DNA-empowered synthetic cells as minimalistic life forms.

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

DNA-Based Signaling Networks for Transient Colloidal Co-Assemblies.

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

Switchable Hydrophobic Pockets in DNA Protocells Enhance Chemical Conversion.

Synthetic cell models help us understand living cells and the origin of life. Key aspects of living cells are crowded interiors where secondary structures, such as the cytoskeleton and membraneless organelles/condensates, can form. These can form dynamically and serve structural or functional purposes, such as protection from heat shock or as crucibles for various biochemical reactions. Inspired by these phenomena, we introduce a crowded all-DNA protocell and encapsulate a temperature-switchable DNA-b-polymer block copolymer, in which the synthetic polymer phase-segregates at elevated temperatures. We find that thermoreversible phase segregation of the synthetic polymer occurs via bicontinuous phase separation, resulting in artificial organelle structures that can reorient into larger domains depending on the viscoelastic properties of the protocell interior. Fluorescent sensors confirm the formation of hydrophobic compartments, which enhance the reactivity of bimolecular reactions. This study leverages the strengths of biological and synthetic polymers to construct advanced biohybrid artificial cells that provide insights into phase segregation under crowded conditions and the formation of organelles and microreactors in response to environmental stress.

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

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

Signal-processing and adaptive prototissue formation in metabolic DNA protocells.

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

Enabling Superhydrophobicity-Guided Superwicking in Metal Alloys via a Nanosecond Laser-Based Surface Treatment Method.

Enabling capillary wicking on bulk metal alloys is challenging due to processing complexity at different size scales. This work presents a laser-chemical surface treatment to fabricate superwicking patterns guided by a superhydrophobic region over a large-area metal alloy surface. The laser-chemical surface treatment generates surface micro/nanostructures and desirable surface chemistry simultaneously. The superhydrophobic surface was first fabricated over the whole surface by laser treatment under water confinement and fluorosilane treatment; subsequently, superwicking stripes were processed by a second laser treatment in air and cyanosilane treatment. The resultant surface shows superwicking regions surrounded by superhydrophobic regions. During the process, superwicking regions possess dual-scale structures and polar nitrile surface chemistry. In contrast, random nanoscale structures and fluorocarbon chemistry are generated on the superhydrophobic region of the aluminum alloy 6061 substrates. The resultant superwicking region demonstrates self-propelling anti-gravity liquid transport for methanol and water. The combination of the capillary effect of the dual-scale surface microgrooves and the water affinitive nitrile group contributes toward the self-propelling movement of water and methanol at the superwicking region. The initial phase of wicking followed Washburn dynamics, whereas it entered a non-linear regime in the later phase. The wicking height and rate are regulated by microgroove geometry and spacing.

Effect of silver electrode wetting state on oxygen reduction electrochemistry.

Surface wettability plays an important role in heterogeneous electrocatalysis. Here we report a facile laser ablation strategy to directly modify the wettability of the silver catalyst surface and investigate its effect on oxygen reduction reaction (ORR). A broad range tuning of 2e-/4e- ORR pathways was achieved, with hydrophilic silver surfaces (contact angle (θw) 31.1°± 0.6°) showing high activity and selectivity towards 4e- reduction of oxygen to water.

A Modular Fluorescent Probe for Viscosity and Polarity Sensing in DNA Hybrid Mesostructures.

There exists a critical need in biomedical molecular imaging and diagnostics for molecular sensors that report on slight changes to their local microenvironment with high spatial fidelity. Herein, a modular fluorescent probe, termed StyPy, is rationally designed which features i) an enormous and tunable Stokes shift based on twisted intramolecular charge transfer (TICT) processes with no overlap, a broad emission in the far-red/near-infrared (NIR) region of light and extraordinary quantum yields of fluorescence, ii) a modular applicability via facile para-fluoro-thiol reaction (PFTR), and iii) a polarity- and viscosity-dependent emission. This renders StyPy as a particularly promising molecular sensor. Based on the thorough characterization on the molecular level, StyPy reports on the viscosity change in all-DNA microspheres and indicates the hydrophilic and hydrophobic compartments of hybrid DNA-based mesostructures consisting of latex beads embedded in DNA microspheres. Moreover, the enormous Stokes shift of StyPy enables one to detect multiple fluorophores, while using only a single laser line for excitation in DNA protocells. The authors anticipate that the presented results for multiplexing information are of direct importance for advanced imaging in complex soft matter and biological systems.

Functional and morphological adaptation in DNA protocells via signal processing prompted by artificial metalloenzymes.

For life to emerge, the confinement of catalytic reactions within protocellular environments has been proposed to be a decisive aspect to regulate chemical activity in space1. Today, cells and organisms adapt to signals2-6 by processing them through reaction networks that ultimately provide downstream functional responses and structural morphogenesis7,8. Re-enacting such signal processing in de novo-designed protocells is a profound challenge, but of high importance for understanding the design of adaptive systems with life-like traits. We report on engineered all-DNA protocells9 harbouring an artificial metalloenzyme10 whose olefin metathesis activity leads to downstream morphogenetic protocellular responses with varying levels of complexity. The artificial metalloenzyme catalyses the uncaging of a pro-fluorescent signal molecule that generates a self-reporting fluorescent metabolite designed to weaken DNA duplex interactions. This leads to pronounced growth, intraparticular functional adaptation in the presence of a fluorescent DNA mechanosensor11 or interparticle protocell fusion. Such processes mimic chemically transduced processes found in cell adaptation and cell-to-cell adhesion. Our concept showcases new opportunities to study life-like behaviour via abiotic bioorthogonal chemical and mechanical transformations in synthetic protocells. Furthermore, it reveals a strategy for inducing complex behaviour in adaptive and communicating soft-matter microsystems, and it illustrates how dynamic properties can be upregulated and sustained in micro-compartmentalized media.

Design of Chemical Surface Treatment for Laser-Textured Metal Alloys to Achieve Extreme Wetting Behavior.

Extreme wetting activities of laser-textured metal alloys have received significant interest due to their superior performance in a wide range of commercial applications and fundamental research studies. Fundamentally, extreme wettability of structured metal alloys depends on both the surface structure and surface chemistry. However, compared with the generation of physical topology on the surface, the role of surface chemistry is less explored for the laser texturing processes of metal alloys to tune the wettability. This work introduces a systematic design approach to modify the surface chemistry of laser textured metal alloys to achieve various extreme wettabilities, including superhydrophobicity/superoleophobicity, superhydrophilicity/superoleophilicity, and coexistence of superoleophobicity and superhydrophilicity. Microscale trenches are first created on the aluminum alloy 6061 surfaces by nanosecond pulse laser surface texturing. Subsequently, the textured surface is immersion-treated in several chemical solutions to attach target functional groups on the surface to achieve the final extreme wettability. Anchoring fluorinated groups (-CF2- and -CF3) with very low dispersive and nondispersive surface energy leads to superoleophobicity and superhydrophobicity, resulting in repelling both water and diiodomethane. Attachment of the polar nitrile (-C≡N) group with very high nondispersive and high dispersive surface energy achieves superhydrophilicity and superoleophilicity by drawing water and diiodomethane molecules in the laser-textured capillaries. At last, anchoring fluorinated groups (-CF2- and -CF3) and polar sodium carboxylate (-COONa) together leads to very low dispersive and very high nondispersive surface energy components. It results in the coexistence of superoleophobicity and superhydrophilicity, where the treated surface attracts water but repels diiodomethane.

Choosing sides: unusual ultrafast charge transfer pathways in an asymmetric electron-accepting cyclophane that binds an electron donor.

Constructing functional molecular systems for solar energy conversion and quantum information science requires a fundamental understanding of electron transfer in donor-bridge-acceptor (D-B-A) systems as well as competitive reaction pathways in acceptor-donor-acceptor (A-D-A) and acceptor-donor-acceptor' (A-D-A') systems. Herein we present a supramolecular complex comprising a tetracationic cyclophane having both phenyl-extended viologen (ExV2+) and dipyridylthiazolothiazole (TTz2+) electron acceptors doubly-linked by means of two p-xylylene linkers (TTzExVBox4+), which readily incorporates a perylene (Per) guest in its cavity (Per ⊂ TTzExVBox4+) to establish an A-D-A' system, in which the ExV2+ and TTz2+ units serve as competing electron acceptors with different reduction potentials. Photoexcitation of the Per guest yields both TTz+˙-Per+˙-ExV2+ and TTz2+-Per+˙-ExV+˙ in <1 ps, while back electron transfer in TTz2+-Per+˙-ExV+˙ proceeds via the unusual sequence TTz2+-Per+˙-ExV+˙ → TTz+˙-Per+˙-ExV2+ → TTz2+-Per-ExV2+. In addition, selective chemical reduction of TTz2+ gives Per ⊂ TTzExVBox3+˙, turning the complex into a D-B-A system in which photoexcitation of TTz+˙ results in the reaction sequence 2*TTz+˙-Per-ExV2+ → TTz2+-Per-ExV+˙ → TTz+˙-Per-ExV2+. Both reactions TTz2+-Per+˙-ExV+˙ → TTz+˙-Per+˙-ExV2+ and TTz2+-Per-ExV+˙ → TTz+˙-Per-ExV2+ occur with a (16 ± 1 ps)-1 rate constant irrespective of whether the bridge molecule is Per+˙ or Per. These results are explained using the superexchange mechanism in which the ionic states of the perylene guest serve as virtual states in each case and demonstrate a novel supramolecular platform for studying the effects of bridge energetics within D-B-A systems.

Pathway-controlled formation of mesostructured all-DNA colloids and superstructures.

DNA has traditionally been used for the programmable design of nanostructures by exploiting its sequence-defined supramolecular recognition. However, control on larger length scales or even hierarchical materials that translate to the macroscale remain difficult to construct. Here, we show that the polymer character of single-stranded DNA (ssDNA) can be activated via a nucleobase-specific lower critical solution temperature, which provides a unique access to mesoscale structuring mechanisms on larger length scales. We integrate both effects into ssDNA multiblock copolymers that code sequences for phase separation, hybridization and functionalization. Kinetic pathway guidance using temperature ramps balances the counteracting mesoscale phase separation during heating with nanoscale duplex recognition during cooling to yield a diversity of complex all-DNA colloids with control over the internal dynamics and of their superstructures. Our approach provides a facile and versatile platform to add mesostructural layers into hierarchical all-DNA materials. The high density of addressable ssDNA blocks opens routes for applications such as gene delivery, artificial evolution or spatially encoded (bio)materials.

Noninvasive Substitution of K+ Sites in Cyclodextrin Metal-Organic Frameworks by Li+ Ions.

Co-crystallization of K+ and Li+ ions with γ-cyclodextrin (γ-CD) has been shown to substitute the K+ ion sites partially by Li+ ions, while retaining the structural integrity and accessible porosity of CD-MOF-1 (MOF, metal-organic framework). A series of experiments, in which the K+/Li+ ratio was varied with respect to that of γ-CD, have been conducted in order to achieve the highest possible proportion of Li+ ions in the framework. Attempts to obtain a CD-MOF containing only Li+ ions resulted in nonporous materials. The structural occupancy on the part of the Li+ ions in the new CD-MOF has been confirmed by single-crystal X-ray analysis by determining the vacancies of K+-ion sites and accounting for the cation/γ-CD ratio in CD-MOF-1. The proportion of Li+ ions has also been confirmed by elemental analysis, whereas powder X-ray diffraction has established the stability of the extended framework. This noninvasive synthetic approach to generating mixed-metal CD-MOFs is a promising method for obtaining porous framework unattainable de novo. Furthermore, the CO2 and H2 capture capacities of the Li+-ion-substituted CD-MOF have been shown to exceed the highest sorption capacities reported so far for CD-MOFs.

Supramolecular Double-Helix Formation by Diastereoisomeric Conformations of Configurationally Enantiomeric Macrocycles.

Solid-state superstructures, resulting from assemblies programmed by homochirality, are attracting considerable attention. In addition, artificial double-helical architectures are being investigated, especially in relation to the ways in which homochiral small molecules can be induced to yield helical forms as a result of chiral induction. Herein, we report the highly specific self-assembly upon crystallization of a double-helical superstructure from an enantiopure macrocyclic dimer which adopts two diastereoisomeric conformations in a molar ratio of 1.5:1 in dimethyl sulfoxide. These two conformational diastereoisomers self-organize-and self-sort-in the crystalline phase in equimolar proportions to form two single-handed helices which are complementary to each other, giving rise to the assembly of a double helix that is stabilized by intermolecular [C-H···O] and π-π stacking interactions. The observed self-sorting phenomenon occurs on going from a mixed-solvent system containing two equilibrating conformational diastereoisomers, presumably present in unequal molar proportions, into the solid state. The diastereoisomeric conformations are captured upon crystallization in a 1:1 molar ratio in the double-helical superstructure, whose handedness is dictated by the choice of the enantiomeric macrocyclic dimer. The interconversion of the two conformational diastereoisomers derived from each configurationally enantiomeric macrocycle was investigated in CD3SOCD3 solution by variable-temperature 1H NMR spectroscopy (VT NMR) and circular dichroism (VT CD). The merging of the resonances for the protons corresponding to the two diastereoisomers at a range of coalescence temperatures in the VT NMR spectra and occurrence of the isosbestic points in the VT CD spectra indicate that the two diastereoisomers are interconverting slowly in solution on the 1H NMR time scale but rapidly on the laboratory time scale. To the best of our knowledge, the self-assembly of such solid-state superstructures from two conformational diastereoisomers of a homochiral macrocycle is a rare, if not unique, occurrence.

Cation-Dependent Gold Recovery with α-Cyclodextrin Facilitated by Second-Sphere Coordination.

Herein, we report an alkali metal cation-dependent approach to gold recovery, facilitated by second-sphere coordination with eco-friendly α-cyclodextrin (α-CD). Upon mixing eight salts composed of Na(+), K(+), Rb(+), or Cs(+) cations and [AuX4](-) (X = Cl/Br) anions with α-, ß-, or γ-CD in water, co-precipitates form selectively from the three (out of 24) aqueous solutions containing α-CD with KAuBr4, RbAuBr4, and CsAuBr4, from which the combination of α-CD and KAuBr4 affords the highest yield. Single-crystal X-ray analyses reveal that in 20 of the 24 adducts CD and [AuX4](-) anions form 2:1 sandwich-type second-sphere adducts driven partially by [C-H···X-Au] interactions between [AuX4](-) anions and the primary faces of two neighboring CDs. In the adduct formed between α-CD and KAuBr4, a [K(OH2)6](+) cation is encapsulated inside the cavity between the secondary faces of two α-CDs, leading to highly efficient precipitation owing to the formation of a cation/anion alternating ion wire residing inside a continuous α-CD nanotube. By contrast, in the other 19 adducts, the cations are coordinated by OH groups and glucopyranosyl ring O atoms in CDs. The strong coordination of Rb(+) and Cs(+) cations by these ligands, in conjunction with the stereoelectronically favorable binding of [AuBr4](-) anions with two α-CDs, facilitates the co-precipitation of the two adducts formed between α-CD with RbAuBr4 and CsAuBr4. In order to develop an efficient process for green gold recovery, the co-precipitation yield of α-CD and KAuBr4 has been optimized regarding both the temperature and the molar ratio of α-CD to KAuBr4.

Chiral Redox-Active Isosceles Triangles.

Designing small-molecule organic redox-active materials, with potential applications in energy storage, has received considerable interest of late. Herein, we report on the synthesis, characterization, and application of two rigid chiral triangles, each of which consist of non-identical pyromellitic diimide (PMDI) and naphthalene diimide (NDI)-based redox-active units. (1)H and (13)C NMR spectroscopic investigations in solution confirm the lower symmetry (C2 point group) associated with these two isosceles triangles. Single-crystal X-ray diffraction analyses reveal their rigid triangular prism-like geometries. Unlike previously investigated equilateral triangle containing three identical NDI subunits, both isosceles triangles do not choose to form one-dimensional supramolecular nanotubes by dint of [C-H···O] interaction-driven columnar stacking. The rigid isosceles triangle, composed of one NDI and two PMDI subunits, forms-in the presence of N,N-dimethylformamide-two different types of intermolecular NDI-NDI and NDI-PMDI π-π stacked dimers with opposite helicities in the solid state. Cyclic voltammetry reveals that both isosceles triangles can accept reversibly up to six electrons. Continuous-wave electron paramagnetic resonance and electron-nuclear double-resonance spectroscopic investigations, supported by density functional theory calculations, on the single-electron reduced radical anions of the isosceles triangles confirm the selective sharing of unpaired electrons among adjacent redox-active NDI subunit(s) within both molecules. The isosceles triangles have been employed as electrode-active materials in organic rechargeable lithium-ion batteries. The evaluation of the structure-performance relationships of this series of diimide-based triangles reveals that the increase in the number of NDI subunits, replacing PMDI ones, within the molecules improves the electrochemical cell performance of the batteries.

Supramolecular Gelation of Rigid Triangular Macrocycles through Rings of Multiple C-H···O Interactions Acting Cooperatively.

When equimolar solutions of the enantiomeric naphthalenediimide-based highly rigid triangles R-Δ and S-Δ in ClCH2CH2Cl are mixed, the racemate rac-Δ forms an organogel that is composed of interwoven fibers, resulting from the columnar stacking of the triangles in an alternating R-Δ/S-Δ fashion. Under identical conditions, the pure enantiomers do not form organogels. Density functional theory calculations reveal that the racemic RS dimer is more stable than the RR dimer as a result of the enantiomeric relationship between R-Δ and S-Δ, allowing them to act as two complementary rings comprised of 12 [C-H···O] interactions with an unprecedented and uninterrupted circular ADDAADDAADDA·DAADDAADDAAD alignment of hydrogen bond donors (D) and acceptors (A), in contrast with the square-wave manner in which the RR dimer forms a complementary yet interrupted ADADAD·DADADA circular sequence of six longer [C-H···O] hydrogen bonds. It follows that gelation is favored by weak interactions acting cooperatively in rings under precise stereoelectronic control.

Light-triggered capture and release of DNA and proteins by host-guest binding and electrostatic interaction.

The development of an effective and general delivery method that can be applied to a large variety of structurally diverse biomolecules remains a bottleneck in modern drug therapy. Herein, we present a supramolecular system for the dynamic trapping and light-stimulated release of both DNA and proteins. Self-assembled ternary complexes act as nanoscale carriers, comprising vesicles of amphiphilic cyclodextrin, the target biomolecules and linker molecules with an azobenzene unit and a charged functionality. The non-covalent linker binds to the cyclodextrin by host-guest complexation with the azobenzene. Proteins or DNA are then bound to the functionalized vesicles through multivalent electrostatic attraction. The photoresponse of the host-guest complex allows a light-induced switch from the multivalent state that can bind the biomolecules to the low-affinity state of the free linker, thereby providing external control over the cargo release. The major advantage of this delivery approach is the wide variety of targets that can be addressed by multivalent electrostatic interaction, which we demonstrate on four types of DNA and six different proteins.

Fabrication of hydrophilic polymer nanocontainers by use of supramolecular templates.

Polymer-shelled vesicles are prepared by using cyclodextrin vesicles as supramolecular templates and an adamantane-functionalized poly(acrylic acid) additive anchored via host-guest recognition, followed by cross-linking of carboxylic acid groups on the polymer. The polymer-shelled nanocontainers are highly stable and effective for encapsulating small hydrophilic molecules. We also show that a hollow cross-linked polymer cage can be obtained after dissolution of the template vesicles. The size and shell thickness of the polymer cage can be tuned by variation of template size and polymer length.

Magnetic separation of proteins by a self-assembled supramolecular ternary complex.

The easy and effective separation of proteins from a mixture is crucial in proteomics. A supramolecular method is described to selectively capture and precipitate one protein from a protein mixture upon application of a magnetic field. A multivalent complex self-assembles in a dilute aqueous solution of three components: magnetic nanoparticles capped with cyclodextrin, non-covalent cross-linkers with an adamantane and a carbohydrate moiety, and lectins. The self-assembled ternary complex is precipitated in a magnetic field and readily redispersed with the aid of a non-ionic surfactant and competitive binding agents. This strategy to purify proteins by supramolecular magnetic precipitation is highly selective and efficient.