Kinetics of DNA-coated sticky particles

Non-Invasive, Reliable, and Fast Quantification of DNA Loading on Gold Nanoparticles by a One-Step Optical Measurement

An exquisite, versatile, and reproducible quantification of DNA loading on gold nanoparticles (Au NPs) has long been pursued because this loading influences the analytical, therapeutic, and self-assembly behaviors of DNA-Au NPs. Nevertheless, the existing methods used thus far rely solely on the invasive detachment and subsequent spectroscopic quantification of DNA, which are error-prone and highly dependent on trained personnel. Here, we present a non-invasive optical framework that can determine the number of DNA strands on Au NPs by versatile one-step measurement of the visible absorption spectra of DNA-Au NP solutions without any invasive modifications or downstream processes. Using effective medium theory in conjunction with electromagnetic numerical calculation, the change in DNA loading density, resulting from varying the ion concentration, Au NP size, DNA strand length, and surrounding temperature, can be tracked in situ merely by the one-step measurement of visible absorption spectra, which is otherwise impossible to achieve. Moreover, the simplicity and robustness of this method promote reproducible DNA loading quantification regardless of experimental adeptness, which is in stark contrast with existing invasive and multistep methods. Overall, the optical framework outlined in this work can contribute to democratizing research on DNA-Au NPs and facilitating their rapid adoption in transformative applications.

Self-Assembly of DNA-Grafted Colloids: A Review of Challenges

DNA-mediated self-assembly of colloids has emerged as a powerful tool to assemble the materials of prescribed structure and properties. The uniqueness of the approach lies in the sequence-specific, thermo-reversible hybridization of the DNA-strands based on Watson–Crick base pairing. Grafting particles with DNA strands, thus, results into building blocks that are fully programmable, and can, in principle, be assembled into any desired structure. There are, however, impediments that hinder the DNA-grafted particles from realizing their full potential, as building blocks, for programmable self-assembly. In this short review, we focus on these challenges and highlight the research around tackling these challenges.

Comprehensive view of microscopic interactions between DNA-coated colloids

The self-assembly of DNA-coated colloids into highly-ordered structures offers great promise for advanced optical materials. However, control of disorder, defects, melting, and crystal growth is hindered by the lack of a microscopic understanding of DNA-mediated colloidal interactions. Here we use total internal reflection microscopy to measure in situ the interaction potential between DNA-coated colloids with nanometer resolution and the macroscopic melting behavior. The range and strength of the interaction are measured and linked to key material design parameters, including DNA sequence, polymer length, grafting density, and complementary fraction. We present a first-principles model that screens and combines existing theories into one coherent framework and quantitatively reproduces our experimental data without fitting parameters over a wide range of DNA ligand designs. Our theory identifies a subtle competition between DNA binding and steric repulsion and accurately predicts adhesion and melting at a molecular level. Combining experimental and theoretical results, our work provides a quantitative and predictive approach for guiding material design with DNA-nanotechnology and can be further extended to a diversity of colloidal and biological systems.

A quantitative prediction of DNA-mediated interactions between colloids is crucial to the design of colloidal structures for optical applications. Cui et al. measure the interaction potential with nanometer resolution and propose a theory to accurately predict adhesion and melting at a molecular level.

The nanocaterpillar's random walk: diffusion with ligand-receptor contacts

Particles with ligand-receptor contacts bind and unbind fluctuating "legs" to surfaces, whose fluctuations cause the particle to diffuse. Quantifying the diffusion of such "nanoscale caterpillars" is a challenge, since binding events often occur on very short time and length scales. Here we derive an analytical formula, validated by simulations, for the long time translational diffusion coefficient of an overdamped nanocaterpillar, under a range of modeling assumptions. We demonstrate that the effective diffusion coefficient, which depends on the microscopic parameters governing the legs, can be orders of magnitude smaller than the background diffusion coefficient. Furthermore it varies rapidly with temperature, and reproduces the striking variations seen in existing data and our own measurements of the diffusion of DNA-coated colloids. Our model gives insight into the mechanism of motion, and allows us to ask: when does a nanocaterpillar prefer to move by sliding, where one leg is always linked to the surface, and when does it prefer to move by hopping, which requires all legs to unbind simultaneously? We compare a range of systems (viruses, molecular motors, white blood cells, protein cargos in the nuclear pore complex, bacteria such as Escherichia coli, and DNA-coated colloids) and present guidelines to control the mode of motion for materials design.

Bulk rheology of sticky DNA-functionalized emulsions

We measure by experiment and particle-based simulation the rheology of concentrated, non-Brownian droplet emulsions functionalized with surface-bound single-stranded (ss), "sticky," DNA. In the absence of ssDNA, the emulsion viscosity increases with the dispersed phase volume fraction ϕ, before passing through a liquid-solid transition at a critical ϕ_{c} related to random close packing. Introducing ssDNA leads to a liquid-solid transition at ϕ<ϕ_{c}, the onset being set by the droplet valency N and the ssDNA concentration (or simulated binding strength ε). Using insight from simulation, we identify three key behaviors: (i) jammed suspensions (ϕ>ϕ_{c}≈0.64) show weak effects of functionalization, with elastic rheology instead governed by droplet stiffness; (ii) suspensions with ϕ<ϕ_{c} and N=1, 2 always exhibit viscous rheology, regardless of functionalization; and (iii) for ϕ<ϕ_{c} and N>3, functionalization leads to a controllable viscous-elastic transition. We present state diagrams showing the range of rheological tuning attainable by these means.

Self-Assembly and Crystallization of DNA-Coated Colloids via Linker-Encoded Interactions

Coating colloidal particles with DNA is a promising strategy to make functional nanoscale materials because the particles can be programmed to spontaneously self-assemble into complex, ordered structures. In this Article, we explore the phase behavior and types of structures that can be formed when interactions between DNA-coated colloids are specified by linker DNA strands dispersed in solution. We show that linker-mediated interactions direct the self-assembly of colloids into equilibrium crystal structures. Furthermore, we demonstrate how different linker sequences and concentrations produce different crystal lattices, whose symmetry and compositional order are encoded exclusively by the linker-mediated interactions. These results illustrate how linkers can be used to separate the assembly instructions, encoded in the linkers, from the colloids themselves. We also examine the phase behavior of asymmetric linkers, which bind more strongly to one colloidal species than the other. We find that asymmetry strongly influences the concentration dependence of the colloidal interactions, which we explain using a mean-field model. We also find evidence that asymmetric linkers might help to reduce kinetic bottlenecks to colloidal crystallization. Together, our findings expand the design rules of linker-mediated self-assembly and make connections between the various schemes for programming assembly of DNA-coated colloids reported in the literature.

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

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

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.

Multivalent, multiflavored droplets by design

Nature self-assembles functional materials by programming flexible linear arrangements of molecules and then folding them to make 2D and 3D objects. To understand and emulate this process, we have made emulsion droplets with specific recognition and controlled valence. Uniquely monovalent droplets form dimers: divalent lead to polymer-like chains, trivalent allow for branching, and programmed mixtures of different valences enable a variety of designed architectures and the ability to subsequently close and open structures. Our functional building blocks are a hybrid of micrometer-scale emulsion droplets and nanoscale DNA origami technologies. Functional DNA origami rafts are first added to droplets and then herded into a patch using specifically designated "shepherding" rafts. Additional patches with the same or different specificities can be formed on the same droplet, programming multiflavored, multivalence droplets. The mobile patch can bind to a patch on another droplet containing complementary functional rafts, leading to primary structure formation. Further binding of nonneighbor droplets can produce secondary structures, a third step in hierarchical self-assembly. The use of mobile patches rather than uniform DNA coverage has the advantage of valence control at the expense of slow kinetics. Droplets with controlled flavors and valences enable a host of different material and device architectures.

Using DNA strand displacement to control interactions in DNA-grafted colloids

Grafting DNA oligonucleotides to colloidal particles leads to specific, reversible interactions between those particles. However, the interaction strength varies steeply and monotonically with temperature, hindering the use of DNA-mediated interactions in self-assembly. We show how the dependence on temperature can be modified in a controlled way by incorporating DNA strand-displacement reactions. The method allows us to make multicomponent systems that can self-assemble over a wide range of temperatures, invert the dependence on temperature to design colloidal systems that melt upon cooling, controllably transition between structures with different compositions, or design systems with multiple melting transitions. This wide range of behaviors can be realized simply by adding a small number of DNA strands to the solution, making the approach modular and straightforward to implement. We conclude with practical considerations for designing systems of DNA-mediated colloidal interactions.

Sequential self-assembly of DNA functionalized droplets

Complex structures and devices, both natural and manmade, are often constructed sequentially. From crystallization to embryogenesis, a nucleus or seed is formed and built upon. Sequential assembly allows for initiation, signaling, and logical programming, which are necessary for making enclosed, hierarchical structures. Although biology relies on such schemes, they have not been available in materials science. Here, we demonstrate programmed sequential self-assembly of DNA functionalized emulsions. The droplets are initially inert because the grafted DNA strands are pre-hybridized in pairs. Active strands on initiator droplets then displace one of the paired strands and thus release its complement, which in turn activates the next droplet in the sequence, akin to living polymerization. Our strategy provides time and logic control during the self-assembly process, and offers a new perspective on the synthesis of materials.Natural complex systems are often constructed by sequential assembly but this is not readily available for synthetic systems. Here, the authors program the sequential self-assembly of DNA functionalized emulsions by altering the DNA grafted strands.

Mutation at Expanding Front of Self-Replicating Colloidal Clusters

We construct a scheme for self-replicating square clusters of particles in two spatial dimensions, and validate it with computer simulations in a finite-temperature heat bath. We find that the self-replication reactions propagate through the bath in the form of Fisher waves. Our model reflects existing colloidal systems, but is simple enough to allow simulation of many generations and thereby the first study of evolutionary dynamics in an artificial system. By introducing spatially localized mutations in the replication rules, we show that the mutated cluster population can survive and spread with the expanding front in circular sectors of the colony.

Crystallization of DNA-coated colloids

DNA-coated colloids hold great promise for self-assembly of programmed heterogeneous microstructures, provided they not only bind when cooled below their melting temperature, but also rearrange so that aggregated particles can anneal into the structure that minimizes the free energy. Unfortunately, DNA-coated colloids generally collide and stick forming kinetically arrested random aggregates when the thickness of the DNA coating is much smaller than the particles. Here we report DNA-coated colloids that can rearrange and anneal, thus enabling the growth of large colloidal crystals from a wide range of micrometre-sized DNA-coated colloids for the first time. The kinetics of aggregation, crystallization and defect formation are followed in real time. The crystallization rate exhibits the familiar maximum for intermediate temperature quenches observed in metallic alloys, but over a temperature range smaller by two orders of magnitude, owing to the highly temperature-sensitive diffusion between aggregated DNA-coated colloids.

DNA-coated colloids have failed to achieve their promise of programmable self-assembly because they stick to each other like Velcro. Here Wang et al. overcome this problem by making clickable smooth colloids that are coated with short single-stranded DNA at high density.