A general strategy for the DNA-mediated self-assembly of functional nanoparticles into heterogeneous systems

MicroRNA Detection through DNAzyme-Mediated Disintegration of Magnetic Nanoparticle Assemblies

DNA-assembled nanoparticle superstructures offer numerous bioresponsive properties that can be utilized for point-of-care diagnostics. Functional DNA sequences such as deoxyribozymes (DNAzymes) provide novel bioresponsive strategies and further extend the application of DNA-assembled nanoparticle superstructures. In this work, we describe a microRNA detection biosensor that combines magnetic nanoparticle (MNP) assemblies with DNAzyme-assisted target recycling. The DNA scaffolds of the MNP assemblies contain substrate sequences for DNAzyme and can form cleavage catalytic structures in the presence of target DNA or RNA sequences, leading to rupture of the scaffolds and disintegration of the MNP assemblies. The target sequences are preserved during the cleavage reaction and release into the suspension to trigger the digestion of multiple DNA scaffolds. The high local concentration of substrate sequences in the MNP assemblies reduces the diffusion time for target recycling. The concentration of released MNPs, which is proportional to the concentration of the target, can be quantified by a 405 nm laser-based optomagnetic sensor. For the detection of let-7b in 10% serum, after 1 h of isothermal reaction at 50 °C, we found a linear detection range between 10 pM and 100 nM with a limit of detection of 6 pM. For the quantification of DNA target in buffer solution, a limit of detection of 1.5 pM was achieved. Compared to protein enzyme-based microRNA detection methods, the proposed DNAzyme-based biosensor has an increased stability, a reduced cost and a possibility to be used in living cells, all of which are valuable features for biosensing applications.

Cooperative Assembly of Asymmetric Carbonaceous Bivalve-Like Superstructures from Multiple Building Blocks

The assembly of superstructures from building blocks is of fundamental importance for engineering materials with distinct morphologies and properties, and deepening our understanding of self-assembly processes in nature. Up to now, it is still a great challenge in materials science to construct multiple-component superstructure with unprecedented architectural complexity and symmetry from molecular. Here, we demonstrate an improved one-pot hydrothermal carbonization of biomass strategy that is capable of fabricating unprecedented asymmetric carbonaceous bivalve-like superstructures with in suit generated solid particles and ordered porous polymers as two kinds of building blocks. In our system, different building blocks can be controllably generated, and they will assemble into complex superstructures through a proposed “cooperative assembly of particles and ordered porous polymers” mechanism. We believe that this assembly principle will open up new potential fields for the synthesis of superstructures with diverse morphologies, compositions, and properties.

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.

Self-Assembly of Quantum Dot-Gold Heterodimer Nanocrystals with Orientational Order

The self-assembly of nanocrystals into ordered superlattices is a powerful strategy for the production of functional nanomaterials. The assembly of well-ordered target structures, however, requires control over the building blocks' size and shape as well as their interactions. While nanocrystals with homogeneous composition are now routinely synthesized with high precision and assembled into various ordered structures, high-quality multicomponent nanocrystals and their ordered assemblies are rarely reported. In this paper, we demonstrate the synthesis of quantum dot-gold (QD-Au) heterodimers. These heterodimers possess a uniform shape and narrow size distribution and are capped with oleylamine and dodecyltrimethylammonium bromide (DTAB). Assembly of the heterodimers results in a superlattice with long-range orientational alignment of dimers. Using synchrotron-based X-ray measurements, we characterize the complex superstructure formed from the dimers. Molecular dynamics simulations of a coarse-grained model suggest that anisotropic interactions between the quantum dot and gold components of the dimer drive superlattice formation. The high degree of orientational order demonstrated in this work is a potential route to nanomaterials with useful optoelectronic properties.

Creating two self-assembly micro-environments to achieve supercrystals with dual structures using polyhedral nanoparticles

Organizing nanoparticles into supercrystals comprising multiple structures remains challenging. Here, we achieve one assembly with dual structures for Ag polyhedral building blocks, comprising truncated cubes, cuboctahedra, truncated octahedra, and octahedra. We create two micro-environments in a solvent evaporation-driven assembly system: one at the drying front and one at the air/water interface. Dynamic solvent flow concentrates the polyhedra at the drying front, generating hard particle behaviors and leading to morphology-dependent densest-packed bulk supercrystals. In addition, monolayers of nanoparticles adsorb at the air/liquid interface to minimize the air/liquid interfacial energy. Subsequent solvent evaporation gives rise to various structurally diverse dual-structure supercrystals. The topmost monolayers feature distinct open crystal structures with significantly lower packing densities than their densest-packed supercrystals. We further highlight a 3.3-fold synergistic enhancement of surface-enhanced Raman scattering efficiency arising from these dual-structure supercrystals as compared to a uniform one.

Crystals with multiple structures often perform special functions in nature, inspiring the creation of synthetic analogues. Here, the authors subject polyhedral nanoparticles to two self-assembly micro-environments to realize supercrystals with dual structures, in which the order of the surface layer differs from the bulk structure.

Covalently bonded multimers of Au25(SBut)18 as a conjugated system

Aromatic dithiol linkers were used to prepare aggregates of Au25(SR)18 clusters (SR: thiolate) via ligand exchange reactions. Fractions of different aggregate sizes were separated by size exclusion chromatography (SEC). The aggregates were characterized by UV-vis absorption spectroscopy, matrix assisted laser desorption ionization (MALDI) mass spectrometry, nuclear magnetic resonance (NMR) spectroscopy (including diffusion-ordered spectroscopy, DOSY) and small angle X-ray scattering (SAXS). At a 2 : 1 cluster : dithiol ratio, small aggregates (dimers, trimers) and also larger aggregates consisting of 10-20 Au25 clusters were formed, according to DOSY, besides unreacted (monomeric) Au25(SR)18. MALDI mass spectrometry shows signals consistent with dimers and trimers (doubly charged). The SAXS curves for the small aggregates can be well fitted by a pearl-necklace model. For the bigger aggregates the SAXS curves evidence a characteristic separation distance between the clusters within the aggregates, which is imposed by the length of the linker. The SAXS curves of these larger aggregates can be well fitted with a core-shell sphere model with a sticky hard-sphere structure factor, in agreement with closely packed aggregates. The absorption spectra of smaller aggregates resemble those of individual Au25(SR)18 clusters; however, and most importantly, the larger aggregates show completely different, less structured spectra with a new band emerging at 840 nm. We assign this drastic change in the absorption spectra and the new band to the electronic coupling between the clusters through the all aromatic linker. In accordance with this view, the aggregates formed with a linker containing methylene groups, thus breaking conjugation, do not show the band at 840 nm. By the addition of monothiols to the larger aggregates their size can be reduced through an "unlinking" reaction. This reaction also affects the band at 840 nm, which moves to higher energy when reducing the aggregate size, as would be expected within a particle in a box model. The electronic coupling between the clusters through the linker is the basis for future applications in nanoelectronics.

Luminescent Gold Nanocluster-Decorated Polymeric Hybrid Particles with Assembly-Induced Emission

Ultrasmall gold atom clusters (<2 nm in diameter) or gold nanoclusters exhibit emergent photonic properties (near-infrared absorption and emission) compared to larger plasmonic gold particles because of the significant quantization of their conduction band. Although single gold nanocluster properties and applications are being increasingly investigated, little is still known about their behavior and properties when assembled into suprastructures, and even fewer studies are investigating their use for biomedical applications. Here, a simple synthetic pathway combines gold nanoclusters with thermosensitive diblock copolymers of poly(ethylene glycol) (PEG) and poly( N-isopropylacrylamide) (PNIPAm) to form a new class of gold-polymer, micelle-forming, hybrid nanoparticle. The nanohybrids' design is uniquely centered on enabling the temperature-dependent self-assembly of gold nanoclusters into the hydrophobic cores of micelles. This nonbulk assembly not only preserves but also enhances the attractive near-infrared photonics of the gold nanoclusters by significantly increasing their native fluorescent signal. In parallel to the fundamental insights into gold nanocluster ordering and assembly, the gold-polymer nanohybrids also demonstrated great potential as fluorescent live-imaging probes in vitro. This innovative material design based on the temperature-dependent, self-assembly of gold nanoclusters within a polymeric micelle's core shows great promise toward bioassays, nanosensors, and nanomedicine.

Protein cage assembly across multiple length scales

Within the materials science community, proteins with cage-like architectures are being developed as versatile nanoscale platforms for use in protein nanotechnology. Much effort has been focused on the functionalization of protein cages with biological and non-biological moieties to bring about new properties of not only individual protein cages, but collective bulk-scale assemblies of protein cages. In this review, we report on the current understanding of protein cage assembly, both of the cages themselves from individual subunits, and the assembly of the individual protein cages into higher order structures. We start by discussing the key properties of natural protein cages (for example: size, shape and structure) followed by a review of some of the mechanisms of protein cage assembly and the factors that influence it. We then explore the current approaches for functionalizing protein cages, on the interior or exterior surfaces of the capsids. Lastly, we explore the emerging area of higher order assemblies created from individual protein cages and their potential for new and exciting collective properties.

An enzyme-free and label-free surface plasmon resonance biosensor for ultrasensitive detection of fusion gene based on DNA self-assembly hydrogel with streptavidin encapsulation

In this research, an enzyme-free and label-free surface plasmon resonance (SPR) biosensing strategy has been developed for ultrasensitive detection of fusion gene based on the heterogeneous target-triggered DNA self-assembly aptamer-based hydrogel with streptavidin (SA) encapsulation. In the presence of target, the capture probes (Cp) immobilized on the chip surface can capture the PML/RARα, forming a Cp-PML/RARα duplex. After that, the aptamer-based network hydrogel nanostructure is formed on the gold surface via target-triggered self-assembly of X shaped polymers. Subsequently, the SA can be encapsulated into hydrogel by the specific binding of SA aptamer, forming the complex with super molecular weight. Thus, the developed strategy achieves dramatic enhancement of the SPR signal. Using PML/RARα "S" subtype as model analyte, the developed biosensing method can detect target down to 45.22 fM with a wide linear range from 100 fM to 10 nM. Moreover, the high efficiency biosensing method shows excellent practical ability to identify the clinical PCR products of PML/RARα. Thus, this proposed strategy presents a powerful platform for ultrasensitive detection of fusion gene and early diagnosis and monitoring of disease.

Pt supraparticles with controllable DNA valences for programmed nanoassembly

Supraparticles are self-limiting nanoparticle ensembles with attractive properties from their unique hierarchical (primary and secondary) structures. Aiming at relieving the bottleneck of the very limited material building blocks in DNA nanotechnology, we herein demonstrate Pt-based supraparticles as catalytic materials for valence-controllable and high density DNA functionalizations toward DNA-programmed nanoassembly.

Modular Self-Assembly of Protein Cage Lattices for Multistep Catalysis

The assembly of individual molecules into hierarchical structures is a promising strategy for developing three-dimensional materials with properties arising from interaction between the individual building blocks. Virus capsids are elegant examples of biomolecular nanostructures, which are themselves hierarchically assembled from a limited number of protein subunits. Here, we demonstrate the bio-inspired modular construction of materials with two levels of hierarchy: the formation of catalytically active individual virus-like particles (VLPs) through directed self-assembly of capsid subunits with enzyme encapsulation, and the assembly of these VLP building blocks into three-dimensional arrays. The structure of the assembled arrays was successfully altered from an amorphous aggregate to an ordered structure, with a face-centered cubic lattice, by modifying the exterior surface of the VLP without changing its overall morphology, to modulate interparticle interactions. The assembly behavior and resultant lattice structure was a consequence of interparticle interaction between exterior surfaces of individual particles and thus independent of the enzyme cargos encapsulated within the VLPs. These superlattice materials, composed of two populations of enzyme-packaged VLP modules, retained the coupled catalytic activity in a two-step reaction for isobutanol synthesis. This study demonstrates a significant step toward the bottom-up fabrication of functional superlattice materials using a self-assembly process across multiple length scales and exhibits properties and function that arise from the interaction between individual building blocks.

DNA Nanotechnology-Enabled Drug Delivery Systems

Over the past decade, we have seen rapid advances in applying nanotechnology in biomedical areas including bioimaging, biodetection, and drug delivery. As an emerging field, DNA nanotechnology offers simple yet powerful design techniques for self-assembly of nanostructures with unique advantages and high potential in enhancing drug targeting and reducing drug toxicity. Various sequence programming and optimization approaches have been developed to design DNA nanostructures with precisely engineered, controllable size, shape, surface chemistry, and function. Potent anticancer drug molecules, including Doxorubicin and CpG oligonucleotides, have been successfully loaded on DNA nanostructures to increase their cell uptake efficiency. These advances have implicated the bright future of DNA nanotechnology-enabled nanomedicine. In this review, we begin with the origin of DNA nanotechnology, followed by summarizing state-of-the-art strategies for the construction of DNA nanostructures and drug payloads delivered by DNA nanovehicles. Further, we discuss the cellular fates of DNA nanostructures as well as challenges and opportunities for DNA nanostructure-based drug delivery.

On-Particle Rolling Circle Amplification-Based Core-Satellite Magnetic Superstructures for MicroRNA Detection

Benefiting from the specially tailored properties of the building blocks as well as of the scaffolds, DNA-assembled core-satellite superstructures have gained increasing interest in drug delivery, imaging, and biosensing. The load of satellites plays a vital role in core-satellite superstructures, and it determines the signal intensity in response to a biological/physical stimulation/actuation. Herein, for the first time, we utilize on-particle rolling circle amplification (RCA) to prepare rapidly responsive core-satellite magnetic superstructures with a high load of magnetic nanoparticle (MNP) satellites. Combined with duplex-specific nuclease-assisted target recycling, the proposed magnetic superstructures hold great promise in sensitive and rapid microRNA detection. The long single-stranded DNA produced by RCA serving as the scaffold of the core-satellite superstructure can be hydrolyzed by duplex-specific nuclease in the presence of target microRNA, resulting in a release of MNPs that can be quantified in an optomagnetic sensor. The proposed biosensor has a simple mix-separate-measure strategy. For let-7b detection, the proposed biosensor offers a wide linear detection range of approximately 5 orders of magnitude with a detection sensitivity of 1 fM. Moreover, it has the capability to discriminate single-nucleotide mismatches and to detect let-7b in cell extracts and serum, thus showing considerable potential for clinical applications.

Self-assembly of 3D porous architectures from energetic nanoparticles for enhanced energetic performances

3D architectures with porous network of energetic molecules were designed and constructed by introduce a general approach through two-step self-assembly process.

Nanoparticle Superlattices: The Roles of Soft Ligands

Nanoparticle superlattices are periodic arrays of nanoscale inorganic building blocks including metal nanoparticles, quantum dots and magnetic nanoparticles. Such assemblies can exhibit exciting new collective properties different from those of individual nanoparticle or corresponding bulk materials. However, fabrication of nanoparticle superlattices is nontrivial because nanoparticles are notoriously difficult to manipulate due to complex nanoscale forces among them. An effective way to manipulate these nanoscale forces is to use soft ligands, which can prevent nanoparticles from disordered aggregation, fine-tune the interparticle potential as well as program lattice structures and interparticle distances - the two key parameters governing superlattice properties. This article aims to review the up-to-date advances of superlattices from the viewpoint of soft ligands. We first describe the theories and design principles of soft-ligand-based approach and then thoroughly cover experimental techniques developed from soft ligands such as molecules, polymer and DNA. Finally, we discuss the remaining challenges and future perspectives in nanoparticle superlattices.

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.

Low-Temperature Crystal Structures of the Hard Core Square Shoulder Model

In many cases, the stability of complex structures in colloidal systems is enhanced by a competition between different length scales. Inspired by recent experiments on nanoparticles coated with polymers, we use Monte Carlo simulations to explore the types of crystal structures that can form in a simple hard-core square shoulder model that explicitly incorporates two favored distances between the particles. To this end, we combine Monte Carlo-based crystal structure finding algorithms with free energies obtained using a mean-field cell theory approach, and draw phase diagrams for two different values of the square shoulder width as a function of the density and temperature. Moreover, we map out the zero-temperature phase diagram for a broad range of shoulder widths. Our results show the stability of a rich variety of crystal phases, such as body-centered orthogonal (BCO) lattices not previously considered for the square shoulder model.

DNA Grafting and Arrangement on Oxide Surfaces for Self-Assembly of Al and CuO Nanoparticles

DNA-directed assembly of nano-objects as a means to manufacture advanced nanomaterial architectures has been the subject of many studies. However, most applications have dealt with noble metals as there are fundamental difficulties to work with other materials. In this work, we propose a generic and systematic approach for functionalizing and characterizing oxide surfaces with single-stranded DNA oligonucleotides. This protocol is applied to aluminum and copper oxide nanoparticles due to their great interest for the fabrication of highly energetic heterogeneous nanocomposites. The surface densities of streptavidin and biotinylated DNA oligonucleotides are precisely quantified combining atomic absorption spectroscopy with conventional dynamic light scattering and fluorometry and maximized to provide a basis for understanding the grafting mechanism. First, the streptavidin coverage is consistently below 20% of the total surface for both nanoparticles. Second, direct and unspecific grafting of DNA single strands onto Al and CuO nanoparticles largely dominates the overall functionalization process: ∼95% and 90% of all grafted DNA strands are chemisorbed on the CuO and Al nanoparticle surfaces, respectively. Measurements of hybridization efficiency indicate that only ∼5 and ∼10% of single-stranded oligonucleotides grafted onto the CuO and Al surfaces are involved in the hybridization process, corresponding precisely to the streptavidin coverage, as evidenced by the occupancy of 0.9 and 1.2 oligonucleotides per protein. The hybridization efficiency of single-stranded oligonucleotides chemisorbed on CuO and Al without streptavidin coating decreases to only ∼2%, justifying the use of streptavidin despite its poor surface occupancy. Finally, the structure of directly chemisorbed DNA strands onto oxide surfaces is examined and discussed.

Interfacial Self-Assembly of Polyelectrolyte-Capped Gold Nanoparticles

We report on pH- and salt-responsive assembly of nanoparticles capped with polyelectrolytes at vapor-liquid interfaces. Two types of alkylthiol-terminated poly(acrylic acid) (PAAs, varying in length) are synthesized and used to functionalize gold nanoparticles (AuNPs) to mimic similar assembly effects of single-stranded DNA-capped AuNPs using synthetic polyelectrolytes. Using surface-sensitive X-ray scattering techniques, including grazing incidence small-angle X-ray scattering (GISAXS) and X-ray reflectivity (XRR), we demonstrate that PAA-AuNPs spontaneously migrate to the vapor-liquid interfaces and form Gibbs monolayers by decreasing the pH of the suspension. The Gibbs monoalyers show chainlike structures of monoparticle thickness. The pH-induced self-assembly is attributed to the protonation of carboxyl groups and to hydrogen bonding between the neighboring PAA-AuNPs. In addition, we show that adding MgCl₂ to PAA-AuNP suspensions also induces adsorption at the interface and that the high affinity between magnesium ions and carboxyl groups leads to two- and three-dimensional clusters that yield partial surface coverage and poorer ordering of NPs at the interface. We also examine the assembly of PAA-AuNPs in the presence of a positively charged Langmuir monolayer that promotes the attraction of the negatively charged capped NPs by electrostatic forces. Our results show that synthetic polyelectrolyte-functionalized nanoparticles exhibit interfacial self-assembly behavior similar to that of DNA-functionalized nanoparticles, providing a pathway for nanoparticle assembly in general.

Interaction Heterogeneity can Favorably Impact Colloidal Crystal Nucleation

Colloidal particles with short-ranged attractions, e.g., micron-scale spheres functionalized with single-stranded DNA oligomers, are susceptible to becoming trapped in disordered configurations even when a crystalline arrangement is the ground state. Moreover, for reasons that are not well understood, seemingly minor variations in the particle formulation can lead to dramatic changes in the crystallization outcome. We demonstrate, using a combination of equilibrium and nonequilibrium computer simulations, that interaction heterogeneity-variations in the energetic interactions among different particle pairs in the population-may favorably impact crystal nucleation. Specifically, interaction heterogeneity is found to lower the free energy barrier to nucleation via the formation of clusters comprised preferentially of strong-binding particle pairs. Moreover, gelation is inhibited by "spreading out over time" the nucleation process, resulting in a reduced density of stable nuclei, allowing each to grow unhindered and larger. Our results suggest a simple and robust approach for enhancing colloidal crystallization near the "sticky sphere" limit, and support the notion that differing extents of interaction heterogeneity arising from various particle functionalization protocols may contribute to the otherwise unexplained variations in crystallization outcomes reported in the literature.

Probing Laser-Induced Heterogeneous Microenvironment Changes in Room-Temperature Ionic Liquids

Modulating the heterogeneous microenvironment in room-temperature ionic liquids (RTILs) by external stimuli is an important approach for understanding and designing external field-induced chemical reactions in natural and applied systems. Here, we report for the first time the redistribution of oxygen molecules related to microstructure changes in RTILs induced by an external laser field, which is probed simultaneously by the triplet-state dynamics of porphyrin. A remarkably long-lived triplet state of porphyrin is observed with changes of microstructures after irradiation, suggesting that charge-shifted O₂ molecules are induced by the external field and/or rearranged intrinsic ions move from nonpolar domains into the polar domains of RTILs through electrostatic interactions. The results suggest that heterogeneous systems like ionic liquids in the presence of external stimuli can be designed for reaction systems associated with not only O₂ but also for CO₂ , CS₂ , etc. and many other similar solvent molecules for many promising applications.

Coherent amplification of X-ray scattering from meso-structures

Small-angle X-ray scattering (SAXS) often includes an unwanted background, which increases the required measurement time to resolve the sample structure. This is undesirable in all experiments, and may make measurement of dynamic or radiation-sensitive samples impossible. Here, we demonstrate a new technique, applicable when the scattering signal is background-dominated, which reduces the requisite exposure time. Our method consists of exploiting coherent interference between a sample with a designed strongly scattering 'amplifier'. A modified angular correlation function is used to extract the symmetry of the interference term; that is, the scattering arising from the interference between the amplifier and the sample. This enables reconstruction of the sample's symmetry, despite the sample scattering itself being well below the intensity of background scattering. Thus, coherent amplification is used to generate a strong scattering term (well above background), from which sample scattering is inferred. We validate this method using lithographically defined test samples.

Assembly of a functional and responsive microstructure by heat bonding of DNA-grafted colloidal brick

A micromachine constructed to possess various chemical and mechanical functions is one of the ultimate targets of technology. Conventional lithographic processes can be used to form complicated structures. However, they are basically limited to rigid and static structures with poor surface properties. Here, we demonstrate a novel method for assembling responsive and functional microstructures from diverse particles modified with DNA strands. The DNA strands are designed to form hairpins at room temperature and denature when heated. Structures are assembled through the simultaneous manipulation and heating of particles with "hot" optical tweezers, which incorporates the particles one by one. The flexible connection formed by DNA strands allows the responsive deformation of the structures with local controllability of the structural flexibility. We assembled a microscopic robot arm actuated by an external magnet, a hinge structure with a locally controlled connection flexibility and a three-dimensional double helix structure. The method is simple and can also be applied to build complex biological tissues from cells.

Multiplexible Wash-Free Immunoassay Using Colloidal Assemblies of Magnetic and Photoluminescent Nanoparticles

Colloidal assemblies of nanoparticles possess both the intrinsic and collective properties of their constituent nanoparticles, which are useful in applications where ordinary nanoparticles are not well suited. Here, we report an immunoassay technique based on colloidal nanoparticle assemblies made of iron oxide nanoparticles (magnetic substrate) and manganese-doped zinc sulfide (ZnS:Mn) nanoparticles (photoluminescent substrate), both of which are functionalized with antibodies to capture target proteins in a sandwich assay format. After magnetic isolation of the iron oxide nanoparticle assemblies and their bound ZnS:Mn nanoparticle assemblies (MZSNAs), photoluminescence of the remaining MZSNAs is measured for the protein quantification, eliminating the need for washing steps and signal amplification. Using human C-reactive protein as a model biomarker, we achieve a detection limit of as low as 0.7 pg/mL, which is more than 1 order of magnitude lower than that of enzyme-linked immunosorbent assay (9.1 pg/mL) performed using the same pair of antibodies, while using only one-tenth of the antibodies. We also confirm the potential for multiplex detection by using two different types of photoluminescent colloidal nanoparticle assemblies simultaneously.

Altering DNA-Programmable Colloidal Crystallization Paths by Modulating Particle Repulsion

Colloidal crystal engineering with DNA can be used to realize precise control over nanoparticle (NP) arrangement. Here, we investigate a case of DNA-based assembly where the properties of DNA as a polyelectrolyte brush are employed to alter a hybridization-driven NP crystallization pathway. Using the coassembly of DNA-conjugated proteins and spherical gold nanoparticles (AuNPs) as a model system, we explore how steric repulsion between noncomplementary, neighboring NPs due to overlapping DNA shells can influence their ligand-directed behavior. Specifically, our experimental data coupled with coarse-grained molecular dynamics (MD) simulations reveal that, by changing factors related to NP repulsion, two structurally distinct outcomes can be achieved. When steric repulsion between DNA-AuNPs is significantly greater than that between DNA-proteins, a lower packing density crystal lattice is favored over the structure that is predicted by design rules based on DNA hybridization considerations alone. This is enabled by the large difference in DNA density on AuNPs versus proteins and can be tuned by modulating the flexibility, and thus conformational entropy, of the DNA on the constituent particles. At intermediate ligand flexibility, the crystallization pathways are energetically similar, and the structural outcome can be adjusted using the density of DNA duplexes on DNA-AuNPs and by screening the Coulomb potential between them. Such lattices are shown to undergo dynamic reorganization upon changing the salt concentration. These data help elucidate the structural considerations necessary for understanding repulsive forces in DNA-mediated assembly and lay the groundwork for using them to increase architectural diversity in engineering colloidal crystals.

Oriented assembly of anisotropic nanoparticles into frame-like superstructures

It is fascinating but challenging for nanoscientists to organize nanoparticles (NPs) into ordered architectures just as it is for chemists to manipulate atoms and molecules to form functional molecules and supramolecules. We explore a strategy to assemble anisotropic NPs into open frame-like superstructures via oriented attachment (OA), experimentally realizing a nanoscale analog to the bonding behavior in M₈L₁₂-type supramolecular cubes. We highlight the role of NP shape in the OA-involved assembly for constructing predictable superstructures. In addition, the frame-like superstructures can retain their basic structure when undergoing postcrystallization of the building blocks as well as annealing for conversion toward functional electrocatalytic materials. Our work enables fundamental insights into directional "bonding" among NPs and adds to the growing body of knowledge for bottom-up assembly of anisotropic NPs into sophisticated functional materials.

Supra-Nanoparticle Functional Assemblies through Programmable Stacking

The quest for the by-design assembly of material and devices from nanoscale inorganic components is well recognized. Conventional self-assembly is often limited in its ability to control material morphology and structure simultaneously. Here, we report a general method of assembling nanoparticles in a linear "pillar" morphology with regulated internal configurations. Our approach is inspired by supramolecular systems, where intermolecular stacking guides the assembly process to form diverse linear morphologies. Programmable stacking interactions were realized through incorporation of DNA coded recognition between the designed planar nanoparticle clusters. This resulted in the formation of multilayered pillar architectures with a well-defined internal nanoparticle organization. By controlling the number, position, size, and composition of the nanoparticles in each layer, a broad range of nanoparticle pillars were assembled and characterized in detail. In addition, we demonstrated the utility of this stacking assembly strategy for investigating plasmonic and electrical transport properties.

Target guided synthesis using DNA nano-templates for selectively assembling a G-quadruplex binding c-MYC inhibitor

The development of small molecules is essential to modulate the cellular functions of biological targets in living system. Target Guided Synthesis (TGS) approaches have been used for the identification of potent small molecules for biological targets. We herein demonstrate an innovative example of TGS using DNA nano-templates that promote Huisgen cycloaddition from an array of azide and alkyne fragments. A G-quadruplex and a control duplex DNA nano-template have been prepared by assembling the DNA structures on gold-coated magnetic nanoparticles. The DNA nano-templates facilitate the regioselective formation of 1,4-substituted triazole products, which are easily isolated by magnetic decantation. The G-quadruplex nano-template can be easily recovered and reused for five reaction cycles. The major triazole product, generated by the G-quadruplex inhibits c-MYC expression by directly targeting the c-MYC promoter G-quadruplex. This work highlights that the nano-TGS approach may serve as a valuable strategy to generate target-selective ligands for drug discovery.

Identification of inhibitors can be accelerated by using the target as a template for ligand formation. Here the authors show that DNA-functionalised magnetic nanoparticles guide templating of G-quadruplex binding c-MYC inhibitors from an array of building blocks, and can be isolated by magnetic decanting.

Structure and Dynamics of a N-Methylfulleropyrrolidine-Mediated Gold Nanocomposite: A Spectroscopic Ruler

A mechanistic understanding of the structure and dynamics of a chemically tunable N-methylfulleropyrrolidine (8-NMFP)-assisted gold nanocomposite and its aggregation via a controllable interparticle interaction is reported as a function of the molar ratio and pH of the medium. Electronic structure calculations adopting density functional theory methods implied electrostatic interactions to play a dominant role between 8-NMFP and citrate-capped gold nanoparticles. MM⁺ molecular mechanics force field computations revealed intermolecular gold-gold interactions, contributing toward the formation of spherical composite aggregates. Corroborating these, optical absorption spectra showed the usual surface plasmon band along with a higher-wavelength feature at ∼600-650 nm, indicative of the aggregated nanocomposite. pH-controlled reversible tuning of the plasmonic features in the composite was evident in a pH interval ∼5-6.8, revealing prevalent interparticle electrostatic interactions. In addition, photoluminescence (PL) and time-correlated single-photon counting studies revealed a strong nanocomposite interaction with a pure fluorescent dye, Rhodamine B, indicating excitation energy transfer from the dye to the composite. The dye upon interaction with the nanocomposite showed a significant quenching of its PL intensity and shortening of lifetime. Energy coupling between the metal nanoparticle composite and the emitting molecular dipole resulted in a long-range surface energy transfer (SET) from the donor dye to the surface plasmon modes of the nanoparticle following a donor-acceptor distance dependence of 1/r⁴. This molecular beacon with correlation between the nanoscale structure and the nonradiative nanometal SET can be used as a spectroscopic/molecular ruler in probing advanced functional materials.

Assembling and ordering polymer-grafted nanoparticles in three dimensions

Taking advantage of the aqueous biphasic behavior of polyethylene glycol (PEG)/salts, recent experiments have demonstrated self-assembly and crystallization of PEG-grafted gold nanoparticles (PEG-AuNPs) into tunable two-dimensional (2D) supercrystals by adjusting salt concentration (for instance, K₂CO₃). In those studies, combined experimental evidence and theoretical analysis have pointed out the possibility that similar strategies can lead to three-dimensional (3D) formation of ordered nanoparticle precipitates. Indeed, a detailed small-angle X-ray scattering (SAXS) study reported herein reveals the spontaneous formation of PEG-AuNPs assemblies in high-concentration salt solutions that exhibit short-range 3D order compatible with fcc symmetry. We argue that the assembly into fcc crystals is driven by partnering nearest-neighbors to minimize an effective surface-tension gradient at the boundary between the polymer shell and the high-salt media. We report SAXS and other results on PEG-AuNPs of various Au core diameters in the range of 10 to 50 nm and analyze them in the framework of brush-polymer theory revealing a systematic prediction of the nearest-neighbor distance in the 3D assemblies.

pH-Responsive Coassembly of Oligo(ethylene glycol)-Coated Gold Nanoparticles with External Anionic Polymers via Hydrogen Bonding

Stimuli-responsive assembly of gold nanoparticles (AuNPs) with precise control of the plasmonic properties, assembly size, and stimuli responsivity has shown potential benefits with regard to biosensing devices and drug-delivery systems. Here we present a new pH-responsive coassembly system of oligo(ethylene glycol) (OEG)-coated AuNPs with anionic polymers as an external mediator via hydrogen bonding in water. Hydrogen-bond-driven coassemblies of OEG-AuNPs with poly(acrylic acid) (PAA) were confirmed by the monitoring of plasmonic peaks and hydrodynamic diameters. In this system, the protonation of anionic polymers on change in pH triggered the formation of hydrogen bond between the OEG-AuNPs and polymers, providing sensitive pH responsivity. The plasmonic properties and assembly size are affected by both the ratio of PAA to AuNPs and the molecular weight of PAAs. In addition, the attachment of hydrophobic groups to the surface ligand or anionic polymer changed the responsive pH range. These results demonstrated that the coassembly with an external mediator via hydrogen bonding provides a stimuli-responsive assembly system with tunable plasmonic properties, assembly size, and stimuli responsivity.

Self-Assembly of Complex Multimetal Nanostructures from Perforated Lamellar Block Copolymer Thin Films

We introduce a facile and effective fabrication of complex multimetallic nanostructures through block copolymer self-assembly. Two- and three-dimensional complex nanostructures, such as "nanomesh," "double-layered nanomeshes," and "surface parallel cylinders on nanomesh," can be fabricated using the self-assembly of perforated lamellar morphology in block copolymer thin films. Simultaneous integration of various metallic elements, including Pt, Au, and Co, into the self-assembled morphologies generates multimetal complex nanostructures with highly interconnected morphology and a large surface. The resultant metal nanostructures with a large surface area, robust electrical connectivity, and well-defined alloy composition demonstrate a high-performance electrochemical catalysis for hydrogen evolution reaction (current density: 6.27 mA/cm²@0.1 V and Tafel slope: 43 mV/dec).

Robust X-ray angular correlations for the study of meso-structures

As self-assembling nanomaterials become more sophisticated, it is becoming increasingly important to measure the structural order of finite-sized assemblies of nano-objects. These mesoscale clusters represent an acute challenge to conventional structural probes, owing to the range of implicated size scales (10 nm to several micrometres), the weak scattering signal and the dynamic nature of meso-clusters in native solution environments. The high X-ray flux and coherence of modern synchrotrons present an opportunity to extract structural information from these challenging systems, but conventional ensemble X-ray scattering averages out crucial information about local particle configurations. Conversely, a single meso-cluster scatters too weakly to recover the full diffraction pattern. Using X-ray angular cross-correlation analysis, it is possible to combine multiple noisy measurements to obtain robust structural information. This paper explores the key theoretical limits and experimental challenges that constrain the application of these methods to probing structural order in real nanomaterials. A metric is presented to quantify the signal-to-noise ratio of angular correlations, and it is used to identify several experimental artifacts that arise. In particular, it is found that background scattering, data masking and inter-cluster interference profoundly affect the quality of correlation analyses. A robust workflow is demonstrated for mitigating these effects and extracting reliable angular correlations from realistic experimental data.

Polarization-Dependent Optical Response in Anisotropic Nanoparticle-DNA Superlattices

DNA-programmable assembly has been used to prepare superlattices composed of octahedral and spherical nanoparticles, respectively. These superlattices have the same body-centered cubic lattice symmetry and macroscopic rhombic dodecahedron crystal habit but tunable lattice parameters by virtue of the DNA length, allowing one to study and determine the effect of nanoscale structure and lattice parameter on the light-matter interactions in the superlattices. Backscattering measurements and finite-difference time-domain simulations have been used to characterize these two classes of superlattices. Superlattices composed of octahedral nanoparticles exhibit polarization-dependent backscattering but via a trend that is opposite to that observed in the polarization dependence for analogous superlattices composed of spherical nanoparticles. Electrodynamics simulations show that this polarization dependence is mainly due to the anisotropy of the nanoparticles and is observed only if the octahedral nanoparticles are well-aligned within the superlattices. Both plasmonic and photonic modes are identified in such structures, both of which can be tuned by controlling the size and shape of the nanoparticle building blocks, the lattice parameters, and the overall size of the three-dimensional superlattices (without changing habit).

Epitaxy: Programmable Atom Equivalents Versus Atoms

The programmability of DNA makes it an attractive structure-directing ligand for the assembly of nanoparticle (NP) superlattices in a manner that mimics many aspects of atomic crystallization. However, the synthesis of multilayer single crystals of defined size remains a challenge. Though previous studies considered lattice mismatch as the major limiting factor for multilayer assembly, thin film growth depends on many interlinked variables. Here, a more comprehensive approach is taken to study fundamental elements, such as the growth temperature and the thermodynamics of interfacial energetics, to achieve epitaxial growth of NP thin films. Both surface morphology and internal thin film structure are examined to provide an understanding of particle attachment and reorganization during growth. Under equilibrium conditions, single crystalline, multilayer thin films can be synthesized over 500 × 500 μm² areas on lithographically patterned templates, whereas deposition under kinetic conditions leads to the rapid growth of glassy films. Importantly, these superlattices follow the same patterns of crystal growth demonstrated in atomic thin film deposition, allowing these processes to be understood in the context of well-studied atomic epitaxy and enabling a nanoscale model to study fundamental crystallization processes. Through understanding the role of epitaxy as a driving force for NP assembly, we are able to realize 3D architectures of arbitrary domain geometry and size.

Macroscopic and tunable nanoparticle superlattices

We describe a robust method to assemble nanoparticles into highly ordered superlattices by inducing aqueous phase separation of neutral capping polymers. Here we demonstrate the approach with thiolated polyethylene-glycol-functionalized gold nanoparticles (PEG-AuNPs) in the presence of salts (for example, K₂CO₃) in solutions that spontaneously migrate to the liquid-vapor interface to form a Gibbs monolayer. We show that by increasing salt concentration, PEG-AuNP monolayers transform from two-dimensional (2D) gas-like to liquid-like phase and eventually, beyond a threshold concentration, to a highly ordered hexagonal structure, as characterized by surface sensitive synchrotron X-ray reflectivity and grazing incidence X-ray diffraction. Furthermore, the method allows control of the inplane packing in the crystalline phase by varying the K₂CO₃ and PEG-AuNPs concentrations and the length of PEG. Using polymer-brush theory, we argue that the assembly and crystallization is driven by the need to reduce surface tension between PEG and the salt solution. Our approach of taking advantage of the phase separation of PEG in salt solutions is general (i.e., can be used with any nanoparticles) leads to high-quality macroscopic and tunable crystals. Finally, we discuss how the method can also be applied to the design of orderly 3D structures.

DNA Functionalization of Nanoparticles

DNA-nanoparticle conjugates are hybrid nanoscale objects that integrate different types of DNA molecules and inorganic nanoparticles with a typical architecture of a DNA shell around an inorganic core. Such incorporation provides particles with unique properties of DNA, addressability and recognition, but, at the same time, allows exploiting the properties of the particle's inorganic core. Thus, these hybrid nano-objects are advantageous for rational fabrication of functional materials and for biomedical applications. Here, we describe several established DNA functionalization procedures for different types of surface ligands and nanoparticle core materials.

Colloidal Cluster Assembly into Ordered Superstructures via Engineered Directional Binding

Recent experimental studies have demonstrated a facile route for fabricating large numbers of geometrically uniform colloidal clusters out of submicron DNA-functionalized spheres. These clusters are ideally suited for use as anisotropic building blocks for hierarchical assembly of superstructures with symmetries that are otherwise inaccessible with simple spherical particles. We study computationally the self-assembly of cubic, tetrahedral, and octahedral clusters mediated by "bond spheres" that dock with the clusters at specific preferential sites, providing robust and well-defined directional bonding. We analyze the assembly process with a combination of direct molecular dynamics simulations of superstructure growth and state-of-the-art umbrella sampling techniques to compute nucleation free energy profiles. The simulations confirm the versatility and robustness of hierarchical cluster assembly but also reveal potential obstacles in the form of energetically accessible defect states. We find and study solutions for bypassing these defects that rely on appropriate selection of particle size and interparticle interaction as a function of building block shape and, therefore, provide operational guidelines for future experimental demonstrations.

Modular assembly of superstructures from polyphenol-functionalized building blocks

The organized assembly of particles into superstructures is typically governed by specific molecular interactions or external directing factors associated with the particle building blocks, both of which are particle-dependent. These superstructures are of interest to a variety of fields because of their distinct mechanical, electronic, magnetic and optical properties. Here, we establish a facile route to a diverse range of superstructures based on the polyphenol surface-functionalization of micro- and nanoparticles, nanowires, nanosheets, nanocubes and even cells. This strategy can be used to access a large number of modularly assembled superstructures, including core-satellite, hollow and hierarchically organized supraparticles. Colloidal-probe atomic force microscopy and molecular dynamics simulations provide detailed insights into the role of surface functionalization and how this facilitates superstructure construction. Our work provides a platform for the rapid generation of superstructured assemblies across a wide range of length scales, from nanometres to centimetres.

Magneto-Optical Response of Cobalt Interacting with Plasmonic Nanoparticle Superlattices

The magneto-optical Kerr effect is a striking phenomenon whereby the optical properties of a material change under an applied magnetic field. Though promising for sensing and data storage technology, these properties are typically weak in magnitude and are inherently limited by the bulk properties of the active magnetic material. In this work, we theoretically demonstrate that plasmonic thin-film assemblies on a cobalt substrate can achieve tunable transverse magneto-optical (TMOKE) responses throughout the visible and near-infrared (300-900 nm). In addition to exhibiting wide spectral tunability, this response can be varied in sign and magnitude by changing the plasmonic volume fraction (1-20%), the composition and arrangement of the assembly, and the shape of the nanoparticle inclusions. Of particular interest is the newly discovered sensitivity of the sign and intensity of the TMOKE spectrum to collective metallic plasmonic behavior in silver, mixed silver-gold, and anisotropic superlattices.

Controlling DNA-nanoparticle serum interactions

Understanding the interaction of molecularly assembled nanoparticles with physiological fluids is critical to their use for in vivo delivery of drugs and contrast agents. Here, we systematically investigated the factors and mechanisms that govern the degradation of DNA on the nanoparticle surface in serum. We discovered that a higher DNA density, shorter oligonucleotides, and thicker PEG layer increased protection of DNA against serum degradation. Oligonucleotides on the surface of nanoparticles were highly resistant to DNase I endonucleases, and degradation was carried out exclusively by protein-mediated exonuclease cleavage and full-strand desorption. These results enabled the programming of the degradation rates of the DNA-assembled nanoparticle system from 0.1 to 0.7 h^-1 and the engineering of superstructures that can release two different preloaded dye molecules with distinct kinetics and half-lives ranging from 3.3 to 9.8 h. This study provides a general framework for investigating the serum stability of DNA-containing nanostructures. The results advance our understanding of engineering principles for designing nanoparticle assemblies with controlled in vivo behavior and present a strategy for storage and multistage release of drugs and contrast agents that can facilitate the diagnosis and treatment of cancer and other diseases.

DNA-Mediated Self-Organization of Polymeric Nanocompartments Leads to Interconnected Artificial Organelles

Self-organization of nanocomponents was mainly focused on solid nanoparticles, quantum dots, or liposomes to generate complex architectures with specific properties, but intrinsically limited or not developed enough, to mimic sophisticated structures with biological functions in cells. Here, we present a biomimetic strategy to self-organize synthetic nanocompartments (polymersomes) into clusters with controlled properties and topology by exploiting DNA hybridization to interconnect polymersomes. Molecular and external factors affecting the self-organization served to design clusters mimicking the connection of natural organelles: fine-tune of the distance between tethered polymersomes, different topologies, no fusion of clustered polymersomes, and no aggregation. Unexpected, extended DNA bridges that result from migration of the DNA strands inside the thick polymer membrane (about 12 nm) represent a key stability and control factor, not yet exploited for other synthetic nano-object networks. The replacement of the empty polymersomes with artificial organelles, already reported for single polymersome architecture, will provide an excellent platform for the development of artificial systems mimicking natural organelles or cells and represents a fundamental step in the engineering of molecular factories.

Tuning the Drug Loading and Release of DNA-Assembled Gold-Nanorod Superstructures

The use of DNA to assemble inorganic nanoparticles into superstructures is an emerging strategy to build non-toxic delivery vehicles for targeting diseases in the body. The impact of the core-satellite nanosystem design in mediating drug storage, drug release (via heat), and killing of HeLa cells in culture is investigated.