Clustering versus percolation in the assembly of colloids coated with long DNA

Competitive Supramolecular Associations Mediate the Viscoelasticity of Binary Hydrogels

Supramolecular polymers are known to form strong and resilient hydrogels which can take up large amounts of water while exhibiting ease of processing and self-healing. They also possess similarities with networks of biological macromolecules. The combination of these features makes supramolecular polymers ideal candidates for studying mechanisms and consequences of self-assembly, which are relevant to biological materials. At the same time, this renders investigations of mixed hydrogels based on different supramolecular compounds necessary, since this substantially widens their applicability. Here, we address unusual viscoelastic properties of a class of binary hydrogels made by mixing fibrillar supramolecular polymers that are formed from two compounds: 1,3,5-benzene-tricarboxamide decorated with aliphatic chains terminated by tetra(ethylene glycol) (BTA) and a 20 kg/mol telechelic poly(ethylene glycol) decorated with the same hydrogen bonding BTA motif on both ends (BTA-PEG-BTA). Using a suite of experimental and simulation techniques, we find that the respective single-compound-based supramolecular systems form very different networks which exhibit drastically different rheology. More strikingly, mixing the compounds results in a non-monotonic dependence of modulus and viscosity on composition, suggesting a competition between interactions of the two compounds, which can then be used to fine-tune the mechanical properties. Simulations offer insight into the nature of this competition and their remarkable qualitative agreement with the experimental results is promising for the design of mixed hydrogels with desired and tunable properties. Their combination with a sensitive dynamic probe (here rheology) offer a powerful toolbox to explore the unique properties of binary hydrogel mixtures.

Thermally reversible nanoparticle gels with tuneable porosity showing structural colour

We present colloidal gels formed from dispersions of PEG- and PEG+DNA-coated silica nanoparticles showing structural colour. The PEG- and PEG+DNA-coated silica colloids are functionalized using exclusively covalent bonds in aqueous conditions. Both sets of colloids self-assemble into thermally-reversible colloidal gels with porosity that can be tuned by changing the colloid volume fraction, although the interaction potentials of the colloids in the two systems are different. Confocal microscopy and image analysis tools are used to characteraize the gels' microstructures. Optical reflection spectroscopy is employed to study the underlying gel nanostructure and to characterize the optical response of the gels. X-ray nanotomography is used to visualize the nanoscale phase separation between the colloid-rich gel branches and the colloid-free gel pores. These nanoparticle gels open new routes for creating structural colour where the gel structure is decoupled from the form factor of the individual colloids. This approach can be extended to create unexplored three dimensional macroscale materials with length scales spanning hundreds of nanometers, which has been difficult to achieve using other methods.

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.

Polymer based nanoformulation of methylglyoxal as an antimicrobial agent: efficacy against resistant bacteria

Functionalized polymer conjugated nanoformulations of methylglyoxal demonstrated broad-spectrum antimicrobial activity, leading to new generation antimicrobial agents and minimizing the environment risks.

Internal structure of nanoparticle dimers linked by DNA

We construct nanoparticle dimers linked by DNA. These dimers are basic units in a possible multiscale, hierarchical assembly and serve as a model system to understand DNA-mediated interactions, especially in the nontrivial regime when the nanoparticle and DNA are comparable in their sizes. We examine the structure of nanoparticle dimers in detail by a combination of scattering experiments and molecular simulations. We find that, for a given DNA length, the interparticle separation within the dimer is controlled primarily by the number of linking DNA. We summarize our findings in a simple model that captures the interplay of the number of DNA bridges, their length, the particle's curvature, and the excluded volume effects. We demonstrate the applicability of the model to our results, without any free parameters. As a consequence, the increase of dimer separation with increasing temperature can be understood as a result of changing the number of connecting DNA.

Modeling the crystallization of spherical nucleic acid nanoparticle conjugates with molecular dynamics simulations

We use molecular dynamics simulations to study the crystallization of spherical nucleic-acid (SNA) gold nanoparticle conjugates, guided by sequence-specific DNA hybridization events. Binary mixtures of SNA gold nanoparticle conjugates (inorganic core diameter in the 8-15 nm range) are shown to assemble into BCC, CsCl, AlB(2), and Cr(3)Si crystalline structures, depending upon particle stoichiometry, number of immobilized strands of DNA per particle, DNA sequence length, and hydrodynamic size ratio of the conjugates involved in crystallization. These data have been used to construct phase diagrams that are in excellent agreement with experimental data from wet-laboratory studies.

Cytotoxic origin of copper(II) oxide nanoparticles: comparative studies with micron-sized particles, leachate, and metal salts

The work investigates the source of toxicity of copper oxide nanoparticles (CuO NPs) with respect to its leaching characteristic and speciation. Complexation-mediated leaching of CuO NPs by amino acids was identified as the source of toxicity toward Escherichia coli, the model microorganism used in the current study. The leached copper-peptide complex induces a multiple-fold increase in intracellular reactive oxygen species generation and reduces the fractions of viable cells, resulting in the overall inhibition of biomass growth. The cytotoxicity of the complex leachate is however different from that of equivalent soluble copper salts (nitrates and sulfates). A pH-dependent copper speciation during the addition of copper salts gives rise to uncoordinated copper ions, which in turn result in greater toxicity and cell lysis, the latter of which was not observed for CuO NPs even at comparable pH. Since leaching did not occur with micrometer-sized CuO, no cytotoxicty effect was observed, thus highlighting the prominence of materials toxicity at the nanoscale.

Design rule for colloidal crystals of DNA-functionalized particles

We report a Monte Carlo simulation study of the phase behavior of colloids coated with long, flexible DNA chains. We find that an important change occurs in the phase diagram when the number of DNAs per colloid is decreased below a critical value. In this case, the triple point disappears and the condensed phase that coexists with the vapor is always liquid. Our simulations thus explain why, in the dilute solutions typically used in experiments, colloids coated with a small number of DNA strands cannot crystallize. We understand this behavior in terms of the discrete nature of DNA binding.

Designing colloidal ground-state patterns using short-range isotropic interactions

DNA-coated colloids are a popular model system for self-assembly through tunable interactions. The DNA-encoded linkages between particles theoretically allow for very high specificity, but generally no directionality or long-range interactions. We introduce a two-dimensional lattice model for particles of many different types with short-range isotropic interactions that are pairwise specific. For this class of models, of which the DNA-coated colloids are one example, we address the fundamental question whether it is possible to reliably design the interactions so that the ground state is unique and corresponds to a given crystal structure. First, we determine lower limits for the interaction range between particles, depending on the complexity of the desired pattern and the underlying lattice. Then, we introduce a proof-of-principle "recipe" for determining the pairwise interactions that exactly satisfies this minimum criterion, and we show that it is sufficient to uniquely determine the ground state for a large class of crystal structures. Finally, we verify these results using Monte Carlo simulations.

Theoretical description of a DNA-linked nanoparticle self-assembly

Nanoparticles tethered with DNA strands are promising building blocks for bottom-up nanotechnology, and a theoretical understanding is important for future development. Here we build on approaches developed in polymer physics to provide theoretical descriptions for the equilibrium clustering and dynamics, as well as the self-assembly kinetics of DNA-linked nanoparticles. Striking agreement is observed between the theory and molecular modeling of DNA-tethered nanoparticles.

Quantitative study of the association thermodynamics and kinetics of DNA-coated particles for different functionalization schemes

Surface functionalization with complementary single-stranded DNA sticky ends is increasingly used for guiding the self-assembly of nano- and micrometer-sized particles into larger scale ordered structures. Here we present measurements, formulas, and graphs that allow one to quantitatively predict the association behavior of DNA-coated particles from readily available Web-based data. From experiments it appears that the suspension behavior is very sensitive to the grafting details, such as the length and flexibility of the tether constructs and the particles' surface coverage. Thus, if one wants to control the interactions and assembly processes, insight is needed into the structural and dynamical features of the DNA coatings. We demonstrate how a straightforward measurement of the particles' association-dissociation kinetics during selected temperature cycles, combined with a simple quantitative model, can reveal the relevant properties. We used this method in a systematic study where we varied the temperature cycle, the bead concentration, the particles' surface coverage, and the DNA construct. Among other things, we find that the backbone that tethers the sticky ends to the surface can have a significant impact on the particles' dissociation properties, as it affects the total number of interparticle bonds and the configurational entropy cost associated with these bonds. We further find that, independent of the tether backbone, self-complementary "palindromic" sticky ends readily form intraparticle hairpins and loops, which greatly affect the particles' association behavior. Such secondary structure formation is increasingly important in faster temperature quenches, at lower particle concentration, and at lower surface coverage. The latter observations are especially useful for the design of so-called self-protected DNA-mediated interactions, which we pioneered recently and for which we expect to find an increasing use, as they enable more versatile assembly schemes.

Aggregation-disaggregation transition of DNA-coated colloids: experiments and theory

Colloids coated with complementary single-stranded DNA "sticky ends" associate and dissociate upon heating. Recently, microscopy experiments have been carried out where this association-dissociation transition has been investigated for different types of DNA and different DNA coverages [R. Dreyfus, M. E. Leunissen, R. Sha, A. V. Tkachenko, N. C. Seeman, D. J. Pine, and P. M. Chaikin, Phys. Rev. Lett. 102, 048301 (2009)]. It has been shown that this transition can be described by a simple quantitative model which takes into account the features of the tethered DNA on the particles and unravels the importance of an entropy cost due to DNA confinement between the surfaces. In this paper, we first present an extensive description of the experiments that were carried out. A step-by-step model is then developed starting from the level of statistical mechanics of tethered DNA to that of colloidal aggregates. This model is shown to describe the experiments with excellent agreement for the temperature and width of the transition, which are both essential properties for complex self-assembly processes.

Self-assembly scenarios of patchy colloidal particles in two dimensions

We have investigated the self-assembly scenario of patchy colloidal particles in a two-dimensional system. The energetically most favourable ordered particle arrangements have been identified via an optimization tool that is based on genetic algorithms. Assuming different simple models for patchy colloidal particles, which include binary mixtures as well as attraction and repulsion between the patches, we could identify a broad variety of highly non-trivial ordered structures. The strategies of the systems to self-assemble become evident from a systematic variation of the pressure: (i) saturation of patch bonds at low pressure and close packing at high pressure and (ii) for intermediate pressure values, the strategy is governed by a trade-off between these two energetic aspects. The present study is yet another demonstration of the efficiency and the high reliability of genetic algorithms as versatile optimization tools.

Direct observation of size fractionation during colloidal crystallization

We present a confocal microscopy study of the quasi-two-dimensional crystallization of a binary mixture of spherical colloids coated with long DNA strands. Our experiments show that in the crystalline phase the two colloidal species are completely demixed. Analysis of the lattice spacings in the two types of colloidal crystal shows that the diameters of the two species of colloids differ by 10%. We argue that the demixing in the crystalline phase is due to size segregation during crystallization. This phenomenon had been predicted in several theoretical studies. To our knowledge, the present study provides the first 'real-space' experimental confirmation of this effect.

Valency dependence of polymorphism and polyamorphism in DNA-functionalized nanoparticles

Nanoparticles (NP) functionalized with single-stranded DNA (ssDNA) offer a route to custom-designed, self-assembled nanomaterials with potentially unusual properties. The bonding selectivity of DNA guarantees one-to-one binding to form double-stranded DNA (dsDNA), and an appropriate base sequence results in head-to-tail binding linking NP into networks. We explore the phase behavior and structure of a model for NP functionalized with between 3 and 6 short ssDNA through simulations of a coarse-grained molecular model, allowing us to examine both the role of the number of attached strands (valency) and their relative orientations. The NP assemble into networks where the number of NP links is controlled by the number of attached strands. The large length scale of the DNA links relative to the core NP size opens the possibility for the formation of interpenetrating networks that give rise to multiple thermodynamically distinct states. We find that the 3-functionalized NP have only a single phase transition between a dilute solution of NPs and an assembled network state. 4-Functionalized NP (with tetrahedral symmetry) exhibit four amorphous phases, or polyamorphism, each higher density phase consisting of an additional interpenetrating network. The two investigated geometries of 5-functionalized NP both exhibit two phase transitions and three amorphous phases. Like the 4-functionalized NP, the highest density phase consists of interpenetrating networks, demonstrating that regular symmetry is not a prerequisite for interpenetration to produce thermodynamically distinct phases. The width of the coexistence regions for all phase transitions increases with increasing functionality. Finally, for 6-functionalized NP with octahedral symmetry, the possibility of observing disordered phases with significantly bonded particles is preempted by the formation of ordered crystal phases. Interestingly, the extreme softness of the potential combined with the directional interaction allows for the formation of (at least) six distinct crystalline structures (i.e., polymorphism) consisting of up to six interpenetrating simple cubic lattices.

Simple quantitative model for the reversible association of DNA coated colloids

We investigate the reversible association of micrometer-sized colloids coated with complementary single-stranded DNA "sticky ends" as a function of the temperature and the sticky end coverage. We find that even a qualitative description of the dissociation transition curves requires the inclusion of an entropic cost. We develop a simple general model for this cost in terms of the configurational entropy loss due to binding and confinement of the tethered DNA between neighboring particles. With this easy-to-use model, we demonstrate for different kinds of DNA constructs quantitative control over the dissociation temperature and the sharpness of the dissociation curve, both essential properties for complex self-assembly processes.

Liquid-vapor transition driven by bond disorder

We report grand-canonical Monte Carlo simulations of an equimolar mixture of hard colloids coated with long polymers that have a complementary functionalization. Such systems have the potential to function as self-healing materials. Under conditions where the complementary polymer ends are strongly associated, we observe a first-order vapor-liquid transition from a dilute gas of colloidal dimers to a dense, liquid-like phase. This transition is driven exclusively by the increase in entropy associated with bond disorder-an effect that was predicted theoretically by Zilman et al. [Phys. Rev. Lett. 91, 015901 (2003)10.1103/PhysRevLett.91.015901]. Our simulations rationalize experimental observations by Schmatko et al. [Soft Matter 03 (2007) 703.].