Direct measurement of DNA-mediated adhesion between lipid bilayers

Polysaccharide functionalization reduces lipid vesicle stiffness

The biophysical properties of lipid vesicles are important for their stability and integrity, key parameters that control the performance when these vesicles are used for drug delivery. The vesicle properties are determined by the composition of lipids used to form the vesicle. However, for a given lipid composition, they can also be tailored by tethering polymers to the membrane. Typically, synthetic polymers like polyethyleneglycol are used to increase vesicle stability, but the use of polysaccharides in this context is much less explored. Here, we report a general method for functionalizing lipid vesicles with polysaccharides by binding them to cholesterol. We incorporate the polysaccharides on the outer membrane leaflet of giant unilamellar vesicles (GUVs) and investigate their effect on membrane mechanics using micropipette aspiration. We find that the presence of the glycolipid functionalization produces an unexpected softening of GUVs with fluid-like membranes. By contrast, the functionalization of GUVs with polyethylene glycol does not reduce their stretching modulus. This work provides the potential means to study membrane-bound meshworks of polysaccharides similar to the cellular glycocalyx; moreover, it can be used for tuning the mechanical properties of drug delivery vehicles.

Lipid vesicle-based molecular robots

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

Modulating Lipid Membrane Morphology by Dynamic DNA Origami Networks

Membrane morphology and its dynamic adaptation regulate many cellular functions, which are often mediated by membrane proteins. Advances in DNA nanotechnology have enabled the realization of various protein-inspired structures and functions with precise control at the nanometer level, suggesting a viable tool to artificially engineer membrane morphology. In this work, we demonstrate a DNA origami cross (DOC) structure that can be anchored onto giant unilamellar vesicles (GUVs) and subsequently polymerized into micrometer-scale reconfigurable one-dimensional (1D) chains or two-dimensional (2D) lattices. Such DNA origami-based networks can be switched between left-handed (LH) and right-handed (RH) conformations by DNA fuels and exhibit potent efficacy in remodeling the membrane curvatures of GUVs. This work sheds light on designing hierarchically assembled dynamic DNA systems for the programmable modulation of synthetic cells for useful applications.

DNA-assisted selective electrofusion (DASE) of Escherichia coli and giant lipid vesicles

Synthetic biology and cellular engineering require chemical and physical alterations, which are typically achieved by fusing target cells with each other or with payload-carrying vectors. On one hand, electrofusion can efficiently induce the merging of biological cells and/or synthetic analogues via the application of intense DC pulses, but it lacks selectivity and often leads to uncontrolled fusion. On the other hand, synthetic DNA-based constructs, inspired by natural fusogenic proteins, have been shown to induce a selective fusion between membranes, albeit with low efficiency. Here we introduce DNA-assisted selective electrofusion (DASE) which relies on membrane-anchored DNA constructs to bring together the objects one seeks to merge, and applying an electric impulse to trigger their fusion. The DASE process combines the efficiency of standard electrofusion and the selectivity of fusogenic nanostructures, as we demonstrate by inducing and characterizing the fusion of spheroplasts derived from Escherichia coli bacteria with cargo-carrying giant lipid vesicles.

Amphiphilic DNA nanostructures for bottom-up synthetic biology

DNA nanotechnology enables the construction of sophisticated biomimetic nanomachines that are increasingly central to the growing efforts of creating complex cell-like entities from the bottom-up. DNA nanostructures have been proposed as both structural and functional elements of these artificial cells, and in many instances are decorated with hydrophobic moieties to enable interfacing with synthetic lipid bilayers or regulating bulk self-organisation. In this feature article we review recent efforts to design biomimetic membrane-anchored DNA nanostructures capable of imparting complex functionalities to cell-like objects, such as regulated adhesion, tissue formation, communication and transport. We then discuss the ability of hydrophobic modifications to enable the self-assembly of DNA-based nanostructured frameworks with prescribed morphology and functionality, and explore the relevance of these novel materials for artificial cell science and beyond. Finally, we comment on the yet mostly unexpressed potential of amphiphilic DNA-nanotechnology as a complete toolbox for bottom-up synthetic biology - a figurative and literal scaffold upon which the next generation of synthetic cells could be built.

Biomechanics as driver of aggregation of tethers in adherent membranes

Cell adhesion is an important cellular process and is mediated by adhesion proteins residing on the cell membrane. Sometimes, two types of linker proteins are involved in adhesion, and they can segregate to form domains through a poorly understood size-exclusion process. We present an experimental and theoretical study of adhesion via linkers of two different sizes, realised in a mimetic model-system, based on giant unilamellar vesicles interacting with supported lipid bilayers. Here, adhesion is mediated by DNA linkers with two different lengths, but with the same binding enthalpy. We study the organisation of these linkers into domains as a function of relative fraction of long and short DNA constructs. Experimentally, we find that, irrespective of the composition, the adhesion domains are uniform with coexisting DNA bridge types, despite their relative difference in length of 9 nm. However, simulations suggest formation of nanodomains of the minority fraction at short length scales, which is below the optical resolution of the microscope. The nano-aggregation is more significant for long bridges, which are also more stable.

DNA self-organization controls valence in programmable colloid design

Just like atoms combine into molecules, colloids can self-organize into predetermined structures according to a set of design principles. Controlling valence-the number of interparticle bonds-is a prerequisite for the assembly of complex architectures. The assembly can be directed via solid "patchy" particles with prescribed geometries to make, for example, a colloidal diamond. We demonstrate here that the nanoscale ordering of individual molecular linkers can combine to program the structure of microscale assemblies. Specifically, we experimentally show that covering initially isotropic microdroplets with N mobile DNA linkers results in spontaneous and reversible self-organization of the DNA into Z(N) binding patches, selecting a predictable valence. We understand this valence thermodynamically, deriving a free energy functional for droplet-droplet adhesion that accurately predicts the equilibrium size of and molecular organization within patches, as well as the observed valence transitions with N Thus, microscopic self-organization can be programmed by choosing the molecular properties and concentration of binders. These results are widely applicable to the assembly of any particle with mobile linkers, such as functionalized liposomes or protein interactions in cell-cell adhesion.

Direct visualization of superselective colloid-surface binding mediated by multivalent interactions

Reliably distinguishing between cells based on minute differences in receptor density is crucial for cell-cell or virus-cell recognition, the initiation of signal transduction, and selective targeting in directed drug delivery. Such sharp differentiation between different surfaces based on their receptor density can only be achieved by multivalent interactions. Several theoretical and experimental works have contributed to our understanding of this "superselectivity." However, a versatile, controlled experimental model system that allows quantitative measurements on the ligand-receptor level is still missing. Here, we present a multivalent model system based on colloidal particles equipped with surface-mobile DNA linkers that can superselectively target a surface functionalized with the complementary mobile DNA-linkers. Using a combined approach of light microscopy and Foerster resonance energy transfer (FRET), we can directly observe the binding and recruitment of the ligand-receptor pairs in the contact area. We find a nonlinear transition in colloid-surface binding probability with increasing ligand or receptor concentration. In addition, we observe an increased sensitivity with weaker ligand-receptor interactions, and we confirm that the timescale of binding reversibility of individual linkers has a strong influence on superselectivity. These unprecedented insights on the ligand-receptor level provide dynamic information into the multivalent interaction between two fluidic membranes mediated by both mobile receptors and ligands and will enable future work on the role of spatial-temporal ligand-receptor dynamics on colloid-surface binding.

Avidity and surface mobility in multivalent ligand-receptor binding

Targeted drug delivery relies on two physical processes: the selective binding of a therapeutic particle to receptors on a specific cell membrane, followed by transport of the particle across the membrane. In this article, we address some of the challenges in controlling the thermodynamics and dynamics of these two processes by combining a simple experimental system with a statistical mechanical model. Specifically, we characterize and model multivalent ligand-receptor binding between colloidal particles and fluid lipid bilayers, as well as the surface mobility of membrane-bound particles. We show that the mobility of the receptors within the fluid membrane is key to both the thermodynamics and dynamics of binding. First, we find that the particle-membrane binding free energy-or avidity-is a strongly nonlinear function of the ligand-receptor affinity. We attribute the nonlinearity to a combination of multivalency and recruitment of fluid receptors to the binding site. Our results also suggest that partial wrapping of the bound particles by the membrane enhances avidity further. Second, we demonstrate that the lateral mobility of membrane-bound particles is also strongly influenced by the recruitment of receptors. Specifically, we find that the lateral diffusion coefficient of a membrane-bound particle is dominated by the hydrodynamic drag against the aggregate of receptors within the membrane. These results provide one of the first direct validations of the working theoretical framework for multivalent interactions. They also highlight that the fluidity and elasticity of the membrane are as important as the ligand-receptor affinity in determining the binding and transport of small particles attached to membranes.

Microfluidic Formation of Honeycomb-Patterned Droplets Bounded by Interface Bilayers via Bimodal Molecular Adsorption

Assembled water-in-oil droplets bounded by lipid bilayers are used in synthetic biology as minimal models of cell tissue. Microfluidic devices successfully generate monodispersed droplets and assemble them via droplet interface bilayesr (DIB) formation. However, a honeycomb pattern of DIB-bounded droplets, similar to epithelial tissues, remains unrealized because the rapid DIB formation between the droplets hinders their ability to form the honeycomb pattern. In this paper, we demonstrate the microfluidic formation of a honeycomb pattern of DIB-bounded droplets using two surfactants with different adsorption rates on the droplet surface. A non-DIB forming surfactant (sorbitan monooleate, Span 80) was mixed with a lipid (1,2-dioleoyl-sn-glycero-3-phosphocholine, PC), whose adsorption rate on the droplet surface and saturated interfacial tension were lower than those of Span 80. By changing the surfactant composition, we established the conditions under which the droplets initially form a honeycomb pattern and subsequently adhere to each other via DIB formation to minimize the interfacial energy. In addition, the reconstituted membrane protein nanopores at the DIBs were able to transport molecules. This new method, using the difference in the adsorption rates of two surfactants, allows the formation of a honeycomb pattern of DIB-bounded droplets in a single step, and thus facilitates research using DIB-bounded droplet assemblies.

An exported kinase family mediates species-specific erythrocyte remodelling and virulence in human malaria

The most severe form of human malaria is caused by Plasmodium falciparum. Its virulence is closely linked to the increase in rigidity of infected erythrocytes and their adhesion to endothelial receptors, obstructing blood flow to vital organs. Unlike other human-infecting Plasmodium species, P. falciparum exports a family of 18 FIKK serine/threonine kinases into the host cell, suggesting that phosphorylation may modulate erythrocyte modifications. We reveal substantial species-specific phosphorylation of erythrocyte proteins by P. falciparum but not by Plasmodium knowlesi, which does not export FIKK kinases. By conditionally deleting all FIKK kinases combined with large-scale quantitative phosphoproteomics we identified unique phosphorylation fingerprints for each kinase, including phosphosites on parasite virulence factors and host erythrocyte proteins. Despite their non-overlapping target sites, a network analysis revealed that some FIKKs may act in the same pathways. Only the deletion of the non-exported kinase FIKK8 resulted in reduced parasite growth, suggesting the exported FIKKs may instead support functions important for survival in the host. We show that one kinase, FIKK4.1, mediates both rigidification of the erythrocyte cytoskeleton and trafficking of the adhesin and key virulence factor PfEMP1 to the host cell surface. This establishes the FIKK family as important drivers of parasite evolution and malaria pathology.

First-order 'hyper-selective' binding transition of multivalent particles under force

Multivalent particles bind to targets via many independent ligand-receptor bonding interactions. This microscopic design spans length scales in both synthetic and biological systems. Classic examples include interactions between cells, virus binding, synthetic ligand-coated micrometer-scale vesicles or smaller nano-particles, functionalised polymers, and toxins. Equilibrium multivalent binding is a continuous yet super-selective transition with respect to the number of ligands and receptors involved in the interaction. Increasing the ligand or receptor density on the two particles leads to sharp growth in the number of bound particles at equilibrium. Here we present a theory and Monte Carlo simulations to show that applying mechanical force to multivalent particles causes their adsorption/desorption isotherm on a surface to become sharper and more selective, with respect to variation in the number of ligands and receptors on the two objects. When the force is only applied to particles bound to the surface by one or more ligands, then the transition can become infinitely sharp and first-order-a new binding regime which we term 'hyper-selective'. Force may be imposed by, e.g. flow of solvent around the particles, a magnetic field, chemical gradients, or triggered uncoiling of inert oligomers/polymers tethered to the particles to provide a steric repulsion to the surface. This physical principle is a step towards 'all or nothing' binding selectivity in the design of multivalent constructs.

Liposomal adhesion via electrostatic interactions and osmotic deflation increase membrane tension and lipid diffusion coefficient

Membrane adhesion is a ubiquitous phenomenon in cells and is related to various biological events such as migration, morphogenesis, and differentiation. To understand the physicochemical aspects of membrane adhesion, liposome-liposome adhesion and liposome-substrate adhesion have been studied. Although membrane adhesion has been shown to increase membrane tension and inhibit lipid diffusion, the relationship between these changes and the degree of membrane adhesion have not been quantified. Here, we analyzed the dependence of membrane tension and lipid diffusion on the degree of membrane adhesion, i.e., area fraction of the adherent region. For this purpose, we developed a simple method to prepare adhered liposomes by simple electrostatic interactions between the membranes and by osmotic deflation. We found that the membrane tension of the adhered liposomes increases slightly with an increase in the area fraction of the adherent region. In addition, the lipid diffusion coefficient of the adhered liposomes is larger than that of isolated liposomes, which is consistent with the theoretical prediction. The analysis provides a framework to understand the correlation between cell adhesion and bio-membrane properties such as membrane tension and molecular diffusion.

Programmable interactions with biomimetic DNA linkers at fluid membranes and interfaces

At the heart of the structured architecture and complex dynamics of biological systems are specific and timely interactions operated by biomolecules. In many instances, biomolecular agents are spatially confined to flexible lipid membranes where, among other functions, they control cell adhesion, motility and tissue formation. Besides being central to several biological processes, multivalent interactions mediated by reactive linkers confined to deformable substrates underpin the design of synthetic-biological platforms and advanced biomimetic materials. Here we review recent advances on the experimental study and theoretical modelling of a heterogeneous class of biomimetic systems in which synthetic linkers mediate multivalent interactions between fluid and deformable colloidal units, including lipid vesicles and emulsion droplets. Linkers are often prepared from synthetic DNA nanostructures, enabling full programmability of the thermodynamic and kinetic properties of their mutual interactions. The coupling of the statistical effects of multivalent interactions with substrate fluidity and deformability gives rise to a rich emerging phenomenology that, in the context of self-assembled soft materials, has been shown to produce exotic phase behaviour, stimuli-responsiveness, and kinetic programmability of the self-assembly process. Applications to (synthetic) biology will also be reviewed.

Kinetics of Nanoparticle-Membrane Adhesion Mediated by Multivalent Interactions

Multivalent adhesive interactions mediated by a large number of ligands and receptors underpin many biological processes, including cell adhesion and the uptake of particles, viruses, parasites, and nanomedical vectors. In materials science, multivalent interactions between colloidal particles have enabled unprecedented control over the phase behavior of self-assembled materials. Theoretical and experimental studies have pinpointed the relationship between equilibrium states and microscopic system parameters such as the ligand-receptor binding strength and their density. In regimes of strong interactions, however, kinetic factors are expected to slow down equilibration and lead to the emergence of long-lived out-of-equilibrium states that may significantly influence the outcome of self-assembly experiments and the adhesion of particles to biological membranes. Here we experimentally investigate the kinetics of adhesion of nanoparticles to biomimetic lipid membranes. Multivalent interactions are reproduced by strongly interacting DNA constructs, playing the role of both ligands and receptors. The rate of nanoparticle adhesion is investigated as a function of the surface density of membrane-anchored receptors and the bulk concentration of nanoparticles and is observed to decrease substantially in regimes where the number of available receptors is limited compared to the overall number of ligands. We attribute such peculiar behavior to the rapid sequestration of available receptors after initial nanoparticle adsorption. The experimental trends and the proposed interpretation are supported by numerical simulations.

Single-Vesicle Assays Using Liposomes and Cell-Derived Vesicles: From Modeling Complex Membrane Processes to Synthetic Biology and Biomedical Applications

The plasma membrane is of central importance for defining the closed volume of cells in contradistinction to the extracellular environment. The plasma membrane not only serves as a boundary, but it also mediates the exchange of physical and chemical information between the cell and its environment in order to maintain intra- and intercellular functions. Artificial lipid- and cell-derived membrane vesicles have been used as closed-volume containers, representing the simplest cell model systems to study transmembrane processes and intracellular biochemistry. Classical examples are studies of membrane translocation processes in plasma membrane vesicles and proteoliposomes mediated by transport proteins and ion channels. Liposomes and native membrane vesicles are widely used as model membranes for investigating the binding and bilayer insertion of proteins, the structure and function of membrane proteins, the intramembrane composition and distribution of lipids and proteins, and the intermembrane interactions during exo- and endocytosis. In addition, natural cell-released microvesicles have gained importance for early detection of diseases and for their use as nanoreactors and minimal protocells. Yet, in most studies, ensembles of vesicles have been employed. More recently, new micro- and nanotechnological tools as well as novel developments in both optical and electron microscopy have allowed the isolation and investigation of individual (sub)micrometer-sized vesicles. Such single-vesicle experiments have revealed large heterogeneities in the structure and function of membrane components of single vesicles, which were hidden in ensemble studies. These results have opened enormous possibilities for bioanalysis and biotechnological applications involving unprecedented miniaturization at the nanometer and attoliter range. This review will cover important developments toward single-vesicle analysis and the central discoveries made in this exciting field of research.

Adhesion of like-charged lipid vesicles induced by rod-like counterions

Adhesion of electrically charged lipid vesicles and subsequent formation of multi-vesicle aggregates can be induced by multivalent rod-like counterions. Motivated by recent experimental observations we calculate the equilibrium conformation of two identical vesicles that adhere onto each other. The degree of adhesion reflects the competition between predominantly electrostatic attraction and vesicle bending. Our model assumes the enclosed vesicle volume is allowed to freely adjust and the area of the vesicle membrane is fixed and remains constant. We describe the electrostatic attraction, which arises from the bridging of the rod-like counterions between the two like-charged vesicles, using a recently developed mean-field theory. Bending fluctuation-induced entropic repulsion, depletion forces between the apposed vesicle membranes induced by the rod-like counterions, and van der Waals attraction between the vesicles are estimated to induce only minor shifts in the equilibrium vesicle conformation. Our model predicts the dependence of vesicle adhesion (including its onset) exclusively from material or molecular parameters such as vesicle size and charge, bending stiffness of the membrane, effective length and net charge of the added rod-like counterions, as well as concentrations of rod-like counterions and additional salt content. We demonstrate that the demixing of charged lipids between the adhesion region and the uncomplexed parts of the vesicles has only a minor influence on the degree of adhesion. Our predictions are in qualitative agreement with recent experimental findings.

Micrometer-sized TPM emulsion droplets with surface-mobile binding groups

Colloids coated with lipid membranes have been widely employed for fundamental studies of lipid membrane processes, biotechnological applications such as drug delivery and biosensing, and more recently, for self-assembly. The latter has been made possible by inserting DNA oligomers with covalently linked hydrophobic anchors into the membrane. The lateral mobility of the DNA linkers on micrometer-sized droplets and solid particles has opened the door to creating structures with unprecedented structural flexibility. Here, we investigate micro-emulsions of TPM (3-(trimethoxysilyl)propyl methacrylate) as a platform for lipid monolayers and further functionalization with proteins and DNA oligonucleotides. TPM droplets can be produced with a narrow size distribution and are polymerizable, thus providing supports for model lipid membranes with controlled size and curvature. With fluorescence recovery after photobleaching, we observed that droplet-attached lipids, NeutrAvidin proteins, as well as DNA oligonucleotides all show mobility on the surface. We explored the assembly of micron-sized particles on TPM-droplets by exploiting either avidin-biotin interactions or double-stranded DNA with complementary single-stranded end groups. While the single molecules are mobile, the particles that are attached to them are not. We propose that this is caused by the heterogeneous nature of emulsified TPM, which forms an oligomer network that limits the collective motion of linkers, but allows the surface mobility of individual molecules.

Interaction with prefibrillar species and amyloid-like fibrils changes the stiffness of lipid bilayers

Evaluating the toxicity of self-assembled protein states is a key step towards developing effective strategies against amyloidogenic pathologies such as Alzheimer's and Parkinson's diseases. Such analysis is directly connected to quantitatively probing the stability of the cellular membrane upon interaction with different protein states. Using a combination of spectroscopic techniques, morphological observations, and spectral analysis of membrane fluctuations, we identify different destabilisation routes for giant unilamellar vesicles interacting with native-like states, prefibrillar species and amyloid-like fibrils of α-lactalbumin. These effects range from substantially lowering the bending rigidity of the membranes to irreversible structural changes and complete disruption of the lipid bilayers. Our findings clearly indicate how the wide heterogeneity in structures occurring during protein aggregation can result in different destabilisation pathways, acting on different length scales and not limited to enhanced membrane permeability.

Entropy Stabilizes Floppy Crystals of Mobile DNA-Coated Colloids

Grafting linkers with open ends of complementary single-stranded DNA makes a flexible tool to tune interactions between colloids, which facilitates the design of complex self-assembly structures. Recently, it has been proposed to coat colloids with mobile DNA linkers, which alleviates kinetic barriers without high-density grafting, and also allows the design of valency without patches. However, the self-assembly mechanism of this novel system is poorly understood. Using a combination of theory and simulation, we obtain phase diagrams for the system in both two and three dimensional spaces, and find stable floppy square and CsCl crystals when the binding strength is strong, even in the infinite binding strength limit. We demonstrate that these floppy phases are stabilized by vibrational entropy, and "floppy" modes play an important role in stabilizing the floppy phases for the infinite binding strength limit. This special entropic effect in the self-assembly of mobile DNA-coated colloids is very different from conventional molecular self-assembly, and it offers a new axis to help design novel functional materials using mobile DNA-coated colloids.

Membrane Adhesion through Bridging by Multimeric Ligands

Ligand/receptor multivalent interactions have been exploited to drive self-assembly of nanoparticles, hard colloids, and, more recently, compliant units including emulsion droplets and lipid vesicles. In deformable liposomes, formation of links between two membranes produces morphological changes depending on the amount of ligands in the environment. Here, we study a proof-of-concept biosensing system in which single lipid vesicles adhere to a flat supported lipid bilayer, both decorated with membrane-anchored biotinylated receptors. Adhesion is driven by multivalent streptavidin (SA) ligands forming bridges between the vesicles and the supported bilayer. Upon changing the concentration of ligands, we characterize the morphological and mechanical changes of the vesicles, including the formation of a stable adhesion patch, membrane tension, and the kinetics of bridge rupture/formation. We observe vesicle binding only within a specific range of ligand concentrations: adhesion does not occur if the amount of SA is either too low or too high. A theoretical model is presented, elucidating the mechanism underlying this observation, particularly, the role of SA multivalency in determining the onset of adhesion. We elaborate on how the behavior of membranes studied here could be exploited in next-generation (bio)molecular analytical devices.

Nanoscale hydration dynamics of DNA-lipid blend dry films: DNA-size dependency

In this study, nanoscale hydration dynamics of DNA-lipid blend dry films are investigated via small angle X-ray diffraction. Compared to the hydration of lipid films, fragmented short DNA strands and counterions in stacked lipid layers dramatically accelerate both the relaxation of the lamellar distance to a metastable interval and the subsequent peeling-off process of lipid bilayers. Moreover, genome-sized long DNA and counterions accelerate the relaxation process, but suppress the peeling-off process and simultaneously induce a damped-oscillation of the lamellar interval; this is probably due to the viscoelastic properties of the entangled long DNA dissolved in hydrated water between the stacked lipid bilayers. This study's findings can pave the way for producing cell-sized liposomes, which efficiently encapsulate any arbitrary sized DNA through natural swelling.

Melting transition in lipid vesicles functionalised by mobile DNA linkers

We study phase behaviour of lipid-bilayer vesicles functionalised by ligand-receptor complexes made of synthetic DNA by introducing a modelling framework and a dedicated experimental platform. In particular, we perform Monte Carlo simulations that combine a coarse grained description of the lipid bilayer with state of art analytical models for multivalent ligand-receptor interactions. Using density of state calculations, we derive the partition function in pairs of vesicles and compute the number of ligand-receptor bonds as a function of temperature. Numerical results are compared to microscopy and fluorimetry experiments on large unilamellar vesicles decorated by DNA linkers carrying complementary overhangs. We find that vesicle aggregation is suppressed when the total number of linkers falls below a threshold value. Within the model proposed here, this is due to the higher configurational costs required to form inter-vesicle bridges as compared to intra-vesicle loops, which are in turn related to membrane deformability. Our findings and our numerical/experimental methodologies are applicable to the rational design of liposomes used as functional materials and drug delivery applications, as well as to study inter-membrane interactions in living systems, such as cell adhesion.

Specific and Reversible DNA-Directed Self-Assembly of Modular Vesicle-Droplet Hybrid Materials

Modular hybrid structures functionalized to assemble in a controlled manner possess diverse properties necessary for a new generation of complex materials and applications. Here, we functionalized giant unilamellar vesicles and emulsion droplets with biotinylated single-stranded DNA oligonucleotides using streptavidin as an intermediary linker to demonstrate specific and reversible DNA-directed self-assembly into vesicle-droplet hybrid structures. A low molar percentage of PEGylated phospholipids independent of the DNA-based recognition machinery at the supramolecular surface modulated the stability of the system. The reversibility of the aggregation was demonstrated by heating the hybrid structures above the melting temperature of the conjoining double-stranded DNA in the presence of excess biotin. The application of this general assembly control system to diverse multiphase soft materials provides the mechanism to assemble complex modular hybrid systems in a controllable and reversible way, which may provide an advantage where multifunctionality is a target property.

Controlling Self-Assembly Kinetics of DNA-Functionalized Liposomes Using Toehold Exchange Mechanism

The selectivity of Watson-Crick base pairing has allowed the design of DNA-based functional materials bearing an unprecedented level of accuracy. Examples include DNA origami, made of tiles assembling into arbitrarily complex shapes, and DNA coated particles featuring rich phase behaviors. Frequently, the realization of conceptual DNA-nanotechnology designs has been hampered by the lack of strategies for effectively controlling relaxations. In this article, we address the problem of kinetic control on DNA-mediated interactions between Brownian objects. We design a kinetic pathway based on toehold-exchange mechanisms that enables rearrangement of DNA bonds without the need for thermal denaturation, and test it on suspensions of DNA-functionalized liposomes, demonstrating tunability of aggregation rates over more than 1 order of magnitude. While the possibility to design complex phase behaviors using DNA as a glue is already well recognized, our results demonstrate control also over the kinetics of such systems.

Theory and simulation of DNA-coated colloids: a guide for rational design

By exploiting the exquisite selectivity of DNA hybridization, DNA-coated colloids (DNACCs) can be made to self-assemble in a wide variety of structures. The beauty of this system stems largely from its exceptional versatility and from the fact that a proper choice of the grafted DNA sequences yields fine control over the colloidal interactions. Theory and simulations have an important role to play in the optimal design of self assembling DNACCs. At present, the powerful model-based design tools are not widely used, because the theoretical literature is fragmented and the connection between different theories is often not evident. In this Perspective, we aim to discuss the similarities and differences between the different models that have been described in the literature, their underlying assumptions, their strengths and their weaknesses. Using the tools described in the present Review, it should be possible to move towards a more rational design of novel self-assembling structures of DNACCs and, more generally, of systems where ligand-receptor are used to control interactions.