Valence-programmable nanoparticle architectures

Octo-diamond crystal of nanoscale tetrahedra with interchanging chiral motifs

Despite their simplicity, tetrahedra can assemble into diverse high- and low-density structures. Here we report a low-density 'octo-diamond' structure formed by nanoscale solid tetrahedra with a 64-tetrahedron unit cell containing 8 cubic-diamond subcells. The formed crystal is achiral, but is composed of chiral bilayers with alternating handedness. The left- and right-handed chirality of the bilayers, combined with the plasmonic nature of the gold tetrahedra, produces chiroptical responses at the crystal surface. We uncover that the hydrophobic substrate facilitates the arrangement of tetrahedra into irregular ring-like patterns, creating a critical, uneven topography to stabilize the observed octo-diamond structure. This study reveals a potent way to affect colloidal crystallization through particle-substrate interactions, expanding the nanoparticle self-assembly toolbox.

Nucleic Acid Framework-Enabled Spatial Organization for Biological Applications

Nucleic acid frameworks (NAFs) are artificially prepared from natural nucleic acids with a precise size and structure. DNA origami exhibits controllable 2D lamellar structure and thus is easily used to construct 3D structures with different morphologies. Tetrahedral DNA nanostructures (TDNs) are prepared with four DNA strands that hybridize to each other with a tetrahedral structure. Here we summarize molecular spatial organization with DNA origami and TDNs as models for 2D- and 3D-recombinations, discuss NAF-based biomimicking of proteins and biomembranes, and introduce the identification probes, functional groups, and intercalators for biosensing, bioimaging, and nanomedicine therapy. NAFs are also extended to applications to guide the formation of inorganic nanoparticles with precise size and structure. Thus, the NAFs exhibit special organization, are easy to functionalize, and are becoming an important platform for interdisciplinary study and applications, such as nanotechnology, biochemistry, synthetic biology, and nanomedicine.

Engineering Anisotropy into Organized Nanoscale Matter

Programming the organization of discrete building blocks into periodic and quasi-periodic arrays is challenging. Methods for organizing materials are particularly important at the nanoscale, where the time required for organization processes is practically manageable in experiments, and the resulting structures are of interest for applications spanning catalysis, optics, and plasmonics. While the assembly of isotropic nanoscale objects has been extensively studied and described by empirical design rules, recent synthetic advances have allowed anisotropy to be programmed into macroscopic assemblies made from nanoscale building blocks, opening new opportunities to engineer periodic materials and even quasicrystals with unnatural properties. In this review, we define guidelines for leveraging anisotropy of individual building blocks to direct the organization of nanoscale matter. First, the nature and spatial distribution of local interactions are considered and three design rules that guide particle organization are derived. Subsequently, recent examples from the literature are examined in the context of these design rules. Within the discussion of each rule, we delineate the examples according to the dimensionality (0D-3D) of the building blocks. Finally, we use geometric considerations to propose a general inverse design-based construction strategy that will enable the engineering of colloidal crystals with unprecedented structural control.

Symmetry-Guided Inverse Design of Self-Assembling Multiscale DNA Origami Tilings

Recent advances enable the creation of nanoscale building blocks with complex geometries and interaction specificities for self-assembly. This nearly boundless design space necessitates design principles for defining the mutual interactions between multiple particle species to target a user-specified complex structure or pattern. In this article, we develop a symmetry-based method to generate the interaction matrices that specify the assembly of two-dimensional tilings, which we illustrate using equilateral triangles. By exploiting the allowed 2D symmetries, we develop an algorithmic approach by which any periodic 2D tiling can be generated from an arbitrarily large number of subunit species, notably addressing an unmet challenge of engineering 2D crystals with periodicities that can be arbitrarily larger than the subunit size. To demonstrate the utility of our design approach, we encode specific interactions between triangular subunits synthesized by DNA origami and show that we can guide their self-assembly into tilings with a wide variety of symmetries, using up to 12 unique species of triangles. By conjugating specific triangles with gold nanoparticles, we fabricate gold-nanoparticle supracrystals whose lattice parameter spans up to 300 nm. Finally, to generate economical design rules, we compare the design economy of various tilings. In particular, we show that (1) higher symmetries allow assembly of larger unit cells with fewer subunits and (2) linear supracrystals can be designed more economically using linear primitive unit cells. This work provides a simple algorithmic approach to designing periodic assemblies, aiding in the multiscale assembly of supracrystals of nanostructured "meta-atoms" with engineered plasmonic functions.

Economical routes to size-specific assembly of self-closing structures

Programmable self-assembly has seen an explosion in the diversity of synthetic crystalline materials, but developing strategies that target "self-limiting" assemblies has remained a challenge. Among these, self-closing structures, in which the local curvature defines the finite global size, are prone to polymorphism due to thermal bending fluctuations, a problem that worsens with increasing target size. Here, we show that assembly complexity can be used to eliminate this source of polymorphism in the assembly of tubules. Using many distinct components, we prune the local density of off-target geometries, increasing the selectivity of the tubule width and helicity to nearly 100%. We further show that by reducing the design constraints to target either the pitch or the width alone, fewer components are needed to reach complete selectivity. Combining experiments with theory, we reveal an economical limit, which determines the minimum number of components required to create arbitrary assembly sizes with full selectivity.

Nanocrystal Assemblies: Current Advances and Open Problems

We explore the potential of nanocrystals (a term used equivalently to nanoparticles) as building blocks for nanomaterials, and the current advances and open challenges for fundamental science developments and applications. Nanocrystal assemblies are inherently multiscale, and the generation of revolutionary material properties requires a precise understanding of the relationship between structure and function, the former being determined by classical effects and the latter often by quantum effects. With an emphasis on theory and computation, we discuss challenges that hamper current assembly strategies and to what extent nanocrystal assemblies represent thermodynamic equilibrium or kinetically trapped metastable states. We also examine dynamic effects and optimization of assembly protocols. Finally, we discuss promising material functions and examples of their realization with nanocrystal assemblies.

Catalytic Gold Nanoparticle Assembly Programmed by DNAzyme Circuits

Assembled gold nanoparticle (AuNP) superstructures can generate unique physicochemical characteristics and be used in various applications, thus becoming an attractive research field. Recently, several DNA-assisted gold nanoparticle assembly methods have been rigorously developed that typically require a non-catalytic equimolar molecular assembly to guarantee the designed assembly. Although efficient and accurate, exploring such non-catalytic nanoparticle assemblies in the complex cellular milieu under low trigger concentrations remains challenging. Therefore, developing a catalytic method that facilitates gold nanoparticle assemblies with relatively low DNA trigger concentrations is desirable. In this report, a catalytic method to program gold nanoparticle assemblies by DNAzyme circuits is presented, where only a small number of DNA triggers are able to induce the production of a large number of the desired nanoparticle assemblies. The feasibility of using logic DNAzyme circuits to control catalytic nanoparticle assemblies is experimentally verified. Additionally, catalytic AuNP assembly systems are established with cascading and feedback functions. The work provides an alternative research direction to enrich the tool library of nanoparticle assembly and their application in biosensing and nanomedicine.

A Spatially Programmable DNA Nanorobot Arm to Modulate Anisotropic Gold Nanoparticle Assembly by Enzymatic Excision

Programmable assembly of gold nanoparticle superstructures with precise spatial arrangement has drawn much attention for their unique characteristics in plasmonics and biomedicine. Bio-inspired methods have already provided programmable, molecular approaches to direct AuNP assemblies using biopolymers. The existing methods, however, predominantly use DNA as scaffolds to directly guide the AuNP interactions to produce intended superstructures. New paradigms for regulating AuNP assembly will greatly enrich the toolbox for DNA-directed AuNP manipulation and fabrication. Here, we developed a strategy of using a spatially programmable enzymatic nanorobot arm to modulate anisotropic DNA surface modifications and assembly of AuNPs. Through spatial controls of the proximity of the reactants, the locations of the modifications were precisely regulated. We demonstrated the control of the modifications on a single 15 nm AuNP, as well as on a rectangular DNA origami platform, to direct unique anisotropic AuNP assemblies. This method adds an alternative enzymatic manipulation to DNA-directed AuNP superstructure assembly.

Symmetry-specific characterization of bond orientation order in DNA-assembled nanoparticle lattices

Bond-orientational order in DNA-assembled nanoparticles lattices is explored with the help of recently introduced Symmetry-specific Bond Order Parameters (SymBOPs). This approach provides a more sensitive analysis of local order than traditional scalar BOPs, facilitating the identification of coherent domains at the single bond level. The present study expands the method initially developed for assemblies of anisotropic particles to the isotropic ones or cases where particle orientation information is unavailable. The SymBOP analysis was applied to experiments on DNA-frame-based assembly of nanoparticle lattices. It proved highly sensitive in identifying coherent crystalline domains with different orientations, as well as detecting topological defects, such as dislocations. Furthermore, the analysis distinguishes individual sublattices within a single crystalline domain, such as pair of interpenetrating FCC lattices within a cubic diamond. The results underscore the versatility and robustness of SymBOPs in characterizing ordering phenomena, making them valuable tools for investigating structural properties in various systems.

Controlling the Self-Assembly of DNA Origami Octahedra via Manipulation of Inter-Vertex Interactions

Recent studies have demonstrated novel strategies for the organization of nanomaterials into three-dimensional (3D) ordered arrays with prescribed lattice symmetries using DNA-based self-assembly strategies. In one approach, the nanomaterial is sequestered into DNA origami frames or "material voxels" and then coordinated into ordered arrays based on the voxel geometry and the corresponding directional interactions based on its valency. While the lattice symmetry is defined by the valency of the bonds, a larger-scale morphological development is affected by assembly processes and differences in energies of anisotropic bonds. To facilely model this assembly process, we investigate the self-assembly behavior of hard particles with six interacting vertices via theory and Monte Carlo simulations and exploration of corresponding experimental systems. We demonstrate that assemblies with different 3D crystalline morphologies but the same lattice symmetry can be formed depending on the relative strength of vertex-to-vertex interactions in orthogonal directions. We observed three distinct assembly morphologies for such systems: cube-like, sheet-like, and cylinder-like. A simple analytical theory inspired by well-established ideas in the areas of protein crystallization, based on calculating the second virial coefficient of patchy hard spheres, captures the simulation results and thus represents a straightforward means of modeling this self-assembly process. To complement the theory and simulations, experimental studies were performed to investigate the assembly of octahedral DNA origami frames with varying binding energies at their vertices. X-ray scattering confirms the robustness of the formed nanoscale lattices for different binding energies, while both optical and electron microscopy imaging validated the theoretical predictions on the dependence of the distinct morphologies of assembled state on the interaction strengths in the three orthogonal directions.

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.

Chemical and Physical Properties of Photonic Noble-Metal Nanomaterials

Colloidal noble metal nanoparticles (NPs) are composed of metal cores and organic or inorganic ligand shells. These NPs support size- and shape-dependent plasmonic resonances. They can be assembled from dispersions into artificial metamolecules which have collective plasmonic resonances originating from coupled bright and dark optical electric and magnetic modes that form depending on the size and shape of the constituent NPs and their number, arrangement, and interparticle distance. NPs can also be assembled into extended 2D and 3D metamaterials that are glassy thin films or ordered thin films or crystals, also known as superlattices and supercrystals. The metamaterials have tunable optical properties that depend on the size, shape, and composition of the NPs, and on the number of NP layers and their interparticle distance. Interestingly, strong light-matter interactions in superlattices form plasmon polaritons. Tunable interparticle distances allow designer materials with dielectric functions tailorable from that characteristic of an insulator to that of a metal, and serve as strong optical absorbers or scatterers, respectively. In combination with lithography techniques, these extended assemblies can be patterned to create subwavelength NP superstructures and form large-area 2D and 3D metamaterials that manipulate the amplitude, phase, and polarization of transmitted or reflected light.

DNA-Driven Dynamic Assembly/Disassembly of Inorganic Nanocrystals for Biomedical Imaging

DNA-mediated programming is emerging as an effective technology that enables controlled dynamic assembly/disassembly of inorganic nanocrystals (NC) with precise numbers and spatial locations for biomedical imaging applications. In this review, we will begin with a brief overview of the rules of NC dynamic assembly driven by DNA ligands, and the research progress on the relationship between NC assembly modes and their biomedical imaging performance. Then, we will give examples on how the driven program is designed by different interactions through the configuration switching of DNA-NC conjugates for biomedical applications. Finally, we will conclude with the current challenges and future perspectives of this emerging field. Hopefully, this review will deepen our knowledge on the DNA-guided precise assembly of NCs, which may further inspire the future development of smart chemical imaging devices and high-performance biomedical imaging probes.

Role of Strong Localized vs Weak Distributed Interactions in Disordered Protein Phase Separation

Interaction strength and localization are critical parameters controlling the single-chain and condensed-state properties of intrinsically disordered proteins (IDPs). Here, we decipher these relationships using coarse-grained heteropolymers comprised of hydrophobic (H) and polar (P) monomers as model IDPs. We systematically vary the fraction of P monomers XP and employ two distinct particle-based models that include either strong localized attractions between only H-H pairs (HP model) or weak distributed attractions between both H-H and H-P pairs (HP+ model). To compare different sequences and models, we first carefully tune the attraction strength for all sequences to match the single-chain radius of gyration. Interestingly, we find that this procedure produces similar conformational ensembles, nonbonded potential energies, and chain-level dynamics for single chains of almost all sequences in both models, with some deviations for the HP model at large XP. However, we observe a surprisingly rich phase behavior for the sequences in both models that deviates from the expectation that similarity at the single-chain level will translate to a similar phase-separation propensity. Coexistence between dilute and dense phases is only observed up to a model-dependent XP, despite the presence of favorable interchain interactions, which we quantify using the second virial coefficient. Instead, the limited number of attractive sites (H monomers) leads to the self-assembly of finite-sized clusters of different sizes depending on XP. Our findings strongly suggest that models with distributed interactions favor the formation of liquid-like condensates over a much larger range of sequence compositions compared to models with localized interactions.

Molecular Engineering of Colloidal Atoms

Creation of architectures with exquisite hierarchies actuates the germination of revolutionized functions and applications across a wide range of fields. Hierarchical self-assembly of colloidal particles holds the promise for materialized realization of structural programing and customizing. This review outlines the general approaches to organize atom-like micro- and nanoparticles into prescribed colloidal analogs of molecules by exploiting diverse interparticle driving motifs involving confining templates, interactive surface ligands, and flexible shape/surface anisotropy. Furthermore, the self-regulated/adaptive co-assembly of simple unvarnished building blocks is discussed to inspire new designs of colloidal assembly strategies.

DNA-Patched Nanoparticles for the Self-Assembly of Colloidal Metamaterials

Colloidal metamaterials are highly desired artificial materials that recapitulate the structure of simple molecules. They exhibit exceptional functionalities conferred by the organization of and specific interaction among constituent elements. Harvesting such exquisite attributes for potential applications necessitates establishing precise control over their structural configuration with high precision. Yet, creating molecule-like small clusters of colloidal metamaterials remains profoundly challenging, as a lack of regioselectively encoded surface chemical heterogeneity prevents specific recognition interactions. Herein, we report a new strategy by harnessing magnetic-bead-assisted DNA cluster transferring to create discretely DNA cluster-patched nanoparticles for the self-assembly of colloidal metamaterials. This strategy affords broad generalizability and scalability for robustly patching DNA clusters on nanoparticles unconstrained by geometrical, dimensional, and compositional complexities commonly encountered in colloidal materials at the nano- and microscale. We direct judiciously patched nanoparticles into a wide variety of nanoassemblies and present a case study demonstrating the distinct metamaterial properties in enhancing the spontaneous emission of diamond nanoparticles. This newly invented strategy is readily implementable and extendable to construct a palette of structurally sophisticated and functionality-explicit architecture, paving the way for nanoscale manipulation of colloidal material functionalities with wide-ranging applications for biological sensing, optical engineering, and catalytic chemistry.

Seeking regularity from irregularity: unveiling the synthesis-nanomorphology relationships of heterogeneous nanomaterials using unsupervised machine learning

Nanoscale morphology of functional materials determines their chemical and physical properties. However, despite increasing use of transmission electron microscopy (TEM) to directly image nanomorphology, it remains challenging to quantify the information embedded in TEM data sets, and to use nanomorphology to link synthesis and processing conditions to properties. We develop an automated, descriptor-free analysis workflow for TEM data that utilizes convolutional neural networks and unsupervised learning to quantify and classify nanomorphology, and thereby reveal synthesis-nanomorphology relationships in three different systems. While TEM records nanomorphology readily in two-dimensional (2D) images or three-dimensional (3D) tomograms, we advance the analysis of these images by identifying and applying a universal shape fingerprint function to characterize nanomorphology. After dimensionality reduction through principal component analysis, this function then serves as the input for morphology grouping through unsupervised learning. We demonstrate the wide applicability of our workflow to both 2D and 3D TEM data sets, and to both inorganic and organic nanomaterials, including tetrahedral gold nanoparticles mixed with irregularly shaped impurities, hybrid polymer-patched gold nanoprisms, and polyamide membranes with irregular and heterogeneous 3D crumple structures. In each of these systems, unsupervised nanomorphology grouping identifies both the diversity and the similarity of the nanomaterial across different synthesis conditions, revealing how synthetic parameters guide nanomorphology development. Our work opens possibilities for enhancing synthesis of nanomaterials through artificial intelligence and for understanding and controlling complex nanomorphology, both for 2D systems and in the far less explored case of 3D structures, such as those with embedded voids or hidden interfaces.

Biomolecule-Based Optical Metamaterials: Design and Applications

Metamaterials are broadly defined as artificial, electromagnetically homogeneous structures that exhibit unusual physical properties that are not present in nature. They possess extraordinary capabilities to bend electromagnetic waves. Their size, shape and composition can be engineered to modify their characteristics, such as iridescence, color shift, absorbance at different wavelengths, etc., and harness them as biosensors. Metamaterial construction from biological sources such as carbohydrates, proteins and nucleic acids represents a low-cost alternative, rendering high quantities and yields. In addition, the malleability of these biomaterials makes it possible to fabricate an endless number of structured materials such as composited nanoparticles, biofilms, nanofibers, quantum dots, and many others, with very specific, invaluable and tremendously useful optical characteristics. The intrinsic characteristics observed in biomaterials make them suitable for biomedical applications. This review addresses the optical characteristics of metamaterials obtained from the major macromolecules found in nature: carbohydrates, proteins and DNA, highlighting their biosensor field use, and pointing out their physical properties and production paths.

High-Yield 99mTc Labeling of Gold Nanoparticles Carrying Atropine and Adrenaline

This work focuses on the synthesis, purification, and analytical characterization of novel multifunctional Au NPs radiolabeled with ^99mTc. These mixed-ligand shell Au NPs represent pharmacologically relevant samples for potential application in theragnostics. A ligand using a plain linker with a rather long chain consisting of 10 CH₂ groups and a thiol moiety along with the PADA chelator has been used for both the attachment to the Au NP surface and for the ^99mTc(CO)₃⁺ complexation. We have combined this with our approach of stabilizing Au NP without any PEG or other stabilizing groups. Thus, monoligand shell Au NPs were radiolabeled by different strategies (prelabeling and postlabeling). Additionally, pharmacologically relevant Au NPs were synthesized carrying both a biofunctionalization with either atropine or adrenaline and the ^99mTc radiolabel. All samples were obtained in very good yields (up to 80% of the total activity loaded onto the column) and completely/particularly purified using desalting columns. Detailed analytical characterization of the Au NPs before and after radiolabeling has proven the NPs' robustness throughout the process. Their intact functionalization, shape, and stability was confirmed by transmission electron microscopy (TEM), ultraviolet/visible (UV/vis) spectroscopy, dynamic light scattering (DLS), and infrared (IR) spectroscopy. The presented strategy represents a versatile building block system that can be adapted to a variety of bioactive molecules and may be of high relevance for theragnostic 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.

From Precision Colloidal Hybrid Materials to Advanced Functional Assemblies

ConspectusThe concept of colloids encompasses a wide range of isotropic and anisotropic particles with diverse sizes, shapes, and functions from synthetic nanoparticles, nanorods, and nanosheets to functional biological units. They are addressed in materials science for various functions, while they are ubiquitous in the biological world for multiple functions. A large variety of synthetic colloids have been researched due to their scientific and technological importance; still they characteristically suffer from finite size distributions, imperfect shapes and interactions, and not fully engineered functions. This contrasts with biological colloids that offer precision in their size, shape, and functionality. Materials science has searched for inspiration from the biological world to allow structural control by self-assembly and hierarchy and to identify novel routes for combinations of functions in bio-inspiration.Herein, we first discuss different approaches for highly defined structural control of technically relevant synthetic colloids based on guided assemblies of biological motifs. First, we describe how polydisperse nanoparticles can be assembled within hollow protein cages to allow well-defined assemblies and hierarchical packings. Another approach relies on DNA nanotechnology-based assemblies, where engineered DNA structures allow programmed assembly. Then we will discuss synthetic colloids that have either particularly narrow size dispersity or even atomically precise structures for new assemblies and potential functions. Such colloids can have well-defined packings for membranes allowing high modulus. They can be switchable using light-responsive moieties, and they can initiate packing of larger assemblies of different geometrical shapes. The emphasis is on atomically defined nanoclusters that allow well-defined assemblies by supramolecular interactions, such as directional hydrogen bonding. Finally, we will discuss stimulus-responsive colloids for new functions, even toward complex responsive functions inspired by life. Therein, stimulus-responsive materials inspired by biological learning could allow the next generation of such materials. Classical conditioning is among the simplest biological learning concepts, requiring two stimuli and triggerable memory. Therein we use thermoresponsive hydrogels with plasmonic gold nanoparticles and a spiropyran photoacid as a model. Heating is the unconditioned stimulus leading to melting of the thermoresponsive gel, whereas light (at a specified wavelength) originally leads to reduced pH without plasmonic or structural changes because of steric gel stabilization. Under heat-induced gel melting, light results in pH-decrease and chain-like aggregation of the gold nanoparticles, allowing a new plasmonic response. Thus, simultaneous heating and light irradiation allow conditioning for a newly derived stimulus, where the logic diagram is analogous to Pavlovian conditioning. The shown assemblies demonstrate the different functionalities achievable using colloids when the sizes and the dispersity are controlled.

Two-Stage Assembly of Nanoparticle Superlattices with Multiscale Organization

Self-assembly processes, while promising for enabling the fabrication of complexly organized nanomaterials from nanoparticles, are often limited in creating structures with multiscale order. These limitations are due to difficulties in practically realizing the assembly processes required to achieve such complex organizations. For a long time, a hierarchical assembly attracted interest as a potentially powerful approach. However, due to the experimental limitations, intermediate-level structures are often heterogeneous in composition and structure, which significantly impacts the formation of large-scale organizations. Here, we introduce a two-stage assembly strategy: DNA origami frames scaffold a coordination of nanoparticles into designed 3D nanoclusters, and then these clusters are assembled into ordered lattices whose types are determined by the clusters' valence. Through modulating the nanocluster architectures and intercluster bindings, we demonstrate the successful formation of complexly organized nanoparticle crystals. The presented two-stage assembly method provides a powerful fabrication strategy for creating nanoparticle superlattices with prescribed unit cells.

Binary Superlattices of Gold Nanoparticles in Two Dimensions

We have created two-dimensional (2D) binary superlattices by cocrystallizing gold nanoparticles (AuNPs) of two distinct sizes into √3 × √3 and 2 × 2 complex binary superlattices, derived from the hexagonal structures of the single components. The building blocks of these binary systems are AuNPs that are functionalized with different chain lengths of poly(ethylene glycol) (PEG). The assembly of these functionalized NPs at the air-water interface is driven by the presence of salt, causing PEG-AuNPs to migrate to the aqueous surface and assemble into a crystalline lattice. We have used liquid surface X-ray reflectivity (XR) and grazing incidence small-angle X-ray scattering (GISAXS) to examine the assembly and crystallization at the liquid interface.

Controlling morphology in hybrid isotropic/patchy particle assemblies

Brownian dynamics is used to study self-assembly in a hybrid system of isotropic particles (IPs), combined with anisotropic building blocks that represent special "designer particles." Those are modeled as spherical patchy particles (PPs) with binding only allowed between their patches and IPs. In this study, two types of PPs are considered: Octahedral PPs (Oh-PPs) and Square PPs (Sq-PPs), with octahedral and square arrangements of patches, respectively. The self-assembly is additionally facilitated by the simulated annealing procedure. The resultant structures are characterized by a combination of local correlations in cubatic ordering and a symmetry-specific variation of bond orientation order parameters (SymBOPs). By varying the PP/IP size ratio, we detected a sharp crossover between two distinct morphologies in both types of systems. High symmetry phases, NaCl crystal for Oh-PP and square lattice for Sq-PP, are observed for larger size ratios. For the smaller ones, the dominant morphologies are significantly different, e.g., Oh-PPs form a compact amorphous structure with predominantly face-to-face orientation of neighboring PPs. Unusually, for a morphology without a long-range order, it is still possible to identify well organized coherent clusters of this structure, thanks to the adoption of our SymBOP-based characterization.

Engineering Inorganic Materials with DNA Nanostructures

Nucleic acid nanotechnology lays a foundation for the user-friendly design and synthesis of DNA frameworks of any desirable shape with extreme accuracy and addressability. Undoubtedly, such features make these structures ideal modules for positioning and organizing molecules and molecular components into complex assemblies. One of the emerging concepts in the field is to create inorganic and hybrid materials through programmable DNA templates. Here, we discuss the challenges and perspectives of such DNA nanostructure-driven materials science engineering and provide insights into the subject by introducing various DNA-based fabrication techniques including metallization, mineralization, lithography, casting, and hierarchical self-assembly of metal nanoparticles.

Self-regulated co-assembly of soft and hard nanoparticles

Controlled self-assembly of colloidal particles into predetermined organization facilitates the bottom-up manufacture of artificial materials with designated hierarchies and synergistically integrated functionalities. However, it remains a major challenge to assemble individual nanoparticles with minimal building instructions in a programmable fashion due to the lack of directional interactions. Here, we develop a general paradigm for controlled co-assembly of soft block copolymer micelles and simple unvarnished hard nanoparticles through variable noncovalent interactions, including hydrogen bonding and coordination interactions. Upon association, the hairy micelle corona binds with the hard nanoparticles with a specific valence depending exactly on their relative size and feeding ratio. This permits the integration of block copolymer micelles with a diverse array of hard nanoparticles with tunable chemistry into multidimensional colloidal molecules and polymers. Secondary co-assembly of the resulting colloidal molecules further leads to the formation of more complex hierarchical colloidal superstructures. Notably, such colloidal assembly is processible on surface either through initiating the alternating co-assembly from a micelle immobilized on a substrate or directly grafting a colloidal oligomer onto the micellar anchor.

Colloidal self-assembly enables bottom-up manufacture of materials with designed hierarchies and functions. Here the authors develop a facile method to construct multidimensional colloidal architectures via the association of soft block copolymer micelles with simple unvarnished hard nanoparticles.

Importance of Substrate-Particle Repulsion for Protein-Templated Assembly of Metal Nanoparticles

We study the protein-directed assembly of colloidal gold nanoparticles on de novo designed protein nanofiber templates. Using sequential assembly on glass substrates, we attach positively charged gold nanoparticles to protein nanofibers engineered to have a high density of negatively charged surface residues. Using a combination of electron and optical microscopy, we measure the density of particle attachment and characterize binding specificity. By varying nanoparticle size and pH of the solution, we explore the importance of charge-dependent particle-fiber and particle-substrate interactions. We find an inverse correlation between particle size and attachment density to protein nanofibers, attributed to the balance between size-dependent electrostatic particle-fiber attraction and particle-substrate repulsion. We show pH-dependent particle attachment density and binding specificity in relation to the protonation fraction of each assembly layer. Finally, we employ hyperspectral scattering microscopy to draw conclusions about particle density and interparticle spacings of optically observable particle assemblies.

Trifaceted Mickey Mouse Amphiphiles for Programmable Self-Assembly, DNA Complexation and Organ-Selective Gene Delivery

Instilling segregated cationic and lipophilic domains with an angular disposition in a trehalose-based trifaceted macrocyclic scaffold allows engineering patchy molecular nanoparticles leveraging directional interactions that emulate those controlling self-assembling processes in viral capsids. The resulting trilobular amphiphilic derivatives, featuring a Mickey Mouse architecture, can electrostatically interact with plasmid DNA (pDNA) and further engage in hydrophobic contacts to promote condensation into transfectious nanocomplexes. Notably, the topology and internal structure of the cyclooligosaccharide/pDNA co-assemblies can be molded by fine-tuning the valency and characteristics of the cationic and lipophilic patches, which strongly impacts the transfection efficacy in vitro and in vivo. Outstanding organ selectivities can then be programmed with no need of incorporating a biorecognizable motif in the formulation. The results provide a versatile strategy for the construction of fully synthetic and perfectly monodisperse nonviral gene delivery systems uniquely suited for optimization schemes by making cyclooligosaccharide patchiness the focus.

Designed and biologically active protein lattices

Versatile methods to organize proteins in space are required to enable complex biomaterials, engineered biomolecular scaffolds, cell-free biology, and hybrid nanoscale systems. Here, we demonstrate how the tailored encapsulation of proteins in DNA-based voxels can be combined with programmable assembly that directs these voxels into biologically functional protein arrays with prescribed and ordered two-dimensional (2D) and three-dimensional (3D) organizations. We apply the presented concept to ferritin, an iron storage protein, and its iron-free analog, apoferritin, in order to form single-layers, double-layers, as well as several types of 3D protein lattices. Our study demonstrates that internal voxel design and inter-voxel encoding can be effectively employed to create protein lattices with designed organization, as confirmed by in situ X-ray scattering and cryo-electron microscopy 3D imaging. The assembled protein arrays maintain structural stability and biological activity in environments relevant for protein functionality. The framework design of the arrays then allows small molecules to access the ferritins and their iron cores and convert them into apoferritin arrays through the release of iron ions. The presented study introduces a platform approach for creating bio-active protein-containing ordered nanomaterials with desired 2D and 3D organizations.

Designer Nanomaterials through Programmable Assembly

Nanoparticles have long been recognized for their unique properties, leading to exciting potential applications across optics, electronics, magnetism, and catalysis. These specific functions often require a designed organization of particles, which includes the type of order as well as placement and relative orientation of particles of the same or different kinds. DNA nanotechnology offers the ability to introduce highly addressable bonds, tailor particle interactions, and control the geometry of bindings motifs. Here, we discuss how developments in structural DNA nanotechnology have enabled greater control over 1D, 2D, and 3D particle organizations through programmable assembly. This Review focuses on how the use of DNA binding between nanocomponents and DNA structural motifs has progressively allowed the rational formation of prescribed particle organizations. We offer insight into how DNA-based motifs and elements can be further developed to control particle organizations and how particles and DNA can be integrated into nanoscale building blocks, so-called "material voxels", to realize designer nanomaterials with desired functions.

Rationally Programming Nanomaterials with DNA for Biomedical Applications

DNA is not only a carrier of genetic information, but also a versatile structural tool for the engineering and self-assembling of nanostructures. In this regard, the DNA template has dramatically enhanced the scalability, programmability, and functionality of the self-assembled DNA nanostructures. These capabilities provide opportunities for a wide range of biomedical applications in biosensing, bioimaging, drug delivery, and disease therapy. In this review, the importance and advantages of DNA for programming and fabricating of DNA nanostructures are first highlighted. The recent progress in design and construction of DNA nanostructures are then summarized, including DNA conjugated nanoparticle systems, DNA-based clusters and extended organizations, and DNA origami-templated assemblies. An overview on biomedical applications of the self-assembled DNA nanostructures is provided. Finally, the conclusion and perspectives on the self-assembled DNA nanostructures are presented.

3D DNA Nanostructures: The Nanoscale Architect

Structural DNA nanotechnology is a pioneering biotechnology that presents the opportunity to engineer DNA-based hardware that will mediate a profound interface to the nanoscale. To date, an enormous library of shaped 3D DNA nanostructures have been designed and assembled. Moreover, recent research has demonstrated DNA nanostructures that are not only static but can exhibit specific dynamic motion. DNA nanostructures have thus garnered significant research interest as a template for pursuing shape and motion-dependent nanoscale phenomena. Potential applications have been explored in many interdisciplinary areas spanning medicine, biosensing, nanofabrication, plasmonics, single-molecule chemistry, and facilitating biophysical studies. In this review, we begin with a brief overview of general and versatile design techniques for 3D DNA nanostructures as well as some techniques and studies that have focused on improving the stability of DNA nanostructures in diverse environments, which is pivotal for its reliable utilization in downstream applications. Our main focus will be to compile a wide body of existing research on applications of 3D DNA nanostructures that demonstrably rely on the versatility of their mechanical design. Furthermore, we frame reviewed applications into three primary categories, namely encapsulation, surface templating, and nanomechanics, that we propose to be archetypal shape- or motion-related functions of DNA nanostructures found in nanoscience applications. Our intent is to identify core concepts that may define and motivate specific directions of progress in this field as we conclude the review with some perspectives on the future.

DNA-assembled superconducting 3D nanoscale architectures

Studies of nanoscale superconducting structures have revealed various physical phenomena and led to the development of a wide range of applications. Most of these studies concentrated on one- and two-dimensional structures due to the lack of approaches for creation of fully engineered three-dimensional (3D) nanostructures. Here, we present a 'bottom-up' method to create 3D superconducting nanostructures with prescribed multiscale organization using DNA-based self-assembly methods. We assemble 3D DNA superlattices from octahedral DNA frames with incorporated nanoparticles, through connecting frames at their vertices, which result in cubic superlattices with a 48 nm unit cell. The superconductive superlattice is formed by converting a DNA superlattice first into highly-structured 3D silica scaffold, to turn it from a soft and liquid-environment dependent macromolecular construction into a solid structure, following by its coating with superconducting niobium (Nb). Through low-temperature electrical characterization we demonstrate that this process creates 3D arrays of Josephson junctions. This approach may be utilized in development of a variety of applications such as 3D Superconducting Quantum interference Devices (SQUIDs) for measurement of the magnetic field vector, highly sensitive Superconducting Quantum Interference Filters (SQIFs), and parametric amplifiers for quantum information systems.

Engineering Organization of DNA Nano-Chambers through Dimensionally Controlled and Multi-Sequence Encoded Differentiated Bonds

Engineering the assembly of nanoscale objects into complex and prescribed structures requires control over their binding properties. Such control might benefit from a well-defined bond directionality, the ability to designate their engagements through specific encodings, and the capability to coordinate local orientations. Although much progress has been achieved in our ability to design complex nano-objects, the challenges in creating such nano-objects with fully controlled binding modes and understanding their fundamental properties are still outstanding. Here, we report a facile strategy for creating a DNA nanochamber (DNC), a hollow cuboid nano-object, whose bonds can be fully prescribed and complexly encoded along its three orthogonal axes, giving rise to addressable and differentiated bonds. The DNC can host nanoscale cargoes, which allows for the integration with functional nano-objects and their organization in larger-scale systems. We explore the relationship between the design of differentiated bonds and a formation of one-(1D), two-(2D), and three-(3D) dimensional organized arrays. Through the realization of different binding modes, we demonstrate sequence encoded nanoscale heteropolymers, helical polymers, 2D lattices, and mesoscale 3D nanostructures with internal order, and show that this assembly strategy can be applied for the organization of nanoparticles. We combine experimental investigations with computational simulation to understand the mechanism of structural formation for different types of ordered arrays, and to correlate the bonds design with assembly processes.