Three-dimensional visualization of nanoparticle lattices and multimaterial frameworks

Binding Site Programmable Self-Assembly of 3D Hierarchical DNA Origami Nanostructures

DNA nanotechnology has broad applications in biomedical drug delivery and programmable materials. Characterization of the self-assembly of DNA origami and quantum dots (QDs) is necessary for the development of new DNA-based nanostructures. We use computation and experiment to show that the self-assembly of 3D hierarchical nanostructures can be controlled by programming the binding site number and their positions on DNA origami. Using biotinylated pentagonal pyramid wireframe DNA origamis and streptavidin capped QDs, we demonstrate that DNA origami with 1 binding site at the outer vertex can assemble multimeric origamis with up to 6 DNA origamis on 1 QD, and DNA origami with 1 binding site at the inner center can only assemble monomeric and dimeric origamis. Meanwhile, the yield percentages of different multimeric origamis are controlled by the QD:DNA-origami stoichiometric mixing ratio. DNA origamis with 2 binding sites at the αγ positions (of the pentagon) make larger nanostructures than those with binding sites at the αβ positions. In general, increasing the number of binding sites leads to increases in the nanostructure size. At high DNA origami concentration, the QD number in each cluster becomes the limiting factor for the growth of nanostructures. We find that reducing the QD size can also affect the self-assembly because of the reduced access to the binding sites from more densely packed origamis.

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.

Symmetry-Breaking of Nanoparticle Surface Function Via Conformal DNA Design

Asymmetric surface functionalization of complex nanoparticles to control their directional self-assembly remains a considerable challenge. Here, we demonstrated a conformal DNA design strategy for flexible remodeling of the surface of complex nanoparticles, taking Au nanobipyramids (AuNBPs) as a model. We sheathed one or both tips of AuNBPs into conformal DNA origami with an exceptionally accurate orientation control. Such asymmetrically and symmetrically distributed surface patches possess regioselective, sequence, and site-specific DNA binding capabilities. As a result, we realized a series of prototypical multicomponent "colloidal molecules" made of AuNBPs and Au nanospheres (AuNSs) with defined directionality and number of "bonding valence" as well as 1D and 3D hierarchical assemblies, e.g., inverse core-satellites of AuNBPs and AuNSs, side-by-side and tip-to-tip linear assemblies of AuNBPs, and 3D helical superstructures of AuNBPs with tunable twists. These findings inspire new opportunities for nanoparticle surface engineering and the high-order self-assembly of nanoarchitectures with higher complexity and broadened functionalities.

Co-Assembly of Soft and Hard Nanoparticles into Macroscopic Colloidal Composites with Tailored Mechanical Property and Processability

Colloidal composites, translating the great potential of nanoscale building bricks into macroscopic dimensions, have emerged as an appealing candidate for new materials with applications in optics, energy storage, and biomedicines. However, it remains a key challenge to bridge the size regimes from nanoscopic colloidal particles to macroscale composites possessing mechanical robustness. Herein, a bottom-up approach is demonstrated to manufacture colloidal composites with customized macroscopic forms by virtue of the co-assembly of nanosized soft polymeric micelles and hard inorganic nanoparticles. Upon association, the hairy micellar corona can bind with the hard nanoparticles, linking individual hard constituents together in a soft-hard alternating manner to form a collective entity. This permits the integration of block copolymer micelles with controlled amounts of hard nanoparticles into macroscopic colloidal composites featuring diverse internal microstructures. The resultant composites showed tunable microscale mechanical strength in a range of 90-270 MPa and macroscale mechanical strength in a range of 7-42 MPa for compression and 2-24 MPa for bending. Notably, the incorporation of soft polymeric micelles also imparts time- and temperature-dependent dynamic deformability and versatile capacity to the resulting composites, allowing their application in the low-temperature plastic processing for functional fused silica glass.

Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments

Sophisticated statistical mechanics approaches and human intuition have demonstrated the possibility of self-assembling complex lattices or finite-size constructs. However, attempts so far have mostly only been successful in silico and often fail in experiment because of unpredicted traps associated with kinetic slowing down (gelation, glass transition) and competing ordered structures. Theoretical predictions also face the difficulty of encoding the desired interparticle interaction potential with the experimentally available nano- and micrometer-sized particles. To overcome these issues, we combine SAT assembly (a patchy-particle interaction design algorithm based on constrained optimization) with coarse-grained simulations of DNA nanotechnology to experimentally realize trap-free self-assembly pathways. We use this approach to assemble a pyrochlore three-dimensional lattice, coveted for its promise in the construction of optical metamaterials, and characterize it with small-angle x-ray scattering and scanning electron microscopy visualization.

Diamond-lattice photonic crystals assembled from DNA origami

Colloidal self-assembly allows rational design of structures on the micrometer and submicrometer scale. One architecture that can generate complete three-dimensional photonic bandgaps is the diamond cubic lattice, which has remained difficult to realize at length scales comparable with the wavelength of visible or ultraviolet light. In this work, we demonstrate three-dimensional photonic crystals self-assembled from DNA origami that act as precisely programmable patchy colloids. Our DNA-based nanoscale tetrapods crystallize into a rod-connected diamond cubic lattice with a periodicity of 170 nanometers. This structure serves as a scaffold for atomic-layer deposition of high-refractive index materials such as titanium dioxide, yielding a tunable photonic bandgap in the near-ultraviolet.

Limits of economy and fidelity for programmable assembly of size-controlled triply periodic polyhedra

We propose and investigate an extension of the Caspar-Klug symmetry principles for viral capsid assembly to the programmable assembly of size-controlled triply periodic polyhedra, discrete variants of the Primitive, Diamond, and Gyroid cubic minimal surfaces. Inspired by a recent class of programmable DNA origami colloids, we demonstrate that the economy of design in these crystalline assemblies-in terms of the growth of the number of distinct particle species required with the increased size-scale (e.g., periodicity)-is comparable to viral shells. We further test the role of geometric specificity in these assemblies via dynamical assembly simulations, which show that conditions for simultaneously efficient and high-fidelity assembly require an intermediate degree of flexibility of local angles and lengths in programmed assembly. Off-target misassembly occurs via incorporation of a variant of disclination defects, generalized to the case of hyperbolic crystals. The possibility of these topological defects is a direct consequence of the very same symmetry principles that underlie the economical design, exposing a basic tradeoff between design economy and fidelity of programmable, size controlled assembly.

Imaging 3D chemistry at 1 nm resolution with fused multi-modal electron tomography

Measuring the three-dimensional (3D) distribution of chemistry in nanoscale matter is a longstanding challenge for metrological science. The inelastic scattering events required for 3D chemical imaging are too rare, requiring high beam exposure that destroys the specimen before an experiment is completed. Even larger doses are required to achieve high resolution. Thus, chemical mapping in 3D has been unachievable except at lower resolution with the most radiation-hard materials. Here, high-resolution 3D chemical imaging is achieved near or below one-nanometer resolution in an Au-Fe3O4 metamaterial within an organic ligand matrix, Co3O4-Mn3O4 core-shell nanocrystals, and ZnS-Cu0.64S0.36 nanomaterial using fused multi-modal electron tomography. Multi-modal data fusion enables high-resolution chemical tomography often with 99% less dose by linking information encoded within both elastic (HAADF) and inelastic (EDX/EELS) signals. We thus demonstrate that sub-nanometer 3D resolution of chemistry is measurable for a broad class of geometrically and compositionally complex materials.

Efficient one-pot assembly of higher-order DNA nanostructures by chemically conjugated branched DNA

Chemically conjugated branched DNA was successfully synthesized by a copper-free click reaction to construct sophisticated and higher-order polyhedral DNA nanostructures with pre-defined units in one pot, which can be used as an efficient nanoplatform to precisely organize multiple gold nanoparticles in predesigned patterns.

Beyond nothingness in the formation and functional relevance of voids in polymer films

Voids-the nothingness-broadly exist within nanomaterials and impact properties ranging from catalysis to mechanical response. However, understanding nanovoids is challenging due to lack of imaging methods with the needed penetration depth and spatial resolution. Here, we integrate electron tomography, morphometry, graph theory and coarse-grained molecular dynamics simulation to study the formation of interconnected nanovoids in polymer films and their impacts on permeance and nanomechanical behaviour. Using polyamide membranes for molecular separation as a representative system, three-dimensional electron tomography at nanometre resolution reveals nanovoid formation from coalescence of oligomers, supported by coarse-grained molecular dynamics simulations. Void analysis provides otherwise inaccessible inputs for accurate fittings of methanol permeance for polyamide membranes. Three-dimensional structural graphs accounting for the tortuous nanovoids within, measure higher apparent moduli with polyamide membranes of higher graph rigidity. Our study elucidates the significance of nanovoids beyond the nothingness, impacting the synthesis‒morphology‒function relationships of complex nanomaterials.

Gradient Transformation of the Double Gyroid to the Double Diamond in Soft Matter

Transitions between gyroid and diamond intercatenated double network phases occur in many types of soft matter, but to date, the structural pathway and the crystallographic relationships remain unclear. Slice and view scanning electron microscopy tomography of a diblock copolymer affords monitoring of the evolving shape of the intermaterial dividing surface, allowing structural characterization of both the majority and minority domains. Two trihedral malleable mesoatoms combine to form a single tetrahedral mesoatom in a volume additive manner while preserving network topology, as the types of loops, the number of mesoatoms in a loop, minority domain strut lengths, and directions that connect a given mesoatom to its neighbors evolve across a 150 nm wide transition zone (TZ). The [111]DD direction is coincident with the [110]DG direction so that the (111)DD and (110)DG planes define the boundaries of the TZ. Selection of the particular crystal orientations and direction and width of the transition zone is to minimize the cost of morphing the mesoatoms from one structure to the other, by maximizing like-block continuity and minimizing the variation of the surface curvature and thickness of the domains across the TZ. Such coherent continuity of the independent, intercatenated networks across the transition zone is critical for applications such as graded mechanical trusses where the pair of different networks are joined to provide different mechanical properties for adjacent grains or could serve as a nanoscale anode/cathode allowing super charging and discharging provided the networks are continuous and rigorously separate.

Chemically Conjugated Branched Staples for Super-DNA Origami

DNA origami, comprising a long folded DNA scaffold and hundreds of linear DNA staple strands, has been developed to construct various sophisticated structures, smart devices, and drug delivery systems. However, the size and diversity of DNA origami are usually constrained by the length of DNA scaffolds themselves. Herein, we report a new paradigm of scaling up DNA origami assembly by introducing a novel branched staple concept. Owing to their covalent characteristics, the chemically conjugated branched DNA staples we describe here can be directly added to a typical DNA origami assembly system to obtain super-DNA origami with a predefined number of origami tiles in one pot. Compared with the traditional two-step coassembly system (yields <10%), a much greater yield (>80%) was achieved using this one-pot strategy. The diverse superhybrid DNA origami with the combination of different origami tiles can be also efficiently obtained by the hybrid branched staples. Furthermore, the branched staples can be successfully employed as the effective molecular glues to stabilize micrometer-scale, super-DNA origami arrays (e.g., 10 × 10 array of square origami) in high yields, paving the way to bridge the nanoscale precision of DNA origami with the micrometer-scale device engineering. This rationally developed assembly strategy for super-DNA origami based on chemically conjugated branched staples presents a new avenue for the development of multifunctional DNA origami-based materials.

Three-dimensional nanoscale metal, metal oxide, and semiconductor frameworks through DNA-programmable assembly and templating

Controlling the three-dimensional (3D) nanoarchitecture of inorganic materials is imperative for enabling their novel mechanical, optical, and electronic properties. Here, by exploiting DNA-programmable assembly, we establish a general approach for realizing designed 3D ordered inorganic frameworks. Through inorganic templating of DNA frameworks by liquid- and vapor-phase infiltrations, we demonstrate successful nanofabrication of diverse classes of inorganic frameworks from metal, metal oxide and semiconductor materials, as well as their combinations, including zinc, aluminum, copper, molybdenum, tungsten, indium, tin, and platinum, and composites such as aluminum-doped zinc oxide, indium tin oxide, and platinum/aluminum-doped zinc oxide. The open 3D frameworks have features on the order of nanometers with architecture prescribed by the DNA frames and self-assembled lattice. Structural and spectroscopic studies reveal the composition and organization of diverse inorganic frameworks, as well as the optoelectronic properties of selected materials. The work paves the road toward establishing a 3D nanoscale lithography.

Breaking the size constraint for nano cages using annular patchy particles

Engineering structures like nanocages, shells, and containers, by self-assembly of colloids is a challenging problem. One of the main challenges is to define the shape of the individual subunits to control the radius of the closed shell structures. In this work, we have proposed a simple model for the subunit, which comprises a spheroidal or spherical hardcore decorated with an annular patch. The self-assembly of these building blocks leads to the formation of monodispersed spherical cages (close shells) or containers (curved clusters). For a spheroid with a given bonding range, the curvature of the shell is analytically related to only the patch angle of the building blocks and independent of the shape of the subunits. This model with only one control parameter can be used to engineer cages with the desired radius, which also have been verified using thermodynamic calculations. In the phase diagram of the system, 4 phases are identified which includes gas, closed shell, partially closed (containers) shell and percolated structures. When the diameters of the spherical cages formed are small, we observe an icosahedral symmetry similar to virus capsids. We also observed that the kinetics of the cage formation is very similar to the nucleation and growth kinetics of viruses and is the key factor in determining the yield of closed shells.

Nanoscale Three-Dimensional Network Structure of a Mesoporous Particle Unveiled via Adaptive Multidistance Coherent X-ray Tomography

Mesoporous nanoparticles provide rich platforms to devise functional materials by customizing the three-dimensional (3D) structures of nanopores. With the pore network as a key tuning parameter, the noninvasive and quantitative characterization of these 3D structures is crucial for the rational design of functional materials. This has prompted researchers to develop versatile nanoprobes with a high penetration power to inspect various specimens sized a few micrometers at nanoscale 3D resolutions. Here, with adaptive phase retrievals on independent data sets with different sampling frequencies, we introduce multidistance coherent X-ray tomography as a noninvasive and quantitative nanoprobe to realize high-resolution 3D imaging of micrometer-sized specimens. The 3D density distribution of an entire mesoporous silica nanoparticle was obtained at 13 nm 3D resolution for quantitative physical and morphological analyses of its 3D pore structure. The morphological features of the whole 3D pore network and pore connectivity were examined to gain insight into the potential functions of the particles. The proposed multidistance tomographic imaging scheme with quantitative structural analyses is expected to advance studies of functional materials by facilitating their structure-based rational design.

Controlling Colloidal Crystal Nucleation and Growth with Photolithographically Defined Templates

Colloidal crystallization provides a means to synthesize hierarchical nanostructures by design and to use these complex structures for nanodevice fabrication. In particular, DNA provides a means to program interactions between particles with high specificity, thereby enabling the formation of particle superlattice crystallites with tailored unit cell geometries and surface faceting. However, while DNA provides precise control of particle-particle bonding interactions, it does not inherently present a means of controlling higher-level structural features such as the size, shape, position, or orientation of a colloidal crystallite. While altering assembly parameters such as temperature or concentration can enable limited control of crystallite size and geometry, integrating colloidal assemblies into nanodevices requires better tools to manipulate higher-order structuring and improved understanding of how these tools control the fundamental kinetics and mechanisms of colloidal crystal growth. In this work, photolithography is used to produce patterned substrates that can manipulate the placement, size, dispersity, and orientation of colloidal crystals. By adjusting aspects of the pattern, such as feature size and separation, we reveal a diffusion-limited mechanism governing crystal nucleation and growth. Leveraging this insight, patterns are designed that can produce wafer-scale substrates with arrays of nanoparticle superlattices of uniform size and shape. These design principles therefore bridge a gap between a fundamental understanding of nanoparticle assembly and the fabrication of nanostructures compatible with functional devices.

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.

Hints of Growth Mechanism Left in Supercrystals

Supercrystals of DNA-functionalized nanoparticles are visualized in three dimensions using X-ray ptychographic tomography, and their reciprocal spaces are mapped with small-angle X-ray scattering in order to better understand their internal defect structures. X-ray ptychographic tomography reveals various types of defects in an assembly that otherwise exhibits a single crystalline diffraction pattern. On average, supercrystals composed of smaller nanoparticles are smaller in size than supercrystals composed of larger particles. Additionally, supercrystals composed of small nanoparticles are typically aggregated into larger "necklace-like" structures. Within these larger structures, some but not all pairs of connected domains are coherent in their relative orientations. In contrast, supercrystals composed of larger nanoparticles with longer DNA ligands typically form faceted crystals. The combination of these two complementary X-ray techniques reveals that the crystalline assemblies grow by aggregation of smaller assemblies followed by rearrangement of nanoparticles.

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.

BODIPY as a Multifunctional Theranostic Reagent in Biomedicine: Self-Assembly, Properties, and Applications

The use of boron dipyrromethene (BODIPY) in biomedicine is reviewed. To open, its synthesis and regulatory strategies are summarized, and inspiring cutting-edge work in post-functionalization strategies is highlighted. A brief overview of assembly model of BODIPY is then provided: BODIPY is introduced as a promising building block for the formation of single- and multicomponent self-assembled systems, including nanostructures suitable for aqueous environments, thereby showing the great development potential of supramolecular assembly in biomedicine applications. The frontier progress of BODIPY in biomedical application is thereafter described, supported by examples of the frontiers of biomedical applications of BODIPY-containing smart materials: it mainly involves the application of materials based on BODIPY building blocks and their assemblies in fluorescence bioimaging, photoacoustic imaging, disease treatment including photodynamic therapy, photothermal therapy, and immunotherapy. Lastly, not only the current status of the BODIPY family in the biomedical field but also the challenges worth considering are summarized. At the same time, insights into the future development prospects of biomedically applicable BODIPY are provided.

Accurate real space iterative reconstruction (RESIRE) algorithm for tomography

Tomography has made a revolutionary impact on the physical, biological and medical sciences. The mathematical foundation of tomography is to reconstruct a three-dimensional (3D) object from a set of two-dimensional (2D) projections. As the number of projections that can be measured from a sample is usually limited by the tolerable radiation dose and/or the geometric constraint on the tilt range, a main challenge in tomography is to achieve the best possible 3D reconstruction from a limited number of projections with noise. Over the years, a number of tomographic reconstruction methods have been developed including direct inversion, real-space, and Fourier-based iterative algorithms. Here, we report the development of a real-space iterative reconstruction (RESIRE) algorithm for accurate tomographic reconstruction. RESIRE iterates between the update of a reconstructed 3D object and the measured projections using a forward and back projection step. The forward projection step is implemented by the Fourier slice theorem or the Radon transform, and the back projection step by a linear transformation. Our numerical and experimental results demonstrate that RESIRE performs more accurate 3D reconstructions than other existing tomographic algorithms, when there are a limited number of projections with noise. Furthermore, RESIRE can be used to reconstruct the 3D structure of extended objects as demonstrated by the determination of the 3D atomic structure of an amorphous Ta thin film. We expect that RESIRE can be widely employed in the tomography applications in different fields. Finally, to make the method accessible to the general user community, the MATLAB source code of RESIRE and all the simulated and experimental data are available at  https://zenodo.org/record/7273314 .

A simple solution to the problem of self-assembling cubic diamond crystals

The self-assembly of colloidal diamond (CD) crystals is considered as one of the most coveted goals of nanotechnology, both from the technological and fundamental points of view. For applications, colloidal diamond is a photonic crystal which can open new possibilities of manipulating light for information processing. From a fundamental point of view, its unique symmetry exacerbates a series of problems that are commonly faced during the self-assembly of target structures, such as the presence of kinetic traps and the formation of crystalline defects and alternative structures (polymorphs). Here we demonstrate that all these problems can be systematically addressed via SAT-assembly, a design framework that converts self-assembly into a Boolean satisfiability problem (SAT). Contrary to previous solutions (requiring four or more components), we prove that the assembly of the CD crystal only requires a binary mixture. Moreover, we use molecular dynamics simulations of a system composed by nearly a million nucleotides to test a DNA nanotechnology design that constitutes a promising candidate for experimental realization.

Advancing the Utility of DNA Origami Technique through Enhanced Stability of DNA-Origami-Based Assemblies

Since its discovery in 2006, the DNA origami technique has revolutionized bottom-up nanofabrication. This technique is simple yet versatile and enables the fabrication of nanostructures of almost arbitrary shapes. Furthermore, due to their intrinsic addressability, DNA origami structures can serve as templates for the arrangement of various nanoscale components (small molecules, proteins, nanoparticles, etc.) with controlled stoichiometry and nanometer-scale precision, which is often beyond the reach of other nanofabrication techniques. Despite the multiple benefits of the DNA origami technique, its applicability is often restricted by the limited stability in application-specific conditions. This Review provides an overview of the strategies that have been developed to improve the stability of DNA-origami-based assemblies for potential biomedical, nanofabrication, and other applications.