Re-entrant DNA gels

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.

Dynamic control of DNA condensation

Artificial biomolecular condensates are emerging as a versatile approach to organize molecular targets and reactions without the need for lipid membranes. Here we ask whether the temporal response of artificial condensates can be controlled via designed chemical reactions. We address this general question by considering a model problem in which a phase separating component participates in reactions that dynamically activate or deactivate its ability to self-attract. Through a theoretical model we illustrate the transient and equilibrium effects of reactions, linking condensate response and reaction parameters. We experimentally realize our model problem using star-shaped DNA motifs known as nanostars to generate condensates, and we take advantage of strand invasion and displacement reactions to kinetically control the capacity of nanostars to interact. We demonstrate reversible dissolution and growth of DNA condensates in the presence of specific DNA inputs, and we characterize the role of toehold domains, nanostar size, and nanostar valency. Our results will support the development of artificial biomolecular condensates that can adapt to environmental changes with prescribed temporal dynamics.

Interpenetrated and Bridged Nanocylinders from Self-Assembled Star Block Copolymers

The design of functional polymeric materials with tunable response requires a synergetic use of macromolecular architecture and interactions. Here, we combine experiments with computer simulations to demonstrate how physical properties of gels can be tailored at the molecular level, using star block copolymers with alternating block sequences as a paradigm. Telechelic star polymers containing attractive outer blocks self-assemble into soft patchy nanoparticles, whereas their mirror-image inverted architecture with inner attractive blocks yields micelles. In concentrated solutions, bridged and interpenetrated hexagonally packed nanocylinders are formed, respectively, with distinct structural and rheological properties. The phase diagrams exhibit a peculiar re-entrance where the hexagonal phase melts upon both heating and cooling because of solvent-block and block-block interactions. The bridged nanostructure is characterized by similar deformability, extended structural coherence, enhanced elasticity, and yield stress compared to micelles or typical colloidal gels, which make them promising and versatile materials for diverse applications.

Mechanistic insight into the structure, thermodynamics and dynamics of equilibrium gels of multi-armed DNA nanostars

The unique sequence specificity rule of DNA makes it an ideal molecular building block for constructing periodic arrays and devices with nanoscale accuracy and precision. Here, we present the self-assembly of DNA nanostars having three, four and five arms into a gel phase using a simplistic coarse-grained bead-spring model developed by Z. Xing, C. Ness, D. Frenkel and E. Eiser (Macromolecules, 2019, 52, 504-512). Our simulations show that the DNA nanostars form a thermodynamically stable fully bonded gel phase from an unstructured liquid phase with the lowering of temperature. We characterize the phase transition by calculating several structural features such as the radial distribution function and structure factor. The thermodynamics of gelation is quantified by the potential energy and translational pair-entropy of the system. The phase transition from an arrested gel phase to an unstructured liquid phase has been modelled using a two-state theoretical model. We find that this transition is enthalpy driven, and loss of configuration and translational entropy is counterpoised by enthalpic interaction of the DNA sticky-ends, which gives rise to a gel phase at low temperature. The absolute rotational and translational entropy of the systems, measured using a two-phase thermodynamic model, also substantiates the gel transition. The slowing down of the dynamics upon approaching the transition temperature from a high temperature demonstrates the phase transition to a gel phase. A detailed numerical simulation study of the morphology, dynamics and thermodynamics of DNA gelation can provide guidance for future experiments, is easily extensible to other polymeric systems, and is expected to help in understanding the physics of self-assembly.

DNA Droplets: Intelligent, Dynamic Fluid

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

Entropy-Driven Thermo-gelling Vitrimer

Thermo-gelling polymers have been envisioned as promising smart biomaterials but limited by their weak mechanical and thermodynamic stabilities. Here, we propose a new thermo-gelling vitrimer, which remains at a liquid state because of the addition of protector molecules preventing the crosslinking, and with increasing temperature, an entropy-driven crosslinking occurs to induce the sol-gel transition. Moreover, we find that the activation barrier in the metathesis reaction of vitrimers plays an important role, and experimentally, one can use catalysts to tune the activation barrier to drive the vitrimer to form an equilibrium gel at high temperature, which is not subject to any thermodynamic instability. We formulate a mean-field theory to describe the entropy-driven crosslinking of the vitrimer, which agrees quantitatively with computer simulations and paves the way for the design and fabrication of novel vitrimers for biomedical applications.

Formation of non-base-pairing DNA microgels using directed phase transition of amphiphilic monomers

Programmability of DNA sequences enables the formation of synthetic DNA nanostructures and their macromolecular assemblies such as DNA hydrogels. The base pair-level interaction of DNA is a foundational and powerful mechanism to build DNA structures at the nanoscale; however, its temperature sensitivity and weak interaction force remain a barrier for the facile and scalable assembly of DNA structures toward higher-order structures. We conducted this study to provide an alternative, non-base-pairing approach to connect nanoscale DNA units to yield micrometer-sized gels based on the sequential phase transition of amphiphilic unit structures. Strong electrostatic interactions between DNA nanostructures and polyelectrolyte spermines led to the formation of giant phase-separated aggregates of monomer units. Gelation could be initiated by the addition of NaCl, which weakened the electrostatic DNA-spermine interaction while attractive interactions between cholesterols created stable networks by crosslinking DNA monomers. In contrast to the conventional DNA gelation techniques, our system used solid aggregates as a precursor for DNA microgels. Therefore, in situ gelation could be achieved by depositing aggregates on the desired substrate and subsequently initiating a phase transition. Our approach can expand the utility and functionality of DNA hydrogels by using more complex nucleic acid assemblies as unit structures and combining the technique with top-down microfabrication methods.

The physics of empty liquids: from patchy particles to water

Empty liquids represent a wide class of materials whose constituents arrange in a random network through reversible bonds. Many key insights on the physical properties of empty liquids have originated almost independently from the study of colloidal patchy particles on one side, and a large body of theoretical and experimental research on water on the other side. Patchy particles represent a family of coarse-grained potentials that allows for a precise control of both the geometric and the energetic aspects of bonding, while water has arguably the most complex phase diagram of any pure substance, and a puzzling amorphous phase behavior. It was only recently that the exchange of ideas from both fields has made it possible to solve long-standing problems and shed new light on the behavior of empty liquids. Here we highlight the connections between patchy particles and water, focusing on the modelling principles that make an empty liquid behave like water, including the factors that control the appearance of thermodynamic and dynamic anomalies, the possibility of liquid-liquid phase transitions, and the crystallization of open crystalline structures.

Treatment of kidney clear cell carcinoma, lung adenocarcinoma and glioblastoma cell lines with hydrogels made of DNA nanostars

Overcoming the systemic administration of chemotherapy to reduce drug toxicity and the application of personalised medicine are two of the major challenges in the treatment of cancer. To this aim,...

Building up DNA, bit by bit: a simple description of chain assembly

We simulate the assembly of DNA copolymers from two types of short duplexes (short double strands with a single-stranded overhang at each end), as described by the oxDNA model. We find that the statistics of chain lengths can be well reproduced by a simple theory that treats the association of particles into ideal (i.e., non-interacting) clusters as a reversible chemical reaction. The reaction constants can be predicted either from SantaLucia's theory or from Wertheim's thermodynamic perturbation theory of association for spherical patchy particles. Our results suggest that theories incorporating very limited molecular detail may be useful for predicting the broad equilibrium features of copolymerisation.

The flexibility-based modulation of DNA nanostar phase separation

Phase separation of biomolecules plays key roles in physiological compartmentalization as well as pathological aggregation. A deeper understanding of biomolecular phase separation requires dissection of a relation between intermolecular interactions and resulting phase behaviors. DNA nanostars, multivalent DNA assemblies of which sticky ends define attractive interactions, represent an ideal system to probe this fundamental relation governing phase separation processes. Here, we use DNA nanostars to systematically study how structural flexibility exhibited by interacting species impacts their phase behaviors. We design multiple nanostars with a varying degree of flexibility using single-stranded gaps of different lengths in the arm of each nanostar unit. We find that structural flexibility drastically alters the phase diagram of DNA nanostars in such a way that the phase separation of more flexible structures is strongly inhibited. This result is not due to self-inhibition from the loss of valency but rather ascribed to a generic flexibility-driven change in the thermodynamics of the system. Our work provides not only potential regulatory mechanisms cells may exploit to dynamically control intracellular phase separation but also a route to build synthetic systems of which assembly can be controlled in a signal dependent manner.

Mechanical Properties of DNA Hydrogels: Towards Highly Programmable Biomaterials

DNA hydrogels are self-assembled biomaterials that rely on Watson–Crick base pairing to form large-scale programmable three-dimensional networks of nanostructured DNA components. The unique mechanical and biochemical properties of DNA, along with its biocompatibility, make it a suitable material for the assembly of hydrogels with controllable mechanical properties and composition that could be used in several biomedical applications, including the design of novel multifunctional biomaterials. Numerous studies that have recently emerged, demonstrate the assembly of functional DNA hydrogels that are responsive to stimuli such as pH, light, temperature, biomolecules, and programmable strand-displacement reaction cascades. Recent studies have investigated the role of different factors such as linker flexibility, functionality, and chemical crosslinking on the macroscale mechanical properties of DNA hydrogels. In this review, we present the existing data and methods regarding the mechanical design of pure DNA hydrogels and hybrid DNA hydrogels, and their use as hydrogels for cell culture. The aim of this review is to facilitate further study and development of DNA hydrogels towards utilizing their full potential as multifeatured and highly programmable biomaterials with controlled mechanical properties.

Rational design of hydrogels to enhance osteogenic potential

Bone tissue engineering (BTE) encompasses the field of biomaterials, cells, and bioactive molecules to successfully guide the growth and repair of bone tissue. Current BTE strategies rely on delivering osteogenic molecules or cells via scaffolding materials. However, growth factor- and stem cell-based treatments have several limitations, such as source restriction, low stability, difficulties in predicting long-term efficacy, and high costs, among others. These issues have promoted the development of material-based therapy with properties of accessibility, high stability, tunable efficacy, and low-cost production. Hydrogels are widely used in BTE applications because of their unique hydrophilic nature and tunable physicochemical properties to mimic the native bone environment. However, current hydrogel materials are not ideal candidates due to minimal osteogenic capability on their own. Therefore, recent studies of BTE hydrogels attempt to counterbalance these issues by modifying their biophysical properties. In this article, we review recent progress in the design of hydrogels to instruct osteogenic potential, and present strategies developed to precisely control its bone healing properties.

Gelling without Structuring: A SAXS Study of the Interactions among DNA Nanostars

We evaluate, by means of synchrotron small-angle X-ray scattering, the shape and mutual interactions of DNA tetravalent nanostars as a function of temperature in both the gas-like state and across the gel transition. To this end, we calculate the form factor from coarse-grained molecular dynamics simulations with a novel method that includes hydration effects; we approximate the radial interaction of DNA nanostars as a hard-sphere potential complemented by a repulsive and an attractive Yukawa term; and we predict the structure factors by exploiting the perturbative random phase approximation of the Percus-Yevick equation. Our approach enables us to fit all the data by selecting the particle radius and the width and amplitude of the attractive potential as free parameters. We determine the evolution of the structure factor across gelation and detect subtle changes of the effective interparticle interactions, that we associate to the temperature and concentration dependence of the particle size. Despite the approximations, the approach here adopted offers new detailed insights into the structure and interparticle interactions of this fascinating system.

DNA-GEL, Novel Nanomaterial for Biomedical Applications and Delivery of Bioactive Molecules

Novel DNA materials promise unpredictable perspectives for applications in cell biology. The realization of DNA-hydrogels built by a controlled association of DNA nanostars, whose binding can be tuned with minor changes in the nucleotide sequences, has been recently described. DNA hydrogels, with specific gelation properties that can be reassambled in desired culture media supplemented with drugs, RNA, DNA molecules and other bioactive compounds offer the opportunity to develop a novel nanomaterial for the delivery of single or multiple drugs in tumor tissues as an innovative and promising strategy. We provide here a comprehensive description of different, recently realized DNA-gels with the perspective of stimulating their biomedical application. Finally, we discuss the possibility to design sophisticated 3D tissue-like DNA-gels incorporating cell spheroids or single cells for the assembly of a novel kind of cellular matrix as a preclinical investigation for the implementation of tools for in vivo delivery of bioactive molecules.

Multivalent ion-induced re-entrant transition of carboxylated cellulose nanofibrils and its influence on nanomaterials' properties

In this work, we identify and characterize a new intriguing capability of carboxylated cellulose nanofibrils that could be exploited to design smart nanomaterials with tuned response properties for specific applications. Cellulose nanofibrils undergo a multivalent counter-ion induced re-entrant behavior at a specific multivalent metal salt concentration. This effect is manifested as an abrupt increase in the strength of the hydrogel that returns upon a further increment of salt concentration. We systematically study this phenomenon using dynamic light scattering, small-angle X-ray scattering, and molecular dynamics simulations based on a reactive force field. We find that the transitions in the nanofibril microstructure are mainly because of the perturbing actions of multivalent metal ions that induce conformational changes of the nanocellulosic chains and thus new packing arrangements. These new aggregation states also cause changes in the thermal and mechanical properties as well as wettability of the resulting films, upon water evaporation. Our results provide guidelines for the fabrication of cellulose-based films with variable properties by the simple addition of multivalent ions.

Sequence-based engineering of dynamic functions of micrometer-sized DNA droplets

DNA has the potential to achieve a controllable macromolecular structure, such as hydrogels or droplets formed through liquid-liquid phase separation (LLPS), as the design of its base sequence can result in programmable interactions. Here, we constructed "DNA droplets" via LLPS of sequence-designed DNA nanostructures and controlled their dynamic functions by designing their sequences. Specifically, we were able to adjust the temperature required for the formation of DNA droplets by designing the sequences. In addition, the fusion, fission, and formation of Janus-shaped droplets were controlled by sequence design and enzymatic reactions. Furthermore, modifications of proteins with sequence-designed DNAs allowed for their capture into specific droplets. Overall, our results provide a platform for designing and controlling macromolecular droplets via the information encoded in component molecules and pave the way for various applications of sequence-designed DNA such as cell mimics, synthetic membraneless organelles, and artificial molecular systems.

Tailoring DNA Self-assembly to Build Hydrogels

DNA hydrogels are crosslinked polymeric networks in which DNA is used as the backbone or the crosslinker. These hydrogels are novel biofunctional materials that possess the biological character of DNA and the framed structure of hydrogels. Compared with other kinds of hydrogels, DNA hydrogels exhibit not only high mechanical strength and controllable morphologies but also good recognition ability, designable responsiveness, and programmability. The DNA used in this type of hydrogel acts as a building block for self-assembly or as a responsive element due to its sequence recognition ability and switchable structural transitions, respectively. In this review, we describe recent developments in the field of DNA hydrogels and discuss the role played by DNA in these hydrogels. Various synthetic strategies for and a range of applications of DNA hydrogels are detailed.

On the role of flexibility in linker-mediated DNA hydrogels

Three-dimensional DNA networks, composed of tri- or higher valent nanostars with sticky, single-stranded DNA overhangs, have been previously studied in the context of designing thermally responsive, viscoelastic hydrogels. In this work, we use linker-mediated gels, where the sticky ends of two trivalent nanostars are connected through the complementary sticky ends of a linear DNA duplex. We can design this connection to be either rigid or flexible by introducing flexible, non-binding bases. The additional flexibility provided by these non-binding bases influences the effective elasticity of the percolating gel formed at low temperatures. Here we show that by choosing the right length of the linear duplex and non-binding flexible joints, we obtain a completely different phase behaviour to that observed for rigid linkers. In particular, we use dynamic light scattering as a microrheological tool to monitor the self-assembly of DNA nanostars with linear linkers as a function of temperature. While we observe classical gelation when using rigid linkers, the presence of flexible joints leads to a cluster fluid with a much-reduced viscosity. Using both the oxDNA model and a coarse-grained simulation to investigate the nanostar-linker topology, we hypothesise on the possible structure formed by the DNA clusters. Moreover, we present a systematic study of the strong viscosity increase of aqueous solutions in the presence of these DNA building blocks.

Chirality dependent inverse-melting and re-entrant gelation in α-cyclodextrin/1-phenylethylamine mixtures

Solutions of cyclohexakis-(1→4)-α-d-glucopyranosyl, α-cyclodextrin, αCD, in R-(+)-1-phenylethylamine, αCD/R-PEA, and S-(−)-1-phenylethylamine, αCD/S-PEA, display abnormal phase transitions that strongly depend on supramolecular diastereomeric interactions. While αCD/R-PEA mixtures show one sol–gel inverse-melting phase transition, αCD/S-PEA mixtures show temperature dependent gel–sol–gel re-entrant behavior. NMR, Raman spectroscopy, microscopy and X-ray scattering measurements reveal that hydrogen bond weakening in solution, as well as changes in crystal composition are responsible for entropy increase and gel formation upon heating.

Solutions of α-cyclodextrin in chiral 1-phenylethylamine display abnormal phase transitions. Depending on supramolecular diastereomeric interactions, inverse-melting and re-entrant gels are formed.

Thermal cycling of DNA devices via associative strand displacement

DNA-based devices often operate through a series of toehold-mediated strand-displacement reactions. To achieve cycling, fluidic mixing can be used to introduce 'recovery' strands to reset the system. However, such mixing can be cumbersome, non-robust, and wasteful of materials. Here we demonstrate mixing-free thermal cycling of DNA devices that operate through associative strand-displacement cascades. These cascades are favored at low temperatures due to the primacy of a net increase in base pairing, whereas rebinding of 'recovery' strands is favored at higher temperatures due to the primacy of a net release of strands. The temperature responses of the devices could be modulated by adjustment of design parameters such as the net increase of base pairs and the concentrations of strands. Degradation of function was not observable even after 500 thermal cycles. We experimentally demonstrated simple digital-logic circuits that evaluate at 35°C and reset after transient heating to 65°C. Thus associative strand displacement enables robust thermal cycling of DNA-based devices in a closed system.

Application of DNA Quadruplex Hydrogels Prepared from Polyethylene Glycol-Oligodeoxynucleotide Conjugates to Cell Culture Media

Application of Na+-responsive DNA quadruplex hydrogels, which utilize G-quadruplexes as crosslinking points of poly(ethylene glycol) (PEG) network as cell culture substrate, has been examined. PEG-oligodeoxynucleotide (ODN) conjugate, in which four deoxyguanosine (dG4) residues are tethered to both ends of PEG, was prepared by modified high-efficiency liquid phase (HELP) synthesis of oligonucleotides and used as the macromonomer. When mixed with equal volume of cell culture media, the solution of PEG-ODN turned into stiff hydrogel (G-quadruplex hydrogel) as the result of G-quadruplex formation by the dG4 segments in the presence of Na+. PEG-ODN itself did not show cytotoxicity and the resulting hydrogel was stable enough under cell culture conditions. However, L929 fibroblast cells cultured in G-quadruplex hydrogel remained spherical for a week, yet alive, without proliferation. The cells gradually sedimented through the gel day by day, probably due to the reversible nature of G-quadruplex formation and the resulting slow rearrangement of the macromonomers. Once they reached the bottom glass surface, the cells started to spread and proliferate.

Self-Organization and Flow of Low-Functionality Telechelic Star Polymers with Varying Attraction

We combine state-of-the art synthesis, simulations, and physical experiments to explore the tunable, responsive character of telechelic star polymers as models for soft patchy particles. We focus on the simplest possible system: a star comprising three asymmetric block copolymer arms with solvophilic inner and solvophobic outer blocks. Our dilute solution studies reveal the onset of a second slow mode in the intermediate scattering functions as the temperature decreases below the θ-point of the outer block, as well as the size reduction of single stars upon further decreasing temperature. Clusters comprising multiple stars are formed and their average dimensions, akin to the single star size, counterintuitively decrease upon cooling. A similar phenomenology is observed in simulations upon increasing attraction between the outer blocks and is rationalized as a result of the interplay between interstar associations and steric repulsion between the star cores. Since our simulations are able to describe the experimental findings reliably, we can use them with confidence to make predictions at conditions and flow regimes that are inaccessible experimentally. Specifically, we employ simulations to investigate flow properties of the system at high shear rates, revealing shear thinning behavior caused by the breakup of interstar associations under flow. On the other hand, the zero-shear viscosity obtained experimentally exhibits a rather weak activation energy, which increases upon rising star concentration. These findings demonstrate the unusual properties of telechelic star polymers even in the dilute regime. They also offer a powerful toolbox for designing soft patchy particles and exploring their unprecedented responsive properties further on.

Cold-swappable DNA gels

We report an experimental investigation of an all-DNA gel composed by tetra-functional DNA nanoparticles acting as network nodes and bi-functional ones acting as links. The DNA binding sequence is designed to generate at room and lower temperatures a persistent long-lived network. Exploiting ideas from DNA-nanotechnology, we implement in the binding base sequences an appropriate exchange reaction which allows links to swap, constantly retaining the total number of network links. The DNA gel is thus able to rearrange its topology at low temperature while preserving its fully-bonded configuration.

A Colloid Approach to Self-Assembling Antibodies

Concentrated solutions of monoclonal antibodies have attracted considerable attention due to their importance in pharmaceutical formulations; yet, their tendency to aggregate and the resulting high viscosity pose considerable problems. Here we tackle this problem by a soft condensed matter physics approach, which combines a variety of experimental measurements with a patchy colloid model, amenable of analytical solution. We thus report results of structural antibodies and dynamic properties obtained through scattering methods and microrheological experiments. We model the data using a colloid-inspired approach, explicitly taking into account both the anisotropic shape of the molecule and its charge distribution. Our simple patchy model is able to disentangle self-assembly and intermolecular interactions and to quantitatively describe the concentration-dependence of the osmotic compressibility, collective diffusion coefficient, and zero shear viscosity. Our results offer new insights on the key problem of antibody formulations, providing a theoretical and experimental framework for a quantitative assessment of the effects of additional excipients or chemical modifications and a prediction of the resulting viscosity.

Evolution of Interactions in the Protein Solution As Induced by Mono and Multivalent Ions

The evolution of interactions in the bovine serum albumin (BSA) protein solution on addition of mono and multivalent (di, tri and tetra) counterions has been studied using small-angle neutron scattering (SANS), dynamic light scattering (DLS) and ζ-potential measurements. It is found that in the presence of mono and divalent counterions, protein behavior can be well explained by DLVO theory, combining the contributions of screened Coulomb repulsion with the van der Waals attraction. The addition of mono or divalent salts in protein solution reduces the repulsive barrier and hence the overall interaction becomes attractive, but the system remains in one-phase for the entire concentration range of the salts, added in the system. However, contrary to DLVO theory, the protein solution undergoes a reentrant phase transition from one-phase to a two-phase system and then back to the one-phase system in the presence of tri and tetravalent counterions. The results show that tri and tetravalent (unlike mono and divalent) counterions induce short-range attraction between the protein molecules, leading to the transformation from one-phase to two-phase system. The two-phase is characterized by the fractal structure of protein aggregates. The excess condensation of these higher-valent counterions in the double layer around the BSA causes the reversal of charge of the protein molecules resulting into reentrant of the one-phase, at higher salt concentrations. The complete phase behavior with mono and multivalent ions has been explained in terms of the interplay of electrostatic repulsion and ion-induced short-range attraction between the protein molecules.

Instant hydrogel formation of terpyridine-based complexes triggered by DNA via non-covalent interaction

Biomolecule-based hydrogels have potential use in a wide range of applications such as controlled drug release, tissue engineering, and biofabrication. Herein, driven by specific interactions between ds-DNA (double-stranded DNA) and Zn2+ based metal-complexes, we report that the use of DNA as cross-linkers can enhance interactions between self-assembling Zn2+ complexes containing terpyridine and sugar groups in the generation of bioinspired hydrogels from solutions or suspensions. The gelation process is fast and straightforward without tedious steps and happens at room temperature. Such a hydrogelation process of different Zn2+ complexes endows the visualized and selective DNA analogue discrimination. Several experiments suggest that the strong intercalation binding of Zn2+ complexes with ds-DNA results in the unzipping of ds-DNA into ss-DNA (single-stranded DNA), which further behave as linkers to enhance the intermolecular interactions of self-assembling Zn2+ complex molecules via coordination interactions. This work demonstrates an efficient and universal strategy to prepare hydrogels based on biomolecular recognition. Moreover, the DNA responsive behaviors of Zn2+ complexes are further compared with that of solutions and cells.

Structure and stimuli-responsiveness of all-DNA dendrimers: theory and experiment

We present a comprehensive theoretical and experimental study of the solution phase properties of a DNA-based family of nanoparticles - dendrimer-like DNA molecules (DL-DNA). These charged DNA dendrimers are novel macromolecular aggregates, which hold high promise in targeted self-assembly of soft matter systems in the bulk and at interfaces. To describe the behaviour of this family of dendrimers (with generations ranging from G1 to G7), we use a theoretical model in which base-pairs of a single DL-DNA molecule are modeled by charged monomers, whose interactions are chosen to mimic the equilibrium properties of DNA correctly. Experimental results on the sizes and conformations of DL-DNA are based on static and dynamic light scattering; and molecular dynamics simulations are employed to model the equilibrium properties of DL-DNA, which compare favorably to the findings from experiments while at the same time providing a host of additional information and insight into the molecular structure of the nanostructures. We also examine the salt-responsiveness of these macromolecules, finding that despite the strong screening of electrostatic interactions brought about by the added salt, the macromolecules shrink only slightly, their size robustness stemming from the high bending rigidity of the DNA-segments. The study of these charged dendrimer systems is an important field of research in the area of soft matter due to their potential role for various interdisciplinary applications, ranging from molecular cages and carriers for drug delivery in a living organism to the development of dendrimer- and dendron-based ultra-thin films in the area of nanotechnology. These findings are essential to determine if DL-DNA is a viable candidate for the experimental realization of cluster crystals in the bulk, a novel form of solid with multiple site occupancy.

All-DNA System Close to the Percolation Threshold

We characterize via small-angle neutron scattering the structural properties of a mixture of all-DNA particles with functionalities 4 (A) and 2 (B) constrained by design to reside close to the percolation threshold. DNA base sequences are selected such that A particles can only bind with B ones and that at the studied temperature (10 °C) all AB bonds are formed and long-lived, originating highly polydisperse persistent equilibrium clusters. The concentration dependence of the scattered intensity and its wavevector dependence is exploited to determine the fractal dimension and the size distribution of the clusters, which are found to be consistent with the critical exponents of the 3-D percolation universality class. The value of DNA nanoparticles as nanometric patchy colloids with well-defined functionality, bonding selectivity, and exquisite control of the interaction strength is demonstrated.

Microrheology of DNA hydrogel gelling and melting on cooling

We present systematic characterisation by means of dynamic light scattering and particle tracking techniques of the viscosity and of the linear viscoelastic moduli, G'(ω) and G''(ω), for two different DNA hydrogels. These thermoreversible systems are composed of tetravalent DNA-made nanostars whose sticky sequence is designed to provide controlled interparticle bonding. While the first system forms a gel on cooling, the second one has been programmed to behave as a re-entrant gel, turning again to a fluid solution at low temperature. The frequency-dependent viscous and storage moduli and the viscosity reveal the different viscoelastic behavior of the two DNA hydrogels. Our results show how little variations in the design of the DNA sequences allow tuning of the mechanical response of these biocompatible all-DNA materials.

Dynamics of Vitrimers: Defects as a Highway to Stress Relaxation

We propose a coarse-grained model to investigate stress relaxation in star-polymer networks induced by dynamic bond-exchange processes. We show how the swapping mechanism, once activated, allows the network to reconfigure, exploring distinct topological configurations, all of them characterized by complete extent of reaction. Our results reveal the important role played by topological defects in mediating the exchange reaction and speeding up stress relaxation. The model provides a representation of the dynamics in vitrimers, a new class of polymers characterized by bond-swap mechanisms which preserve the total number of bonds, as well as in other bond-exchange materials.

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.

The Proof Is in the Pidan: Generalizing Proteins as Patchy Particles

The Chinese century egg, or pidan, is a traditional preparation of duck eggs that can be stored for months at room temperature without degradation. Raw eggs are soaked in a strong alkaline and salt solution, and the albumin gradually forms a stable, transparent gel. Here, we show that pidan gels belong to the class of materials formed from "patchy particles". We found that the β-sheet structure of ovalbumin, the major protein constituent of egg white, is preserved during gelation, while α-helical regions undergo a degree of unfolding into unstructured random coils that may form attractive patches. Upon dilution in additional strong base, the phase behavior of pidan gels is consistent with patchy-particle thermodynamics. This protein gel is also physically and structurally similar to the protein gels that form the squid lens. Both systems exhibit patchy thermodynamics, and the constituent proteins share physical features including a structured, charged core, and polar, unstructured "arms" that form attractive patches. Our work provides a path toward rational design of proteins for precisely structured, volume-spanning materials.

Binding branched and linear DNA structures: From isolated clusters to fully bonded gels

The proper design of DNA sequences allows for the formation of well-defined supramolecular units with controlled interactions via a consecution of self-assembling processes. Here, we benefit from the controlled DNA self-assembly to experimentally realize particles with well-defined valence, namely, tetravalent nanostars (A) and bivalent chains (B). We specifically focus on the case in which A particles can only bind to B particles, via appropriately designed sticky-end sequences. Hence AA and BB bonds are not allowed. Such a binary mixture system reproduces with DNA-based particles the physics of poly-functional condensation, with an exquisite control over the bonding process, tuned by the ratio, r, between B and A units and by the temperature, T. We report dynamic light scattering experiments in a window of Ts ranging from 10 °C to 55 °C and an interval of r around the percolation transition to quantify the decay of the density correlation for the different cases. At low T, when all possible bonds are formed, the system behaves as a fully bonded network, as a percolating gel, and as a cluster fluid depending on the selected r.

How to simulate patchy particles⋆

Patchy particles is the name given to a large class of systems of mesoscopic particles characterized by a repulsive core and a discrete number of short-range and highly directional interaction sites. Numerical simulations have contributed significantly to our understanding of the behaviour of patchy particles, but, although simple in principle, advanced simulation techniques are often required to sample the low temperatures and long time-scales associated with their self-assembly behaviour. In this work we review the most popular simulation techniques that have been used to study patchy particles, with a special focus on Monte Carlo methods. We cover many of the tools required to simulate patchy systems, from interaction potentials to biased moves, cluster moves, and free-energy methods. The review is complemented by an educationally oriented Monte Carlo computer code that implements all the techniques described in the text to simulate a well-known tetrahedral patchy particle model.

An Accurate Estimate of the Free Energy and Phase Diagram of All-DNA Bulk Fluids

We present a numerical study in which large-scale bulk simulations of self-assembled DNA constructs have been carried out with a realistic coarse-grained model. The investigation aims at obtaining a precise, albeit numerically demanding, estimate of the free energy for such systems. We then, in turn, use these accurate results to validate a recently proposed theoretical approach that builds on a liquid-state theory, the Wertheim theory, to compute the phase diagram of all-DNA fluids. This hybrid theoretical/numerical approach, based on the lowest-order virial expansion and on a nearest-neighbor DNA model, can provide, in an undemanding way, a parameter-free thermodynamic description of DNA associating fluids that is in semi-quantitative agreement with experiments. We show that the predictions of the scheme are as accurate as those obtained with more sophisticated methods. We also demonstrate the flexibility of the approach by incorporating non-trivial additional contributions that go beyond the nearest-neighbor model to compute the DNA hybridization free energy.

Bulk pH-Responsive DNA Quadruplex Hydrogels Prepared by Liquid-Phase, Large-Scale DNA Synthesis

A new pH-responsive hydrogel biomaterial, that is composed of solely two popular biocompatible materials, oligodeoxynucleotides (ODN) and polyethylene glycol (PEG) have been prepared. Merely five deoxycytidine residues were elongated to the ends of linear or 4-arm PEG in ×1000 larger scale than conventional systems by using liquid-phase DNA synthesis technique, and applied them as a macromonomer for the preparation of hydrogels. The syntheses of the conjugates are simply elongating ODN onto the ends of PEG as a semisolid phase substrate using standard phosphoramidite chemistry. The resulting dC5-PEG conjugates gave quite stable and stiff hydrogels triggered by the formation of a unique DNA quadruplex, i-motif. Introduction of only one chemical linkage between two linear conjugates resulted in unexpectedly high thermal stabilities for the melting temperatures of i-motifs themselves. Nonlinearly improved rheological properties compared to the original linear conjugates were also observed, probably because of topological entanglement between macromonomers of fused circles.

Irregular model DNA particles self-assemble into a regular structure

DNA nanoparticles with three-fold coordination have been observed to self-assemble in experiment into a network equivalent to the hexagonal (6.6.6) tiling, and a network equivalent to the 4.8.8 Archimedean tiling. Both networks are built from a single type of vertex. Here we use analytic theory and equilibrium and dynamic simulation to show that a model particle, whose rotational properties lie between those of the vertices of the 6.6.6 and 4.8.8 networks, can self-assemble into a network built from three types of vertex. Important in forming this network is the ability of the particle to rotate when bound, thereby allowing the formation of more than one type of binding motif. The network in question is equivalent to a false tiling, a periodic structure built from irregular polygons, and possesses 40 particles in its unit cell. The emergence of this complex structure, whose symmetry properties are not obviously related to those of its constituent particles, highlights the potential for creating new structures from simple variants of existing nanoparticles.

Interactions in reentrant phase behavior of a charged nanoparticle solution by multivalent ions

The interactions following a reentrant phase transition of charged silica nanoparticles from one phase to two phases and back to one phase by varying the concentration of multivalent counterions have been examined. The observations are far beyond the framework of Debye-Hückel or even nonlinear Poisson-Boltzmann equations and demonstrate the universal behavior of multivalent counterion-driven charge inversion. We show that the interplay of multivalent counterion-induced short-range attraction and long-range electrostatic repulsion between nanoparticles results in reentrant phase behavior.

Effective potentials induced by self-assembly of patchy particles

Effective colloid-colloid interactions can be tailored through the addition of a complex cosolute. Here we investigate the case of a cosolute made by self-assembling patchy particles. Depending on the valence, these particles can form either polymer chains or branched structures. We numerically calculate the effective potential Veff between two colloids immersed in a suspension of reversible patchy particles, exploring a wide region of the cosolute phase diagram and the role of valence. In addition to well-known excluded volume and depletion effects, we find that, under appropriate conditions, Veff is completely attractive but shows an oscillatory character. In the case of polymerizing cosolute, this results from the fact that chains are efficiently confined by the colloids through the onset of local order. This argument is then generalized to the case of particles with higher valence, under the condition that they are still able to maintain a fully bonded organization upon confinement. The resulting effective potentials are relevant for understanding the behavior of complex mixtures in crowded environments, but may also be exploited for tuning colloidal self-assembly at preferred target distances in order to build desired superstructures.