Polarization-Dependent Optical Response in Anisotropic Nanoparticle-DNA Superlattices

Inspired Beyond Nature: Three Decades of Spherical Nucleic Acids and Colloidal Crystal Engineering with DNA

The conception, synthesis, and invention of a nanostructure, now known as the spherical nucleic acid, or SNA, in 1996 marked the advent of a new field of chemistry. Over the past three decades, the SNA and its analogous anisotropic equivalents have provided an avenue for us to think about some of the most fundamental concepts in chemistry in new ways and led to technologies that are significantly impacting fields from medicine to materials science. A prime example is colloidal crystal engineering with DNA, the framework for using SNAs and related structures to synthesize programmable matter. Herein, we document the evolution of this framework, which was initially inspired by nature, and describe how it now allows researchers to chart paths to move beyond it, as programmable matter with real-world significance is envisioned and created.

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.

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

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

Photonic band structure calculation of 3D-finite nanostructured supercrystals

Computational modeling of plasmonic periodic structures are challenging due to their multiscale nature. On one hand, nanoscale building blocks require very fine spatial discretization of the computation domain to describe the near-field nature of the localized surface plasmons. On the other hand, the microscale supercrystals require large simulation domains. To tackle this challenge, two approaches are generally taken: (i) an effective medium approach, neglecting the nanoscale effects and (ii) the use of a unit cell with periodic boundary conditions, neglecting the overall habit of the supercrystal. The latter, which is used to calculate the photonic band structure of these supercrystals, fails to describe the photonic properties arising from their finite-size such as Fabry-Pérot modes (FPMs), whispering gallery modes (WGMs), and decrease of the photonic mode lifetime. Here, we developed a computational approach, based on the finite-difference time-domain method to accurately calculate the photonic band structures of finite supercrystals. We applied this new approach to 3D periodic microstructures of Au nanoparticles with cubic, spherical, and rhombic dodecahedral habits and discuss how their photonic band structures differ from those of infinite structures. Finally, we compared the photonic band structures to reflectance spectra and describe phenomena such as FPMs, WGMs, and polaritonic bandgaps.

A Deep Learning Framework Discovers Compositional Order and Self-Assembly Pathways in Binary Colloidal Mixtures

Binary colloidal superlattices (BSLs) have demonstrated enormous potential for the design of advanced multifunctional materials that can be synthesized via colloidal self-assembly. However, mechanistic understanding of the three-dimensional self-assembly of BSLs is largely limited due to a lack of tractable strategies for characterizing the many two-component structures that can appear during the self-assembly process. To address this gap, we present a framework for colloidal crystal structure characterization that uses branched graphlet decomposition with deep learning to systematically and quantitatively describe the self-assembly of BSLs at the single-particle level. Branched graphlet decomposition is used to evaluate local structure via high-dimensional neighborhood graphs that quantify both structural order (e.g., body-centered-cubic vs face-centered-cubic) and compositional order (e.g., substitutional defects) of each individual particle. Deep autoencoders are then used to efficiently translate these neighborhood graphs into low-dimensional manifolds from which relationships among neighborhood graphs can be more easily inferred. We demonstrate the framework on in silico systems of DNA-functionalized particles, in which two well-recognized design parameters, particle size ratio and interparticle potential well depth can be adjusted independently. The framework reveals that binary colloidal mixtures with small interparticle size disparities (i.e., A- and B-type particle radius ratios of r _A/r _B = 0.8 to r _A/r _B = 0.95) can promote the self-assembly of defect-free BSLs much more effectively than systems of identically sized particles, as nearly defect-free BCC-CsCl, FCC-CuAu, and IrV crystals are observed in the former case. The framework additionally reveals that size-disparate colloidal mixtures can undergo nonclassical nucleation pathways where BSLs evolve from dense amorphous precursors, instead of directly nucleating from dilute solution. These findings illustrate that the presented characterization framework can assist in enhancing mechanistic understanding of the self-assembly of binary colloidal mixtures, which in turn can pave the way for engineering the growth of defect-free BSLs.

Programmable Matter: The Nanoparticle Atom and DNA Bond

Colloidal crystal engineering with DNA has led to significant advances in bottom-up materials synthesis and a new way of thinking about fundamental concepts in chemistry. Here, programmable atom equivalents (PAEs), comprised of nanoparticles (the "atoms") functionalized with DNA (the "bonding elements"), are assembled through DNA hybridization into crystalline lattices. Unlike atomic systems, the "atom" (e.g., the nanoparticle shape, size, and composition) and the "bond" (e.g., the DNA length and sequence) can be tuned independently, yielding designer materials with unique catalytic, optical, and biological properties. In this review, nearly three decades of work that have contributed to the evolution of this class of programmable matter is chronicled, starting from the earliest examples based on gold-core PAEs, and then delineating how advances in synthetic capabilities, DNA design, and fundamental understanding of PAE-PAE interactions have led to new classes of functional materials that, in several cases, have no natural equivalent.

Spatial Separation of Plasmonic Hot-Electron Generation and a Hydrodehalogenation Reaction Center Using a DNA Wire

Using hot charge carriers far from a plasmonic nanoparticle surface is very attractive for many applications in catalysis and nanomedicine and will lead to a better understanding of plasmon-induced processes, such as hot-charge-carrier- or heat-driven chemical reactions. Herein we show that DNA is able to transfer hot electrons generated by a silver nanoparticle over several nanometers to drive a chemical reaction in a molecule nonadsorbed on the surface. For this we use 8-bromo-adenosine introduced in different positions within a double-stranded DNA oligonucleotide. The DNA is also used to assemble the nanoparticles into nanoparticles ensembles enabling the use of surface-enhanced Raman scattering to track the decomposition reaction. To prove the DNA-mediated transfer, the probe molecule was insulated from the source of charge carriers, which hindered the reaction. The results indicate that DNA can be used to study the transfer of hot electrons and the mechanisms of advanced plasmonic catalysts.

DNA-Grafted 3D Superlattice Self-Assembly

The exploitation of new methods to control material structure has historically been dominating the material science. The bottom-up self-assembly strategy by taking atom/molecule/ensembles in nanoscale as building blocks and crystallization as a driving force bring hope for material fabrication. DNA-grafted nanoparticle has emerged as a "programmable atom equivalent" and was employed for the assembly of hierarchically ordered three-dimensional superlattice with novel properties and studying the unknown assembly mechanism due to its programmability and versatility in the binding capabilities. In this review, we highlight the assembly strategies and rules of DNA-grafted three-dimensional superlattice, dynamic assembly by different driving factors, and discuss their future applications.

DNA origami single crystals with Wulff shapes

DNA origami technology has proven to be an excellent tool for precisely manipulating molecules and colloidal elements in a three-dimensional manner. However, fabrication of single crystals with well-defined facets from highly programmable, complex DNA origami units is a great challenge. Here, we report the successful fabrication of DNA origami single crystals with Wulff shapes and high yield. By regulating the symmetries and binding modes of the DNA origami building blocks, the crystalline shapes can be designed and well-controlled. The single crystals are then used to induce precise growth of an ultrathin layer of silica on the edges, resulting in mechanically reinforced silica-DNA hybrid structures that preserve the details of the single crystals without distortion. The silica-infused microcrystals can be directly observed in the dry state, which allows meticulous analysis of the crystal facets and tomographic 3D reconstruction of the single crystals by high-resolution electron microscopy.

Position- and Orientation-Controlled Growth of Wulff-Shaped Colloidal Crystals Engineered with DNA

Colloidal crystals have emerged as promising candidates for building optical microdevices. Techniques now exist for synthesizing them with control over their nanoscale features (e.g., particle compositions, sizes, shapes, and lattice parameters and symmetry); however, the ability to tune macroscale structural features, such as the relative positions of crystals to one another and lattice orientations, has yet to be realized. Here, inspiration is drawn from epitaxial growth strategies in atomic crystallization, and patterned substrates are prepared that, when used in conjunction with DNA-mediated nanoparticle crystallization, allow for control over individual Wulff-shaped crystal growth, location, and orientation. In addition, the approach allows exquisite control over the patterned substrate/crystal lattice mismatch, something not yet realized for any epitaxy process. This level of structural control is a significant step toward realizing complex, integrated devices with colloidal crystal components, and this approach provides a model system for further exploration in epitaxy systems.

Microfluidic Synthesis of Hybrid TiO2-Anisotropic Gold Nanoparticles with Visible and Near-Infrared Activity

Anisotropic gold nanoparticles (AuNPs), with their unique physical and optical properties, are emerging as smart and key nanomaterials and are being exploited in many crucial fields. To further improve their range of action, anisotropic AuNPs have been coupled with semiconductors, mainly TiO₂ (titania), receiving great interest as powerful platforms both in biomedicine and in catalytic applications. Such hybrid nanoparticles show new properties that arise from the synergic action of the components and rely on NP size, morphology, and arrangement. Therefore, continuous advances in design and fabrication of new hybrid titania@gold NPs (TiO₂@AuNPs) are urgent and highly desirable. Here, we propose an effective protocol to produce multibranched AuNPs covered by a controlled TiO₂ thin layer, exploiting a one-pot microfluidic process. The proposed method allows the in-flow and reliable synthesis of titania-functionalized-anisotropic gold nanoparticles by avoiding the use of toxic surfactants and controlling the titania shell formation. TiO₂@AuNPs have been fully characterized in terms of morphology, stability, and biocompatibility, and their activity in photocatalysis has been tested and verified.

"Colloid-Atom Duality" in the Assembly Dynamics of Concave Gold Nanoarrows

We use liquid-phase transmission electron microscopy (TEM) to study self-assembly dynamics of charged gold nanoarrows (GNAs), which reveal an unexpected "colloid-atom duality". On one hand, they assemble following the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory for colloids when van der Waals attraction overruns slightly screened electrostatic repulsion. Due to concaveness in shape, GNAs adopt zipper motifs with lateral offset in their assembly matching with our modeling of inter-GNA interaction, which form into unconventional structures resembling degenerate crystals. On the other hand, further screening of electrostatic repulsion leads to merging of clusters assembled from GNAs, reminiscent of the coalescence growth mode in atomic crystals driven by minimization of surface energy, as we measure from the surface fluctuation of clusters. Liquid-phase TEM captures the initial formation of highly curved necks bridging the two clusters. Analysis of the real-time evolution of neck width illustrates the first-time observation of coalescence in colloidal assemblies facilitated by rapid surface diffusion of GNAs. We attribute the duality to the confluence of factors (e.g., nanoscale colloidal interaction, diffusional dynamics) that we access by liquid-phase TEM, taking turns to dominate at different conditions, which is potentially generic to the nanoscale. The atom aspect, in particular, can inspire utilization of atomic crystal synthesis strategies to encode structure and dynamics in nanoscale assembly.

DNA Base Pair Stacking Crystallization of Gold Colloids

We describe a DNA base pair (bp) stacking driven 3D crystallization of 70-80 nm gold nanospheres (Au NSs) into a large-area, face-centered-cubic (FCC) lattice. Although great advances have been achieved over the past decade, DNA nanoparticle (NP) crystallization has relied solely on the base complementary binding. This limits the accessible crystal size particularly for the larger and heavier Au NPs (>50 nm). In this work, we argue that the use of DNA bp-stacking (so-called blunt-end stacking) instead of complementary binding can widen the scope of controlled interparticle interactions used to assemble larger Au colloids into a larger-area crystal. Through the optimization of the melting transition, relatively large Au NSs (e.g., 75 nm) with nearly ideal roundness can be crystallized into FCC crystals with the area of up to approximately 1400 μm². A strong metallodielectric stopband is experimentally observed in the visible range, confirming the high quality of our self-assembled Au colloidal crystals.

Programmable Atom Equivalents: Atomic Crystallization as a Framework for Synthesizing Nanoparticle Superlattices

Decades of research efforts into atomic crystallization phenomenon have led to a comprehensive understanding of the pathways through which atoms form different crystal structures. With the onset of nanotechnology, methods that use colloidal nanoparticles (NPs) as nanoscale "artificial atoms" to generate hierarchically ordered materials are being developed as an alternative strategy for materials synthesis. However, the assembly mechanisms of NP-based crystals are not always as well-understood as their atomic counterparts. The creation of a tunable nanoscale synthon whose assembly can be explained using the context of extensively examined atomic crystallization will therefore provide significant advancement in nanomaterials synthesis. DNA-grafted NPs have emerged as a strong candidate for such a "programmable atom equivalent" (PAE), because the predictable nature of DNA base-pairing allows for complex yet easily controlled assembly. This Review highlights the characteristics of these PAEs that enable controlled assembly behaviors analogous to atomic phenomena, which allows for rational material design well beyond what can be achieved with other crystallization techniques.

Fabrication of Metal Nanostructures on DNA Templates

Metal nanoarchitectures fabrication based on DNA assembly has attracted a good deal of attention. DNA nanotechnology enables precise organization of nanoscale objects with extraordinary structural programmability. The spatial addressability of DNA nanostructures and sequence-dependent recognition allow functional elements to be precisely positioned; thus, novel functional materials that are difficult to produce using conventional methods could be fabricated. This review focuses on the recent development of the fabrication strategies toward manipulating the shape and morphology of metal nanoparticles and nanoassemblies based on the rational design of DNA structures. DNA-mediated metallization, including DNA-templated conductive nanowire fabrication and sequence-selective metal deposition, etc., is briefly introduced. The modifications of metal nanoparticles (NPs) with DNA and subsequent construction of heterogeneous metal nanoarchitectures are highlighted. Importantly, DNA-assembled dynamic metal nanostructures that are responsive to different stimuli are also discussed as they allow the design of smart and dynamic materials. Meanwhile, the prospects and challenges of these shape-and morphology-controlled strategies are summarized.

Density-Gradient Control over Nanoparticle Supercrystal Formation

With the advent of DNA-directed methods to form "single crystal" nanoparticle superlattices, new opportunities for studying the properties of such structures across many length scales now exist. These structure-property relationships rely on the ability of one to deliberately use DNA to control crystal symmetry, lattice parameter, and microscale crystal habit. Although DNA-programmed colloidal crystals consistently form thermodynamically favored crystal habits with a well-defined symmetry and lattice parameter based upon well-established design rules, the sizes of such crystals often vary substantially. For many applications, especially those pertaining to optics, each crystal can represent a single device, and therefore size variability can significantly reduce their scope of use. Consequently, we developed a new method based upon the density difference between two layers of solvents to control nanoparticle superlattice formation and growth. In a top aqueous layer, the assembling particles form a less viscous and less dense state, but once the particles assemble into well-defined rhombic dodecahedral superlattices of a critical size, they sediment into a higher density and higher viscosity sublayer that does not contain particles (aqueous polysaccharide), thereby arresting growth. As a proof-of-concept, this method was used to prepare a uniform batch of Au nanoparticle (20.0 ± 1.6 nm in diameter) superlattices in the form of 0.95 ± 0.20 μm edge length rhombic dodecahedra with body-centered cubic crystal symmetries and a 49 nm lattice parameter (cf. 1.04 ± 0.38 μm without the sublayer). This approach to controlling and arresting superlattice growth yields structures with a 3-fold enhancement in the polydispersity index.

Assembly of three-dimensional binary superlattices from multi-flavored particles

Binary superlattices constructed from nano- or micron-sized colloidal particles have a wide variety of applications, including the design of advanced materials. Self-assembly of such crystals from their constituent colloids can be achieved in practice by, among other means, the functionalization of colloid surfaces with single-stranded DNA sequences. However, when driven by DNA, this assembly is traditionally premised on the pairwise interaction between a single DNA sequence and its complement, and often relies on particle size asymmetry to entropically control the crystalline arrangement of its constituents. The recently proposed "multi-flavoring" motif for DNA functionalization, wherein multiple distinct strands of DNA are grafted in different ratios to different colloids, can be used to experimentally realize a binary mixture in which all pairwise interactions are independently controllable. In this work, we use various computational methods, including molecular dynamics and Wang-Landau Monte Carlo simulations, to study a multi-flavored binary system of micron-sized DNA-functionalized particles modeled implicitly by Fermi-Jagla pairwise interactions. We show how self-assembly of such systems can be controlled in a purely enthalpic manner, and by tuning only the interactions between like particles, demonstrate assembly into various morphologies. Although polymorphism is present over a wide range of pairwise interaction strengths, we show that careful selection of interactions can lead to the generation of pure compositionally ordered crystals. Additionally, we show how the crystal composition changes with the like-pair interaction strengths, and how the solution stoichiometry affects the assembled structures.

Controlled growth and shape-directed self-assembly of gold nanoarrows

Self-assembly of colloidal nanocrystals into complex superstructures offers notable opportunities to create functional devices and artificial materials with unusual properties. Anisotropic nanoparticles with nonspherical shapes, such as rods, plates, polyhedra, and multipods, enable the formation of a diverse range of ordered superlattices. However, the structural complexity and tunability of nanocrystal superlattices are restricted by the limited geometries of the anisotropic nanoparticles available for supercrystal self-assembly. We show that uniform gold nanoarrows (GNAs) consisting of two pyramidal heads connected by a four-wing shaft are readily synthesized through controlled overgrowth of gold nanorods. The distinct concave geometry endows the GNAs with unique packing and interlocking ability and allows for the shape-directed assembly of sophisticated two-dimensional (2D) and 3D supercrystals with unprecedented architectures. Net-like 2D supercrystals are assembled through the face-to-face contact of the GNAs lying on the pyramidal edges, whereas zipper-like and weave-like 2D supercrystals are constructed by the interlocked GNAs lying on the pyramidal {111} facets. Furthermore, multilayer packing of net-like and weave-like 2D assemblies of GNAs leads to non-close-packed 3D supercrystals with varied packing efficiencies and pore structures. Electromagnetic simulation of the diverse nanoarrow supercrystals exhibits exotic patterns of nanoscale electromagnetic field confinement. This study may open new avenues toward tunable self-assembly of nanoparticle superstructures with increased complexity and unusual functionality and may advance the design of novel plasmonic metamaterials for nanophotonics and reconfigurable architectured materials.