Directed assembly of particles using directional DNA interactions

Orientation of Antibody Modified and Reacted on Carboxy-Functionalized Polystyrene Particle Revealed by Zeta Potential Measurement

The comprehensive understanding of the orientation of antibodies on a solid surface is crucial for affinity-based sensing mechanisms. In this study, we demonstrated that the orientation of primary antibodies modified on carboxy-functionalized polystyrene (PS) particles can be analyzed using zeta potential behavior at different pH based on the combined Gouy-Chapman-Stern model and the acid dissociation of carboxy groups and antibodies. We observed that at low surface concentrations of the primary antibody, a side-on orientation was predominant. However, at higher concentrations (approximately 30000 antibodies per PS particle), the orientation shifted to an end-on type due to steric hindrance. Furthermore, the reaction mechanism of the secondary antibody exhibited pH-dependent behavior. At pH > 7, the zeta potential changes were attributed to the antibody-antibody reaction, whereas at pH < 7, adsorption of secondary antibody onto the PS particle was observed, leading to a change in the orientation of the primary antibody modified on the PS particle to an end-on type. The change in zeta potential due to secondary antibody binding indicated a detection limit of 37000 antibodies per PS particle. As a result, we revealed that the analysis of zeta potential behavior enables the evaluation of antibody orientation and the detection of zeptomole order antibodies. This study represents the first demonstration of this capability. We anticipate that the present concept and results will broaden the quantitative application of zeta potential measurements and have significant implications for research areas, including physical chemistry and analytical chemistry.

Synthesis and Assembly of Photoresponsive Colloidal Tubes

Inspired by the sophisticated multicomponent and multistage assembly of proteins and their mixtures in living cells, this study rationally designs and fabricates photoresponsive colloidal tubes that can self-assemble and hybrid-assemble when mixed with colloidal spheres and rods. Time-resolved observation and computer simulation reveal that the assembly is driven by phoretic attraction originating from osmotic pressures. These pressures are induced by the chemical concentration gradients generated by the photochemical reaction caused by colloidal tubes in a H2O2 solution under ultraviolet (UV) irradiation. The assembled structure is dictated by the size and shape of the constituent colloids as well as the intensity of the UV irradiation. Additionally, the resulting assembly can undergo self-propelled motion originating from the broken symmetry of the surrounding concentration gradients. This motion can be steered by a magnetic field and used for microscale cargo delivery. The study demonstrates a facile synthesis method for colloidal tubes and highlights their unique potential for controlled, hierarchical self-assembly and hybrid-assembly.

Utilizing peptide-anchored DNA templates for novel programmable nanoparticle assemblies in biological macromolecules: A review

Biological macromolecules such as proteins and DNA are known to self-assemble into various structural moieties with distinct functions. While nucleic acids are the structural building blocks, peptides exemplify diversity as tailorable biochemical units. Thus, combining the scaffold properties of the biomacromolecule DNA and the functionality of peptides could evolve into a powerful method to obtain tailorable nano assemblies. In this review, we discuss the assembly of non-DNA-coated colloidal NPs on DNA/peptide templates using functional anchors. We begin with strategies for directly attaching metallic NPs to DNA templates to ascertain the functional role of DNA as a scaffold. Followed by methods to assemble peptides onto DNA templates to emphasize the functional versatility of biologically abundant DNA-binding peptides. Next, we focus on studies corroborating peptide self-assembling into macromolecular templates onto which NPs can attach to emphasize the properties of NP-binding peptides. Finally, we discuss the assembly of NPs on a DNA template with a focus on the bifunctional DNA-binding peptides with NP-binding affinity (peptide anchors). This review aims to highlight the immense potential of combining the functional power of DNA scaffolds and tailorable functionalities of peptides for NP assembly and the need to utilize them effectively to obtain tailorable hierarchical NP assemblies.

DNA-mediated regioselective encoding of colloids for programmable self-assembly

How far we can push chemical self-assembly is one of the most important scientific questions of the century. Colloidal self-assembly is a bottom-up technique for the rational design of functional materials with desirable collective properties. Due to the programmability of DNA base pairing, surface modification of colloidal particles with DNA has become fundamental for programmable material self-assembly. However, there remains an ever-lasting demand for surface regioselective encoding to realize assemblies that require specific, directional, and orthogonal interactions. Recent advances in surface chemistry have enabled regioselective control over the formation of DNA bonds on the particle surface. In particular, the structural DNA nanotechnology provides a simple yet powerful design strategy with unique regioselective addressability, bringing the complexity of colloidal self-assembly to an unprecedented level. In this review, we summarize the state-of-art advances in DNA-mediated regioselective surface encoding of colloids, with a focus on how the regioselective encoding is introduced and how the regioselective DNA recognition plays a crucial role in the self-assembly of colloidal structures. This review highlights the advantages of DNA-based regioselective modification in improving the complexity of colloidal assembly, and outlines the challenges and opportunities for the construction of more complex architectures with tailored functionalities.

Packing core-corona particles on a spherical surface

We explore the non-trivial structures that can be obtained by the assembly of repulsive core-corona particles confined on a spherical surface. Using Monte Carlo simulations, we study the low-temperature equilibrium configurations as a function of the size of the confining (spherical) surface for a small number of particles (N ≤ 12) and obtain a large variety of minimal-energy arrangements including anisotropic and chiral structures. For a small cluster (N = 4), we construct a phase diagram in the confining surface radius vs corona range plane that showed regions where configurations with a certain energy are not accessible. Also, a phase diagram in the temperature and confining surface radius plane showed the presence of reentrant phases. The assembly of Platonic and Archimedean solids and the emergence of helical structures are also discussed. When the number of particles is large (N ≥ 100), apart from the appearance of defects, the overall configurations correspond closely to the ones formed in an unconfined two-dimensional case. Interestingly, the present model reproduces the symmetry of experimentally obtained small clusters of colloidal spheres confined at the surface of evaporating liquid droplets which cannot be explained in terms of packing of hard spheres. Thus, our simulations provide insight on the role that the softness of the particles may have in the assembly of clusters of nanoparticles.

Computer simulations of self-assembly of anisotropic colloids

Computer simulations have played a significant role in understanding the physics of colloidal self-assembly, interpreting experimental observations, and predicting novel mesoscopic and crystalline structures. Recent advances in computer simulations of colloidal self-assembly driven by anisotropic or orientation-dependent inter-particle interactions are highlighted in this review. These interactions are broadly classified into two classes: entropic and enthalpic interactions. They mainly arise due to shape anisotropy, surface heterogeneity, compositional heterogeneity, external field, interfaces, and confinements. Key challenges and opportunities in the field are discussed.

Multifarious colloidal structures: new insight into ternary and quadripartite ordered assemblies

DNA-mediated assembly of colloidal particles can be utilized to produce a variety of structures which may have desirable phononic, photonic, or electronic transport properties. Recent developments in linker-mediated assembly processes allow for interactions to be coordinated between many different types of colloidal particles more easily and with fewer unique sequences than direct hybridization. However, the dynamics of colloidal self-assembly becomes increasingly more complex when coordinating interactions between three or more distinct interacting elements. In such cases particle pairs with similar binding energies are allowed to interact unpredictably, and enthalpically degenerate binding sites will be noticeably more present while numerous secondary phases may also result from the self-assembly process. Therefore, it is necessary to develop procedures for predicting feasible superstructure geometries for these systems before they can be implemented in material design. Here we investigate the formation of multifarious ordered structures through self-assembly of multiple types of spherically symmetrical colloidal particles with a variety of interaction matrices. We utilize Molecular Dynamics (MD) simulations to study the growth behavior of systems with different types of interacting elements and different particle sizes, and also predict the formation and stability of the target structures. We also study the phononic spectra of various ternary structures in order to identify the influence of key structural parameters on phonon bandgap frequencies and ranges. Our results provide direct guidelines for designing ternary and quadripartite multifarious colloidal structures, and motivate new directions for future experimental work to target formation of multi-component colloidal superstructures beyond the well-established binary symmetries studied in the past.

Shear-driven rolling of DNA-adhesive microspheres

Many biologically important cell binding processes, such as the rolling of leukocytes in the vasculature, are multivalent, being mediated by large numbers of weak binding ligands. Quantitative agreement between experiments and models of rolling has been elusive and often limited by the poor understanding of the binding and unbinding kinetics of the ligands involved. Here, we present a cell-free experimental model for such rolling, consisting of polymer microspheres whose adhesion to a glass surface is mediated by ligands with well-understood force-dependent binding free energy-short complementary DNA strands. We observe robust rolling activity for certain values of the shear rate and the grafted DNA strands' binding free energy and force sensitivity. The simulation framework developed to model leukocyte rolling, adhesive dynamics, quantitatively captures the mean rolling velocity and lateral diffusivity of the experimental particles using known values of the experimental parameters. Moreover, our model captures the velocity variations seen within the trajectories of single particles. Particle-to-particle variations can be attributed to small, plausible differences in particle characteristics. Overall, our findings confirm that state-of-the-art adhesive dynamics simulations are able to capture the complex physics of particle rolling, boding well for their extension to modeling more complex systems of rolling cells.

Terminal Sequence-Specific Interparticle Attraction between DNA Duplex-Carrying Polystyrene Microparticles in Aqueous Salt Solution Assessed by Optical Tweezers

The dispersion behavior of DNA duplex-carrying colloidal particles in aqueous high-salt solutions shows extraordinary selectivity against the duplex terminal sequence. We investigated the interparticle force between DNA duplex-carrying polystyrene (dsDNA-PS) microparticles in aqueous salt solutions and examined their behavior in relation to the duplex terminal sequences. Force-distance (F-D) curves for a pair of dsDNA-PS particles were recorded with a dual-beam optical tweezers system with the two optically trapped particles closely approaching each other. Interestingly, only 3-5% of the oligo-DNA strands on the dsDNA-PS particles formed a duplex with complementary DNAs, and the F-D curves showed a distinct specificity to the duplex terminal sequences in the interparticle force at a high-NaCl concentration; a clear attraction peak was observed in F-D curves only when the duplex terminal was a complementary base pair. The attractive strength reached 2.6 ± 0.5 pN at 500 mM NaCl and 4.3 ± 1.0 pN at 750 mM NaCl. By sharp contrast, no significant attraction occurred for the particles with mismatched duplex terminals even at 750 mM NaCl. Similar duplex terminal-specificity in the interparticle force was also confirmed for dsDNA-PS particles in divalent MgCl₂ solutions. Considering that the duplex terminal sequences on the dsDNA-PS particles showed only a negligible difference in their surface charges under identical salt conditions, we concluded that the interparticle attraction observed only for the dsDNA-PS particles with complementary duplex terminals is attributable to the salt-facilitated stacking interaction between the paired terminal nucleobases (i.e., blunt-end stacking) on the dsDNA-PS surfaces. Our results thus demonstrate the occurrence of a duplex terminal-specific interparticle force between dsDNA-PS particles under high-salt conditions.

DNA Terminal-Specific Dispersion Behavior of Polystyrene Latex Microparticles Densely Covered with Oligo-DNA Strands Under High-Salt Conditions

We prepared microspheres densely covered with oligo-DNA strands by immobilizing amino-terminated oligo-DNA strands on the surface of carboxylate polystyrene latex (PS) particles via the amide bond formation. The obtained microspheres (ssDNA-PS) stably dispersed in neutral pH buffer containing high concentrations of NaCl. For the ssDNA-PS ≥1 μm diameter, only 3 - 5% of surface-immobilized oligo-DNA could form a duplex with the complementary strands. Nevertheless, the resulting ssDNA-PS showed a distinct duplex terminal dependency in their dispersion behavior under neutral pH and high NaCl conditions; the microspheres with fully-matched duplexes on the surface spontaneously aggregated in a non-crosslinking manner. By contrast, the microspheres with terminal-mismatched duplexes remained dispersed under the identical conditions. These results suggest that the micrometer-scale particles covered with oligo-DNA strands also have high susceptibility to a duplex terminal sequence in their dispersion property, similar to previously reported DNA-functionalized nanoparticles. This property could potentially be used in various applications including analytical purposes.

Two-Dimensional (2D) or Quasi-2D Superstructures from DNA-Coated Colloidal Particles

This contribution describes the synthesis of colloidal di-patch particles functionalized with DNA on the patches and their assembly into colloidal superstructures via cooperative depletion and DNA-mediated interactions. The assembly into flower-like Kagome, brick-wall like monolayer, orthogonal packed single or double layers, wrinkled monolayer, and colloidal honeycomb superstructures can be controlled by tuning the particles' patch sizes and assembly conditions. Based on these experimental results, we generate an empirical phase diagram. The principles revealed by the phase diagram provide guidance in the design of two-dimensional (2D) materials with desired superstructures. Our strategy might be translatable to the assembly of three-dimensional (3D) colloidal structures.

Observation of liquid glass in suspensions of ellipsoidal colloids

Despite the omnipresence of colloidal suspensions, little is known about the influence of colloid shape on phase transformations, especially in nonequilibrium. To date, real-space imaging results at high concentrations have been limited to systems composed of spherical colloids. In most natural and technical systems, however, particles are nonspherical, and their structural dynamics are determined by translational and rotational degrees of freedom. Using confocal microscopy of fluorescently labeled core-shell particles, we reveal that suspensions of ellipsoidal colloids form an unexpected state of matter, a liquid glass in which rotations are frozen while translations remain fluid. Image analysis unveils hitherto unknown nematic precursors as characteristic structural elements of this state. The mutual obstruction of these ramified clusters prevents liquid crystalline order. Our results give insight into the interplay between local structures and phase transformations. This helps to guide applications such as self-assembly of colloidal superstructures and also gives evidence of the importance of shape on the glass transition in general.

Nature-Inspired Emerging Chiral Liquid Crystal Nanostructures: From Molecular Self-Assembly to DNA Mesophase and Nanocolloids

Liquid crystals (LCs) are omnipresent in living matter, whose chirality is an elegant and distinct feature in certain plant tissues, the cuticles of crabs, beetles, arthropods, and beyond. Taking inspiration from nature, researchers have recently devoted extensive efforts toward developing chiral liquid crystalline materials with self-organized nanostructures and exploring their potential applications in diverse fields ranging from dynamic photonics to energy and safety issues. In this review, an account on the state of the art of emerging chiral liquid crystalline nanostructured materials and their technological applications is provided. First, an overview on the significance of chiral liquid crystalline architectures in various living systems is given. Then, the recent significant progress in different chiral liquid crystalline systems including thermotropic LCs (cholesteric LCs, cubic blue phases, achiral bent-core LCs, etc.) and lyotropic LCs (DNA LCs, nanocellulose LCs, and graphene oxide LCs) is showcased. The review concludes with a perspective on the future scope, opportunities, and challenges in these truly advanced functional soft materials and their promising applications.

Reconfigurable Self-Assembly and Kinetic Control of Multiprogrammed DNA-Coated Particles

DNA is a unique molecule for storing information, which is used to provide particular biological instructions. Its function is primarily determined by the sequence of its four nucleobases, which have highly specific base-pairing interactions. This unique feature can be applied to direct the self-assembly of colloids by grafting DNA onto them. Due to the sequence-specific interactions, colloids can be programmed with multiple instructions. Here, we show that particles having multiple DNA strands with different melting profiles can undergo multiple phase transitions and reassemble into different crystalline structures in response to temperature. We include free DNA strands in the medium to selectively switch on and off DNA hybridization depending on temperature. We also demonstrate that DNA hybridization kinetics can be used as a means to achieve targeted assembling structure of colloids. These transitions impart a reconfigurability to colloids in which systems can be transformed an arbitrary number of times using thermal and kinetic control.

Multivalent Patchy Colloids for Quantitative 3D Self-Assembly Studies

We report methods to synthesize sub-micron- and micron-sized patchy silica particles with fluorescently labeled hemispherical titania protrusions, as well as routes to efficiently characterize these particles and self-assemble these particles into non-close-packed structures. The synthesis methods expand upon earlier work in the literature, in which silica particles packed in a colloidal crystal were surface-patterned with a silane coupling agent. Here, hemispherical amorphous titania protrusions were successfully labeled with fluorescent dyes, allowing for imaging by confocal microscopy and super-resolution techniques. Confocal microscopy was exploited to experimentally determine the numbers of protrusions per particle over large numbers of particles for good statistical significance, and these distributions were compared to simulations predicting the number of patches as a function of core particle polydispersity and maximum separation between the particle surfaces. We self-assembled these patchy particles into open percolating gel networks by exploiting solvophobic attractions between the protrusions.

Engineering Surface Patterning of Colloidal Rings through Plateau-Rayleigh Instability

Plateau-Rayleigh (P-R) instability occurring on Brownian colloidal particles is presented. This instability can be used for the surface patterning of Brownian colloidal rings. This idea was realized by employing polystyrene(PS)/SiO₂ core/shell rings, for which PS layer was selectively grown onto the interior surface of SiO₂ rings. The P-R instability was initiated in the ring's dispersion by adding a good solvent of PS. By using both experiments and theory, it is shown that the number of patches is tunable and that it is linearly related to a function of two variables, namely, solvent quantity and contact angle. In particular, one-patch Janus rings and patchy disks were also synthesized at high yields. The patch size of all particles is tunable by step-by-step polymerization and the patches can be functionalized, for example by ATRP grafting with pH-sensitive polymers. This approach can be adapted for the synthesis of other patchy colloids with designated complexity.

Convectively Assembled Monolayers of Colloidal Cubes: Evidence of Optimal Packings

We employ a system of cubic colloids with rounded corners to study the close-packed monolayers that form via convective assembly. We show that by controlled solvent evaporation large densely packed monolayers of colloidal cubes are obtained. Using scanning electron microscopy and particle-tracking algorithms, we investigate the local order in detail and show that the obtained monolayers possess their predicted close-packed optimal packings, the Λ₀-lattice and the Λ₁-lattice, as well as the simple square-lattice and disordered packings. We further show that shape details of the cube corners are important for the final packing symmetry, where the frequency of the Λ₁-lattice increases with decreasing roundness of the corners, whereas the frequency of the Λ₀-lattice is unaffected. The formation of both optimal packings is found to be a consequence of the out-of-equilibrium formation process, which leads to small shifts in rows of cubes, thereby transforming the Λ₁-lattice into the Λ₀-lattice.

Modeling the relative dynamics of DNA-coated colloids

We construct a theoretical model for the dynamics of a microscale colloidal particle, modeled as an interval, moving horizontally on a DNA-coated surface, modelled as a line coated with springs that can stick to the interval. Averaging over the fast DNA dynamics leads to an evolution equation for the particle in isolation, which contains both friction and diffusion. The DNA-induced friction coefficient depends on the physical properties of the DNA, and substituting parameter values typical of a 1 μm colloid coated densely with weakly interacting DNA gives a coefficient about 100 times larger than the corresponding coefficient of hydrodynamic friction. We use a mean-field extension of the model to higher dimensions to estimate the friction tensor for a disc rotating and translating horizontally along a line. When the DNA strands are very stiff and short, the friction coefficient for the disc rolling approaches zero while the friction for the disc sliding remains large. Together, these results could have significant implications for the dynamics of DNA-coated colloids or other ligand-receptor systems, implying that DNA-induced friction between colloids can be stronger than hydrodynamic friction and should be incorporated into simulations, and that it depends nontrivially on the type of relative motion, possibly causing the particles to assemble into out-of-equilibrium metastable states governed by the pathways with the least friction.

DNA-Encoded Protein Janus Nanoparticles

Asymmetric functionality and directional interactions, which are characteristic of noncentrosymmetric particles, such as Janus particles, present an opportunity to encode particles with properties, but also a great synthetic challenge. Here, we exploit the chemical anisotropy of proteins, and the versatile chemistry of DNA to synthesize a protein-based Janus nanoparticle comprised of two proteins encoded with sequence-specific nucleic acid domains, tethered together by an interprotein "DNA bond". We use these novel nanoparticles to realize a new class of three-dimensional superlattice, only possible when two sides of the particle are modified with orthogonal oligonucleotide sequences. The low symmetry, intrinsic to Janus particles, enables the realization of unprecedented multicomponent nanoparticle superlattices with unique, hexagonal layered architectures. In addition, the interprotein "DNA bond" can be modulated to selectively expand the lattice in a single direction. The results presented herein not only emphasize the power of rationally designing nanoscale building blocks to create highly engineered colloidal crystals, but also establish a precedent for applications of multidomain DNA-encoded nanoparticles, especially in the field of colloidal crystallization.

Valence, loop formation and universality in self-assembling patchy particles

Patchy particles have emerged as an attractive model to mimic phase separation and self-assembly of globular proteins solutions, colloidal patchy particles, and molecular fluids where directional interactions are operative. In our previous work, we extensively explored the coupling of directional and isotropic interactions on both the phase separation and self-assembly in a system of patchy particles with five spots. Here, we extend this work to consider different patch valences and isotropic interaction strengths with an emphasis on self-assembly. Although the location of self-assembly transition lines in the temperature-density plane depend on a number of parameters, we find universal behavior of cluster size that is dependent only on the probability of a spot being bound, the patch valence, and the density. Using these principles, we quantify both the mass distribution and the shape for all clusters, as well as clusters containing loops. Following the logical implications of these results, combined with a simplified version of a mean-field theory that incorporates Flory-Stockmayer theory, we find a universal curve for the temperature dependence of cluster mass and a universal curve for the fraction of clusters that contain loops. As the curves are dependent on the particle valence, such results provide a method for parameterizing patchy particle models using experimental data.

Molecular Recognition in the Colloidal World

Colloidal self-assembly is a bottom-up technique to fabricate functional nanomaterials, with paramount interest stemming from programmable assembly of smaller building blocks into dynamic crystalline domains and photonic materials. Multiple established colloidal platforms feature diverse shapes and bonding interactions, while achieving specific orientations along with short- and long-range order. A major impediment to their universal use as building blocks for predesigned architectures is the inability to precisely dictate and control particle functionalization and concomitant reversible self-assembly. Progress in colloidal self-assembly necessitates the development of strategies that endow bonding specificity and directionality within assemblies. Methodologies that emulate molecular and polymeric three-dimensional (3D) architectures feature elements of covalent bonding, while high-fidelity molecular recognition events have been installed to realize responsive reconfigurable assemblies. The emergence of anisotropic 'colloidal molecules', coupled with the ability to site-specifically decorate particle surfaces with supramolecular recognition motifs, has facilitated the formation of superstructures via directional interactions and shape recognition. In this Account, we describe supramolecular assembly routes to drive colloidal particles into precisely assembled architectures or crystalline lattices via directional noncovalent molecular interactions. The design principles are based upon the fabrication of colloidal particles bearing surface-exposed functional groups that can undergo programmable conjugation to install recognition motifs with high fidelity. Modular and versatile by design, our strategy allows for the introduction and integration of molecular recognition principles into the colloidal world. We define noncovalent molecular interactions as site-specific forces that are predictable (i.e., feature selective and controllable complementary bonding partners) and can engage in tunable high-fidelity interactions. Examples include metal coordination and host-guest interactions as well as hydrogen bonding and DNA hybridization. On the colloidal scale, these interactions can be used to drive the reversible formation of open structures. Key to the design is the ability to covalently conjugate supramolecular motifs onto the particle surface and/or noncovalently associate with small molecules that can mediate and direct assembly. Efforts exploiting the binding strength inherent to DNA hybridization for the preparation of reversible open-packed structures are then detailed. We describe strategies that led to the introduction of dual-responsive DNA-mediated orthogonal assembly as well as colloidal clusters that afford distinct DNA-ligated close-packed lattices. Further focus is placed on two essential and related efforts: the engineering of complex superstructures that undergo phase transitions and colloidal crystals featuring a high density of functional anchors that aid in crystallization. The design principles discussed in this Account highlight the synergy stemming from coupling well-established noncovalent interactions common on the molecular and polymeric length scales with colloidal platforms to engineer reconfigurable functional architectures by design. Directional strategies and methods such as those illustrated herein feature molecular control and dynamic assembly that afford both open-packed 1D and 2D lattices and are amenable to 3D colloidal frameworks. Multiple methods to direct colloidal assembly have been reported, yet few are capable of crystallizing 2D and 3D architectures of interest for optical data storage, electronics, and photonics. Indeed, early implications are that [supra]molecular control over colloidal assembly can fabricate rationally structured designer materials from simple fundamental building blocks.