties. Developing out-of-equilibrium materials whose electronic functions are parameterized by a chemical reaction cycle is challenging. Yet, this class of materials is required to construct biomimetic materials. In contrast to traditional chemical reaction cycles that exploit molecularly dissolved building blocks at thermodynamic equilibrium, we show that fiber structures derived from reactive naphthalene diimide (NDI) building blocks can be used as resting states to form far-from-equilibrium conductive hydrogels after the addition of chemical fuels. Upon fueling the NDI-derived fibers, a dual-component activation and deactivation pathway is deduced by kinetic analysis and is absent when using a molecularly dissolved resting state. Investigating the solid-state morphologies of the structures formed throughout the fuel-driven reaction cycle using cryo-EM reveals that the resting thermodynamic fibers evolve to transient thicker fibrils and layered superstructures. We show that the transient redox-active hydrogels exhibit a nearly threefold increase in electrical conductivity upon fuel consumption before reverting to their original value over hours. These far-from-equilibrium materials are potential candidates in applications such as programmable biorobotics and chemical computing.

Transient Allosteric Regulation of Catalysis by Effector Switching in a Pt2L4 Cage

The complexity of allosteric enzymatic regulation continues to inspire synthetic chemists seeking to emulate interconnected biological systems. In this work, a Pt2L4 cage capable of catalyzing the cyclization reaction of an alkynoic tosyl amide is orthogonally coupled to a diacid-catalyzed carbodiimide-hydration cycle. This new Pt-catalyzed cyclization reaction is demonstrated to exhibit electronic regulation by inclusion of different guest effectors. The orthogonal diacid-catalyzed carbodiimide hydration cycle produces transiently diverse guests that influence the rate of the Pt-catalyzed cyclization reaction to different extents. Further complexity can be introduced to the system through displacing the transiently-formed, weakly bound anhydride guest with the stronger binding fumaronitrile, affecting the catalytic rate to a larger extent for the duration of the orthogonal reaction cycle. The modulation of a Pt-catalyzed cyclization reaction can thus be regulated transiently over the course of the reaction- either up- or down-regulating the turnover frequency (TOF)-via coupling with a temporally controllable orthogonal process. This study demonstrates that principles of allosteric enzymatic regulation can also be applied to simple artificial systems.

Selection of Early Life Codons by Ultraviolet Light

How life developed in its earliest stages is a central but notoriously difficult question in science. The earliest lifeforms likely used a reduced set of codon sequences that were progressively completed over time, driven by chemical, physical, and combinatorial constraints. However, despite its importance for prebiotic chemistry, UV radiation has not been considered a selection pressure for the evolution of early codon sequences. In this proof-of-principle study, we quantified the UV susceptibility of large pools of DNA protogenomes and tested the timing of evolutionary incorporation of codon sequences using a Monte Carlo method utilizing sequence-context-dependent damage rates previously determined by high throughput sequencing experiments. We traced the UV-radiation selection pressure on early protogenomes comprising a limited number of codon sequences to late protogenomes with access to all codons. The modeling showed that in just minutes under early sunlight, the choice of the first codons determined whether most of the protogenomes remained intact or became damaged entirely. The results correlated with earlier chemical models of the evolution of the genetic code. Our results show how UV could have played a crucial role in the evolution of the early genetic code for a DNA-based genome and provide the concept for future RNA-based studies.

The second wave of formose research

This review article highlights key developments in the second wave of formose research (from approximately 2000), summarizing approximately 100 relevant studies. Section 1 introduces the basics of formose reaction and its historical context. Section 2 provides a brief overview of the pioneering works from the first wave of formose research (from 1970 to 1990). Section 3 then overviews the second wave of formose research, in which formose reactions under various conditions, mechanistic studies of the formose reaction, formose reactions and the origin of life, and applications of formose reactions are described. Finally, Section 4 offers summary and outlook.

Reactive Brownian Dynamics of Chemically Fueled Droplets: Roles of Attraction and Deactivation Modes

The self-assembly of biological membraneless organelles can be mimicked by active droplets resulting from chemically fueled microphase separation. However, how the nonequilibrium, transient structure of these active droplets can be controlled through the physicochemical input parameters is not yet well understood. In our work, a chemically fueled two-state chemical reaction and subsequent droplet growth and decay are modeled with a reactive Brownian dynamics simulation in two spatial dimensions. In our model, particles that are activated via the consumption of fuel become attractive and can accumulate into droplets. A local-density-dependent distinction of the droplet's 'internal' and 'external' particles allows for structural feedback by giving further control over the deactivation process. The simulation shows that the deactivation of only external particles slows down the decay and stabilizes the droplets, whereas the deactivation of only internal particles can lead to a temporary encapsulation of deactivated particles (in nonequilibrium 'core-shell' structures) where the chemically active particles serve as an outer shell. Additionally, the role of hydrophobicity resembled by the attraction energy ε and the dependency of the nonequilibrium droplet formation on the various parameters of the chemical reaction are investigated. For example, a high attraction energy can lead to transient finite-size crystalline droplets, while other parameter choices indicate bimodal droplet size distributions at specific times. Similarities and differences to related experiments are discussed.

A Urease-Based pH Photoswitch: A General Route to Light-to-pH Transduction

New approaches for the integration of chemical and physical stimuli to control the dynamics of artificial enzymatic reaction networks (ERNs) are needed. Here, we present a general approach to convert a light stimulus into a time-programmed pH response. We developed and characterized a panel of photoswitchable inhibitors of urease. Urease activity, now regulated by light via the photoinhibitors, leads to an increase in pH upon hydrolysis of urea into ammonia. Careful choice of characteristics of light, and concentrations of enzyme, substrate, and photoinhibitor, allowed us to control the timing of the pH transition. Furthermore, as all enzymes have an activity-pH profile, the urease photoinhibitor system can be used to regulate the activities of other enzymes in small reaction networks.

Menthyl acetate powered self-propelled Janus sponge Marangoni motors with self-maintaining surface tension gradients and active mixing

HYPOTHESIS

Small scale Marangoni motors, which self-generate motion by inducing surface tension gradients on water interfaces through release of surface-active "fuels", have recently been proposed as self-powered mixing devices for low volume fluids. Such devices however, often show self-limiting lifespans due to the rapid saturation of surface-active agents. A potential solution to this is the use volatile surface-active agents which do not persist in their environment. Here we investigate menthyl acetate (MA) as a safe, inexpensive and non-persistent fuel for Marangoni motors.

EXPERIMENTS

MA was loaded asymmetrically into millimeter scale silicone sponges. Menthyl acetate reacts slowly with water to produce the volatile surface-active menthol, which induces surface tension gradients across the sponge to drive motion by the Marangoni effect. Videos were taken and trajectories determined by custom software. Mixing was assessed by the ability of Marangoni motors to homogenize milliliter scale aqueous solutions containing colloidal sediments.

FINDINGS

Marangoni motors, loaded with asymmetric "Janus" distributions of menthyl acetate show velocities and rotational speeds up to 30 mm s-1 and 500 RPM respectively, with their functional lifetimes scaling linearly with fuel volume. We show these devices are capable of enhanced mixing of solutions at orders of magnitude greater rates than diffusion alone.

Autocatalytic Reaction Networks: A Pathway to Spatial Temporal Mastery in Dynamic Materials

Autocatalytic reaction present a significant opportunity for the precise spatial and temporal control of dynamic materials, mimicking the characteristics of living matter within autonomous chemical systems. Herein, we have crafted an autocatalytic chemical reaction network (CRN) designed to be incorporated into a dynamic system, allowing for efficient control of both sol(I)-gel and gel-sol(II) transitions through autocatalytic fronts. The CRN incorporates two autocatalytic reactions. The first reaction promotes the formation of disulfide crosslinks while increasing the local pH through base product generation, catalyzing further disulfide bond formation and initiating a polymerization front that transforms the liquid phase into a gel. A subsequent, slower reaction triggered at the gel/air interface, resulted in the breakage of disulfide crosslinks, transforming the gel back into a liquid state through accelerating fronts. The dynamics of these autocatalytic fronts are accurately predicted by a reaction-diffusion model, providing a theoretical framework for system preprogramming. Moreover, our results show that the reversible sol-gel transition can be reliably repeated multiple times. This approach not only enhances our understanding of autocatalytic CRNs but also pioneers a new approach for developing dynamic materials with life-like properties, significantly impacting material science and bioengineering.

Quantification of Biomolecular Condensate Volume Reveals Network Swelling and Dissolution Regimes during Phase Transition

Accurate determination of biomolecular condensate volume reveals that destabilization of condensates can lead to either swelling or shrinking of condensates, giving fundamental insights into the regulation of the volume of cellular condensates. Determination of the volume of biomolecular condensates and coacervate protocells is essential to investigate their precise composition and impact on (bio)chemical reactions that are localized inside the condensates. It is not a straightforward task, as condensates have tiny volumes, are highly viscous, and are prone to wetting. Here, we examine different strategies to determine condensate volume and introduce two new methods, with which condensate volumes of 1 μL or less (volume fraction 0.4%) can be determined with a standard deviation of 0.03 μL. Using these methods, we show that the swelling or shrinking of condensates depends on the degree of physical cross-linking. These observations are supported by Flory-Huggins theory and can have profound effects on condensates in cell biology.

Time-Encoded Information Encryption with pH Clock Guided Broad-Spectrum Emission by Dynamic Assemblies

With growing threats from counterfeiting-based security breaches, multi-level and specific stimuli-responsive anti-counterfeiting devices and message encryption methods have attracted immense research interest. Fluorescence-based encryption from aggregation-induced emission (AIE)-based materials solves the problems to a considerable extent. However, the development of smarter patterns with hierarchical security levels alongside dynamic display is still challenging. To screen out this complication, we bring forward a pH-switchable fluorescent assembly of an AIEgen and an aliphatic acid. We later temporally direct the molecular assembly with the aid of a chemical trigger-regulated pH clock, generating a transitory multicolor emission, including transient white light generation. The pH-dependent emissions were further implemented in constructing smart multi-input fluorescent chemical AND gates. Subsequently, we integrate the time-gated emissive system to develop an advanced multi-dimensionally secure data encryption strategy. This novel approach enhances anti-counterfeiting measures by introducing an additional layer of security based on temporal characteristics.

Cell-Free Gene Expression: Methods and Applications

Cell-free gene expression (CFE) systems empower synthetic biologists to build biological molecules and processes outside of living intact cells. The foundational principle is that precise, complex biomolecular transformations can be conducted in purified enzyme or crude cell lysate systems. This concept circumvents mechanisms that have evolved to facilitate species survival, bypasses limitations on molecular transport across the cell wall, and provides a significant departure from traditional, cell-based processes that rely on microscopic cellular "reactors." In addition, cell-free systems are inherently distributable through freeze-drying, which allows simple distribution before rehydration at the point-of-use. Furthermore, as cell-free systems are nonliving, they provide built-in safeguards for biocontainment without the constraints attendant on genetically modified organisms. These features have led to a significant increase in the development and use of CFE systems over the past two decades. Here, we discuss recent advances in CFE systems and highlight how they are transforming efforts to build cells, control genetic networks, and manufacture biobased products.

Do-Nothing Prebiotic Chemistry: Chemical Kinetics as a Window into Prebiotic Plausibility

ConspectusOrigin of Life research is a fast growing field of study with each year bringing new breakthroughs. Recent discoveries include novel syntheses of life's building blocks, mechanisms of activation and interaction between molecules, and newly identified environments that provide promising conditions for these syntheses and mechanisms. Even with these new findings, firmly grounded in rigorous laboratory experiments, researchers often find themselves uncertain about how to apply them. How can a bridge be built between the laboratory and the geochemical environment? A critical question to ask when seeking to apply new results in origins is: how can this chemistry occur without direct intervention from a chemist? We believe the first step toward answering this question lies in the determination of rate constants and the construction of chemical networks to describe prebiotic chemistry in geochemical environments.So far, our group has measured several rate constants relevant to different prebiotic reaction networks, starting with the synthetic pathways of the cyanosulfidic network. The reactions we explore often involve ultraviolet light-driven photochemistry, facilitated by our StarLab setup that accurately simulates the spectrum of the young Sun and other stars. Our latest work investigates environments with active photochemistry in the absence of cyanide. In this study, we measure the effective rate constant for the production of formate from the reduction of carbon species using sulfite within the context of early Martian waters. The underlying goal of the work done in our group is to predict the likelihood that certain geological conditions will result in a specific set of chemical products. These predictions can be combined with those we have made for the necessary astrophysical conditions in certain origins of life scenarios on extrasolar planets.In the near future we expect that a sufficient number of rate constants will be measured, by our group and others, to allow for aspects of prebiotic chemistry to be predicted using chemical kinetics models. Once these models have been benchmarked against experimental data, our next step will be applying them to natural environments that better mimic the conditions thought to have been present at the onset of life. Following this, we can test these models by comparing their predictions to additional experiments. After refinement, these models will be able to provide guidance on the optimal conditions for conducting laboratory experiments, while helping to minimize and characterize any interference from a chemist.This approach can provide valuable insights into what is possible within geochemical environments, where all chemistry is by necessity do-nothing chemistry.

A possible origin of life in nonpolar environments

Explaining the emergence of life is perhaps the central and most challenging question in modern science. We are proposing a new hypothesis concerning the origins of life. The new hypothesis is based on the assumption that during the emergence of life, evolution had to first involve autocatalytic systems which only subsequently acquired the capacity of genetic heredity. Additionally, the key abiotic and early biotic molecules required in the formation of early life, like cofactors, coenzymes, nucleic bases, prosthetic groups, polycyclic aromatic hydrocarbons (PAHs), some pigments, etc. are poorly soluble in aqueous media. To avoid the latter concentration problem, the new hypothesis assumes that life could have emerged in the nonpolar environments or low water systems, or at the interphase of the nonpolar and polar water phase, from where it was subsequently transferred to the aqueous environment. To support our hypothesis, we assume that hydrocarbons and oil on the Earth have abiotic origins.

Microgels With Electrostatically Controlled Molecular Affinity to Direct Morphogenesis

Concentration gradients of soluble signaling molecules-morphogens-determine the cellular organization in tissue development. Morphogen-releasing microgels have shown potential to recapitulate this principle in engineered tissue constructs, however, with limited control over the molecular cues in space and time. Inspired by the functionality of sulfated glycosaminoglycans (sGAGs) in morphogen signaling in vivo, a library of sGAG-based microgels is developed and designated as µGel Units to Instruct Development (µGUIDEs). Adjustment of the microgel's sGAG sulfation patterns and concentration enabled the programming of electrostatic affinities that control the release of morphogens. Based on computational analyses of molecular transport processes, µGUIDEs provided unprecedented precision in the spatiotemporal modulation of vascular endothelial growth factor (VEGF) gradients in a microgel-in-gel vasculogenesis model and kidney organoid cultures. The versatile approach offers new options for creating morphogen signaling centers to advance the understanding of tissue and organ development.

Multilevel Dynamic System as Molecular Morning-After Timer

Systems chemistry aims to develop molecular systems that display emerging properties arising from their network and absent in their individual constituents. Employing reversible chemistry under thermodynamic control represents a valuable tool for generating dynamic combinatorial libraries of interconverting molecules, which may exhibit intriguing collective behaviour. A simple dynamic combinatorial library was prepared using dithioacetal/thiol/disulfide exchanges. Because of the relative reactivities of these reversible reactions, the library constitutes a two-layer dynamic system with one layer active in an acid medium (thiol/dithioacetal exchange) and one layer active in a basic medium (thiol/disulfide exchange). This property enables the system to respond to momentary changes in acidity of the medium by activating different network regions, channeling some building blocks from one layer to another through shared thiol reagents (nodes). This momentaneous change in wiring affects the final steady state composition of the library, measured the next day, even though the event that caused it vanishes without leaving any residue. Therefore, the final composition of this dynamic system provides information about this transient past perturbation in the environment such as: when it occurred, how long it was, or how intense it was.

Using Hybrid Coating to Fabricate Highly Stable and Expandable Transparent Liquid Marbles

Liquid marbles (LMs) are microliter-scale droplets coated with hydrophobic solid particles. The particle size and hydrophobicity of the surface coating determine their properties, such as transparency, expandability, and resistance to evaporation and coalescence, one or more of which can be critical to their application as microreactors. This study reports the use of a mixture of two different hydrophobic powders for fabrication of LMs for colorimetric assays: trichloro(1H,1H,2H,2H-perfluorooctyl) silane-linked silica gel (modified silica gel (MSG), particle size: 40-75 μm) and hexamethyldisilazane-linked fumed silica (modified fumed silica (MFS), average aggregate length: 200-300 nm). The hybrid coating mixture (MIX) prepared by mixing these MSG and MFS powders in a ratio of 3:7 (w/w), respectively, contained particles of different sizes as well as different hydrophobicity as the silane linked to MSG is more hydrophobic than the one linked to MFS. LMs fabricated using MIX as the surface coating were characterized and compared to LMs coated with MSG or MFS alone. It was observed that MIX LMs were comparable to the MFS LMs in transparency (higher than the MSG LMs), expandability (more than 20 times their initial volume), and stability against evaporation (for more than 4 h at 78% relative humidity at 26 °C). However, in terms of resistance to coalescence, the MIX LMs showed a resistance comparable to that of MSG LMs, much higher than that of MFS LMs. Further experiments demonstrated that it is the presence of the particles of different sizes (MSG particles are ∼100 times larger than MFS) that improves the resistance to coalescence rather than the higher hydrophobicity of the MSG. Three different colorimetric assays were performed in the MIX LMs, and the results obtained were comparable in accuracy and precision to those obtained in a standard polystyrene microwell plate system. Low quantities of the analytes could be detected and quantified, as evidenced by the limit of detection (alkaline phosphatase (AP): 0.18 μg/mL; bovine serum albumin (BSA): 2.28 μg/mL; and chymotrypsin: 3.69 μM) and limit of quantification (AP: 0.59 μg/mL; BSA: 12.29 μg/mL; and chymotrypsin: 7.59 μM) values. Color intensities in LMs were quantified using a smartphone application, which provides the added benefit of an instrument-free approach. These findings highlight the potential of using LMs stabilized with mixtures of nano- and microparticles as robust, versatile microreactors for portable and sensitive colorimetric assays, paving the way for more accessible and efficient diagnostic tools.

Experimental formation of carbonates from perchlorate and sulphate brines: Implications for Jezero crater, Mars

Extensive carbonate precipitation has occurred on Mars. To gain insight into the carbonation mechanisms and formation processes under ancient Martian aqueous conditions, we examine the precipitation of carbonates resulting from atmospheric carbon fixation, focusing on interactions between various brines and silicate and perchlorate solutions in alkaline environments. The micro-scale morphology and composition of the resulting precipitates are analysed using ESEM micrographs, EDX chemical compositional analysis, X-ray diffraction, and micro-Raman spectroscopy. Our findings indicate a significant atmospheric carbonation process involving chlorate and sulphate brines reacting with alkaline perchlorate solutions, leading to the precipitation of calcium carbonate polymorphs, including vaterite, aragonite, and calcite, as well as other carbonates like siderite (iron carbonate) and zaratite (nickel carbonate). Some precipitates exhibit biomorphic structures (such as globular spherical aggregates, fine branched tubes, and flower-like morphologies) that should not be mistaken for fossils. These experiments demonstrate that various precipitates can form simultaneously in a single reaction vessel while being exposed to different micro-scale pH conditions. We propose that systematic laboratory studies of such precipitate reactions should be conducted in preparation for the analysis of the Mars Sample Return collection on Earth, aiding in the interpretation of carbonate presence in natural brine-rock carbonation processes under Martian conditions while also helping to distinguish potential biosignatures from purely geochemical processes.

A novel approach based on supramolecular solvents microextraction for quick detection of perfluoroalkyl acids and their precursors in aquatic food

Per-and polyfluoroalkyl substances (PFASs) have garnered significant attention owing to their prevalence and adverse effects on humans. The direct dietary intake of perfluoroalkyl acids (PFAAs) and PFAAs precursors (pre-PFAAs) biotransformation are considered major contributors to human exposure to PFASs. However, little information is available on analytical methods for the simultaneous detection of PFAAs and pre-PFAAs. In the present study, a single-step sample-treatment-based supramolecular solvents-dispersed liquid-liquid microextraction (SUPRASs-DLLME) technique was established for the analysis of 16 PFAAs and 7 pre-PFAAs in aquatic food. SUPRASs were synthesized using 1-heptanol (3 mL) and tetrahydrofuran (4 mL), which were self-assembled in water. The parameters for microextraction, such as extraction method and enrichment capacity, were optimized. Under the optimum conditions, the limit of detection (LOD) and limit of quantification (LOQ) were 0.03-0.15 ng·g-1 and 0.1-0.5 ng·g-1, respectively. Good linearities (R2 > 0.996) were obtained for all the target compounds, and the recoveries ranged 81.1-120 % with relative standard deviations (RSDs) lower than 20 %. This method was applied to the analysis of 16 PFAAs and 7 pre-PFAAs in aquatic food samples (crabs, prawns, and fish). This study provides a new idea for analyzing other pollutants in biological samples.

Shape transformations in peptide-DNA coacervates driven by enzyme-catalyzed deacetylation

Biomolecular condensates formed by liquid-liquid phase separation (LLPS) are important organizers of biochemistry in living cells. Condensate formation can be dynamically regulated, for example, by protein binding or enzymatic processes. However, how enzymatic reactions can influence condensate shape and control shape transformations is less well understood. Here, we design a model condensate that can be formed by the enzymatic deacetylation of a small peptide by sirtuin-3 in the presence of DNA. Interestingly, upon nucleation condensates initially form gel-like aggregates that gradually transform into spherical droplets, displaying fusion and wetting. This process is governed by sirtuin-3 concentration, as more enzyme results in a faster aggregate-to-liquid transformation of the condensates. The counterintuitive transformation of gel-like to liquid-like condensates with increasing interaction strength between the peptide and DNA is recapitulated by forming condensates with different peptides and nucleic acids at increasing salt concentrations. Close to the critical point where coacervates dissolve, gel-like aggregates are formed with short double stranded DNA, but not with single stranded DNA or weakly binding peptides, even though the coacervate salt resistance is similar. At lower salt concentrations the interaction strength increases, and spherical, liquid-like condensates are formed. We attribute this behavior to bending of the DNA by oppositely charged peptides, which becomes stronger as the system moves further into the two-phase region. Overall, this work shows that enzymes can induce shape transformations of condensates and that condensate material properties do not necessarily reveal their stability.