Session Q47: Focus Session: DNA-Coated Colloid Particles

Heterogeneous 3D Assembly of DNA-encoded Quantum Dots and Gold Nanoparticles

We report the heterogeneous assembly of quantum dots (QDs) and gold nanoparticles (AuNPs) into three-dimensional (3D) superlattices by means of DNA encoding. CdSe/ZnS core-shell QDs were functionalized with stranded (ss) DNA to obtain a stable aqueous dispersion of QD-DNA conjugates, which maintains the optical properties of the original QDs. By introducing AuNPs modified by complementary ssDNA, QD-AuNP aggregates were assembled. Using synchrotron-based small angel X-ray scattering, we found that QD-AuNP assemblies form a body center cubic (BCC) lattice, while each nanoparticle type, QD and AuNP, are positioned in a simple cubic (SC) manner. Distance-dependent optical property of QDs in heterogeneous superlattices was studied by time-resolved fluorescence spectroscopy. The potential applications of the above optically-active nanosystems will also be discussed.   

Self-Assembly of Octopus Nanoparticles into Pre-Programmed Finite Clusters

The precise control of the spatial arrangement of nanoparticles (NP) is often required to take full advantage of their novel optical and electronic properties. NPs have been shown to self-assemble into crystalline structures using either patchy surface regions or complementary DNA strands to direct the assembly. Due to a lack of specificity of the interactions these methods lead to only a limited number of structures. An emerging approach is to bind ssDNA at specific sites on the particle surface making so-called octopus NPs. Using octopus NPs we investigate the inverse problem of the self-assembly of finite clusters. That is, for a given target cluster (e.g., arranging the NPs on the vertices of a dodecahedron) what are the minimum number of complementary DNA strands needed for the robust self-assembly of the cluster from an initially homogeneous NP solution? Based on the results of Brownian dynamics simulations we have compiled a set of design rules for various target clusters including cubes, pyramids, dodecahedrons and truncated icosahedrons. Our approach leads to control over the kinetic pathway and has demonstrated nearly perfect yield of the target.   

DNA-induced 2D-to-1D Phase Transition of Nanoparticle Assemblies at Liquid-Vapor Interface

We have investigated the structure formation and development for two-dimensional assembly of DNA functionalized nanoparticles at liquid-vapor interface. The adsorption of negatively charged DNA-coated particle to the interface was triggered by a positively charged lipid layer. A normal and in-plane structure of the nanoparticle monolayer were probed using in-situ surface scattering methods, x-ray reflectivity and grazing incidence small angle x-ray scattering. We observed the formation of the hexagonally closed packed (HCP) 2D lattice of nanoparticles due to a combination of electrostatic surface-to-particle attraction and interparticle repulsion. Upon an onset of DNA hybridization between particles the phase transition from HCP order to 1D crystalline structure was observed. The control on the interparticle spacing and monolayer confinement were also examined by changing a salt concentration. Our studies demonstrate novel mechanism for transition from ordered 2D to ordered 1D structure due to the domination of DNA-induced attraction over an electrostatic repulsion and open a route for nano-structure manipulations at the interfaces.   

Structural Diversity of DNA-Coated Particle Assemblies

Custom designed nanoparticles (NP) or colloids with specific recognition offer the possibility to control the phase behavior and structure of particle assemblies for a range of applications. One approach to realize these new materials is by attaching DNA to a core particle; the hybridization of double-stranded DNA between particles results in the spontaneous assembly of higher-order structures. Control of the assembled state can be achieved by adjusting several parameters, including sequence selectivity, DNA link orientation, DNA length and flexibility, and the balance between the length of links and non-specific repulsive interactions. I will discuss the results of a coarse-grained molecular model for DNA-linked nanoparticles that helps to rationalize experimental findings and demonstrate new routes to control the assembled structure. We examine how the number and orientation of strands affects the structure, phase behavior, and dynamics. We show that it is possible to realize unusual phase diagrams with many thermodynamically distinct phases, both amorphous and crystal. We further examine the parameters that control the pathways of assembly, which are critical to avoid kinetic bottlenecks. Finally, we discuss strategies to create highly anisoptropic structures using both isotropic and anisotropic core units.   

DNA Mediated Nanoparticle Crystallization: Characterizing How Equilibrium is Reached

DNA programmed self-assembly is becoming one of the most powerful tools for designing nanoparticle crystals due to the exquisite control over lattice size and structure achievable. While in recent years the inventory of crystalline structures accessible through DNA programming has grown, our understanding of the dynamical processes that lead to crystallization is still limited. Using MD we simulate the nucleation and growth of DNA programmed nanoparticle crystallization and characterize the different processes that determine the relaxation times leading to equilibrium. In particular, we classify the topological defects and the processes leading to their annihilation. Implications for experiments as well as for achieving single crystals are also discussed.   

Packing of DNA-assembled Nanocubes and Nanooctahedra

Nanoparticle shape has a profound effect on assembly behavior. However, the contribution of surface-attached molecules can significantly modulate the packing of nanoscale objects, inducing phases markedly different from the known packing rules of macroscopic objects. Our studies uncover the phase behavior of nanocubes and nanooctahedron assembled by DNA-mediated interactions into three-dimensional structures, which were probed in-situ by small angle x-ray scattering. We observed that the packing of these nanoscale anisotropic objects depends strongly on the details of the DNA linkages. Using electron microscopy and optical spectroscopy, we elucidate the factors that drive assembly and dictate the spatial organization of the nano-objects. The relationship between particle shape and the mechanism of phase formation for nanocubes has been also investigated.   

Making DNA competitive: a new strategy to improve the self-assembly properties of DNA-coated particles

We present a new approach to widen the normally very narrow temperature window for equilibrium self-assembly (e.g. crystallization) of DNA-coated particles. Using Monte Carlo simulations, we first show that not only enthalpic but also entropic effects - due to the multi-bond character of the DNA-mediated interactions - play an important role in the overall binding properties of the particles. We then outline a new strategy that exploits the competition between different types of inter-particle DNA linkages to achieve a temperature-dependent switching of the dominant bond type. Depending on the length ratio of the DNA constructs, the bond switching is either energetically driven or controlled by a combinatorial entropy gain, which arises from the large number of possible binding partners for each DNA strand. Importantly, the resulting particle interaction is less strongly temperature dependent than in ``conventional'' systems with only one bond type, thus enhancing the experimental control over self-assembly. Finally, we will also show that in general stable gas-liquid separation is expected to occur only for particles smaller than a few tens of nanometers, which suggests that nanoparticles and micrometer-sized colloids will follow different routes to crystallization.   

DNA Regulated Clusters: Structure and Self-limiting Assembly

We have investigated the structural details of nanoparticle clusters assembled by flexible DNA linkers in dimer clusters using electron microscopy, in-situ x-ray scattering and optical methods. The observed dependence of interparticle distance on a DNA length significantly deviates from the predictions for single chain linkages and previous measurements for superlattices. The observed effect is attributed to a large solid angle of interparticle contact, in agreement with computational results. Our studies further reveal the non-monotonic decrease of interparticle distance for the longer linkers; that suggests nanoparticles confinement by hybridized linkers from opposite particles' hemispheres. The effect is accompanied by inhibited development of nanoclusters and results in a self-limited cluster assembly. The mechanism of dimer formation was investigated in details using the optical methods.   

Kinetics of the Association of DNA Coated Colloids

The self-assembly of DNA coated colloidal particles opens a door to complex colloidal architecture. To understand how particles aggregate due to DNA hybridization between particles is the key to program colloidal aggregation. In this study, we investigate theoretically and experimentally the aggregation time of micron scale particles as a function of DNA coverage and the ion concentration $I$. Our particles coated with streptavidin can attach $\sim$70,000 biotinlated DNA molecules, which have a double strand with 49 base pairs and an 11 base sticky end. At $I$ = 60 mM , particles 100\% fully covered with DNA show an aggregation time of $\tau$ = 6 minutes. For 10\% DNA covered particles at $I$ = 35 mM, $\tau$ = 57 hours. A simple model based on the reaction limited aggregation and electrical repulsion for DNA hybridization is developed and tested. These experiments and the model also allow us to use the microscopic colloidal aggregation to measure nanoscopic hybridization rates.   

Phase Behavior and Magnetic Response of DNA-mediated Gold and Iron Oxide Nanoparticle Assemblies

Gold nanoparticles (NPs) have long been long served as model systems to study phase behavior of DNA-assisted NP assemblies. Incorporation of different types of nano-objects into DNA-NP systems opens attractive possibilities for the material design. Furthermore, it also allows enriching a self-assembly behavior by an introduction of non-specific yet controllable interparticle interactions. Herein, we report the DNA-mediated assembly of a heterogeneous system comprising gold and superparamagnetic iron oxide (IO) NPs. We systematically studied the phase diagram of the assembled systems by varying a system's composition, DNA design and environmental conditions. Our studies show that by controlling a balance between non-specific and DNA-recognition interactions via system design the assembled phase can be switched between a face-centered cubic (fcc) structure of a IO assembly and a superlattice formed by Au-IO core-shells clusters. We also observed that structure of assemblies is responsive to the magnetic field.   

Modeling of DNA-Directed Colloidal Self-Assembly and Crystallization

A series of design rules have recently been developed for using gold nanoparticles conjugated with a dense layer of double stranded DNA chains to assemble a wide variety of nanoparticle superlattice structures [1]. Key design parameters for obtaining different structures in a binary system were shown to be the ratio of the hydrodynamic radii of the DNA-conjugated particles, the ratio of the number of DNA strands per particle, and the self- or non-self-complementary nature of the DNA sequences guiding the assembly process. Guided by those experiments, we have built a coarse grained model that faithfully mimics relative design parameters in the experimental system. Working with nanoparticles in the size range from 8nm to 15nm, overall DNA-nanoparticle hydrodynamic radii of 10nm to 30nm, and the number of DNA strands per particle between 30 and 100, we have developed a simulation method that confirms that these design rules can be used to assemble a variety of different crystal structures. In particular, we have identified FCC, BCC, CsCl, $AlB_2$ and $Cr_3Si$ structures. With these data, we have constructed a detailed phase diagram that closely corresponds to the experimentally obtained phase diagram developed in ref. [1]. [1] R. J. Macfarlane, B. Lee, M. R. Jones, N. Harris, G.   

DNA coated rods: pure Biological materials for self assembly studies

We will present a way of coating Fd virus, a model of colloidal liquid crystal, with DNA. The DNA coating provides new interesting tunable properties to control the liquid crystalline behavior.   

Linear DNA-linked colloidal chains: a model to visualize polymer dynamics

We present the development of synthetic materials consisting of chains of DNA-linked paramagnetic colloids that have rigidity and length specificity. These chains have demonstrated capability for folding and self-assembly. This is classic bead-spring-bead model can be a model system to visualize polymer dynamics. Here, I will describe the formation mechanism and stability of these DNA-linked magnetic particle chains. I will also describe a model that describes the total energy landscape that describes the inter-particle interactions and provides a workable theory toward the optimization of experimental parameters in synthesizing more stable and reliable colloidal assemblies. In addition to stability, we will also present the use of a colloidal worm-like chain (WLC) model system to describe chain dynamics. We measure bending rigidity by monitoring the thermal fluctuations of the chains. We show that the persistence length of the chains can be tuned from 1 to 50 mm (L/LP = 0.002 - 0.1), by changing the length of the DNA used to link adjacent particles from 75 to 15 bases. We also will show that the bending relaxation dynamics of these chains, which match well with theoretical predictions, further supporting the validity of using these colloidal chains as models for semiflexible polymer systems in both equilibrium and dynamic studies.