Regulating phase behavior of nanoparticle assemblies through engineering of DNA-mediated isotropic interactions.

Self-assembly of isotropically interacting particles into desired crystal structures could allow for creating designed functional materials via simple synthetic means. However, the ability to use isotropic particles to assemble different crystal types remains challenging, especially for generating low-coordinated crystal structures. Here, we demonstrate that isotropic pairwise interparticle interactions can be rationally tuned through the design of DNA shells in a range that allows transition from common, high-coordinated FCC-CuAu and BCC-CsCl lattices, to more exotic symmetries for spherical particles such as the SC-NaCl lattice and to low-coordinated crystal structures (i.e., cubic diamond, open honeycomb). The combination of computational and experimental approaches reveals such a design strategy using DNA-functionalized nanoparticles and successfully demonstrates the realization of BCC-CsCl, SC-NaCl, and a weakly ordered cubic diamond phase. The study reveals the phase behavior of isotropic nanoparticles for DNA-shell tunable interaction, which, due to the ease of synthesis is promising for the practical realization of non-close-packed lattices.

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.

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.

DNA origami protection and molecular interfacing through engineered sequence-defined peptoids.

DNA nanotechnology has established approaches for designing programmable and precisely controlled nanoscale architectures through specific Watson-Crick base-pairing, molecular plasticity, and intermolecular connectivity. In particular, superior control over DNA origami structures could be beneficial for biomedical applications, including biosensing, in vivo imaging, and drug and gene delivery. However, protecting DNA origami structures in complex biological fluids while preserving their structural characteristics remains a major challenge for enabling these applications. Here, we developed a class of structurally well-defined peptoids to protect DNA origamis in ionic and bioactive conditions and systematically explored the effects of peptoid architecture and sequence dependency on DNA origami stability. The applicability of this approach for drug delivery, bioimaging, and cell targeting was also demonstrated. A series of peptoids (PE1-9) with two types of architectures, termed as "brush" and "block," were built from positively charged monomers and neutral oligo-ethyleneoxy monomers, where certain designs were found to greatly enhance the stability of DNA origami. Through experimental and molecular dynamics studies, we demonstrated the role of sequence-dependent electrostatic interactions of peptoids with the DNA backbone. We showed that octahedral DNA origamis coated with peptoid (PE2) can be used as carriers for anticancer drug and protein, where the peptoid modulated the rate of drug release and prolonged protein stability against proteolytic hydrolysis. Finally, we synthesized two alkyne-modified peptoids (PE8 and PE9), conjugated with fluorophore and antibody, to make stable DNA origamis with imaging and cell-targeting capabilities. Our results demonstrate an approach toward functional and physiologically stable DNA origami for biomedical applications.

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.

Compact Peptoid Molecular Brushes for Nanoparticle Stabilization.

Controlling the interfaces and interactions of colloidal nanoparticles (NPs) via tethered molecular moieties is crucial for NP applications in engineered nanomaterials, optics, catalysis, and nanomedicine. Despite a broad range of molecular types explored, there is a need for a flexible approach to rationally vary the chemistry and structure of these interfacial molecules for controlling NP stability in diverse environments, while maintaining a small size of the NP molecular shell. Here, we demonstrate that low-molecular-weight, bifunctional comb-shaped, and sequence-defined peptoids can effectively stabilize gold NPs (AuNPs). The generality of this robust functionalization strategy was also demonstrated by coating of silver, platinum, and iron oxide NPs with designed peptoids. Each peptoid (PE) is designed with varied arrangements of a multivalent AuNP-binding domain and a solvation domain consisting of oligo-ethylene glycol (EG) branches. Among designs, a peptoid (PE5) with a diblock structure is demonstrated to provide a superior nanocolloidal stability in diverse aqueous solutions while forming a compact shell (∼1.5 nm) on the AuNP surface. We demonstrate by experiments and molecular dynamics simulations that PE5-coated AuNPs (PE5/AuNPs) are stable in select organic solvents owing to the strong PE5 (amine)-Au binding and solubility of the oligo-EG motifs. At the vapor-aqueous interface, we show that PE5/AuNPs remain stable and can self-assemble into ordered 2D lattices. The NP films exhibit strong near-field plasmonic coupling when transferred to solid substrates.

Effect of mono- and multi-valent ionic environments on the in-lattice nanoparticle-grafted single-stranded DNA.

Polyelectrolyte (PE) chains respond in a complex manner to multivalent salt environments, and this behavior depends on pH, temperature, and the presence of specific counter ions. Although much work has been done to understand the behaviour of free PE chains, it is important to reveal their behaviour on a nanoparticle's surface, where surface constraints, particle geometry, and multi-chain environment can affect their behaviour and contribute to particles' assembly states. Our work investigates, using in situ small-angle X-ray scattering (SAXS), the morphology of PE (single-stranded DNA) chains grafted onto the surface of spherical gold nanoparticles assembled in a lattice in the presence of monovalent, divalent and trivalent salts. For divalent salts, the DNA brush length was found to decrease at a faster rate with salt concentration than in the monovalent salt environment, while trivalent salts led to chain collapse. Using a power law analysis and the modified Daoud-Cotton model, we have obtained insight into the mechanism of a nanoparticle-grafted chain's response to ionic environments. Our analysis suggests that the decrease in brush length is due to the conventional electrostatic screening for monovalent systems, whereas for divalent systems both electrostatic screening and divalent ion bridging must be considered.

Surface patterning of nanoparticles with polymer patches.

Patterning of colloidal particles with chemically or topographically distinct surface domains (patches) has attracted intense research interest. Surface-patterned particles act as colloidal analogues of atoms and molecules, serve as model systems in studies of phase transitions in liquid systems, behave as 'colloidal surfactants' and function as templates for the synthesis of hybrid particles. The generation of micrometre- and submicrometre-sized patchy colloids is now efficient, but surface patterning of inorganic colloidal nanoparticles with dimensions of the order of tens of nanometres is uncommon. Such nanoparticles exhibit size- and shape-dependent optical, electronic and magnetic properties, and their assemblies show new collective properties. At present, nanoparticle patterning is limited to the generation of two-patch nanoparticles, and nanoparticles with surface ripples or a 'raspberry' surface morphology. Here we demonstrate nanoparticle surface patterning, which utilizes thermodynamically driven segregation of polymer ligands from a uniform polymer brush into surface-pinned micelles following a change in solvent quality. Patch formation is reversible but can be permanently preserved using a photocrosslinking step. The methodology offers the ability to control the dimensions of patches, their spatial distribution and the number of patches per nanoparticle, in agreement with a theoretical model. The versatility of the strategy is demonstrated by patterning nanoparticles with different dimensions, shapes and compositions, tethered with various types of polymers and subjected to different external stimuli. These patchy nanocolloids have potential applications in fundamental research, the self-assembly of nanomaterials, diagnostics, sensing and colloidal stabilization.

Engineered Silicon Carbide Three-Dimensional Frameworks through DNA-Prescribed Assembly.

The ability to create nanoengineered silicon carbide (SiC) architectures is important for the diversity of optical, electronic, and mechanical applications. Here, we report a fabrication of periodic three-dimensional (3D) SiC nanoscale architectures using a self-assembled and designed 3D DNA-based framework. The assembly is followed by the templating into silica and subsequent conversion into SiC using a lower temperature pathway (<700 °C) via magnesium reduction. The formed SiC framework lattice has a unit size of about 50 nm and domains over 5 µm, and it preserves the integrity of the original 3D DNA lattice. The spectroscopic and electron microscopy characterizations reveal SiC crystalline morphology of 3D nanoarchitectured lattices, whereas electrical probing shows 2 orders of magnitude enhancements of electrical conductivity over the precursor silica framework. The reported approach offers a versatile methodology toward creating highly structured and spatially prescribed SiC nanoarchitectures through the DNA-programmable assembly and the combination of templating processes.

Divalent Multilinking Bonds Control Growth and Morphology of Nanopolymers.

Assembly of nanoscale objects into linear architectures resembling molecular polymers is a basic organization resulting from divalent interactions. Such linear architectures occur for particles with two binding patches on opposite sides, known as Janus particles. However, unlike molecular systems where valence bonds can be envisioned as pointlike interactions nanoscale patches are often realized through multiple molecular linkages. The relationship between the characteristics of these linkages, the resulting interpatch connectivity, and assembly morphology is not well-explored. Here, we investigate assembly behavior of model divalent nanomonomers, DNA nanocuboid with tailorable multilinking bonds. Our study reveals that the characteristics of individual molecular linkages and their collective properties have a profound effect on nanomonomer reactivity and resulting morphologies. Beyond linear nanopolymers, a common signature of divalent nanomonomers, we observe an effective valence increase as linkages lengthened, leading to the nanopolymer bundling. The experimental findings are rationalized by molecular dynamics simulations.

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.

Ordered three-dimensional nanomaterials using DNA-prescribed and valence-controlled material voxels.

The ability to organize nanoscale objects into well-defined three-dimensional (3D) arrays can translate advances in nanoscale synthesis into targeted material fabrication. Despite successes in nanoparticle assembly, most extant methods are system specific and not fully compatible with biomolecules. Here, we report a platform for creating distinct 3D ordered arrays from different nanomaterials using DNA-prescribed and valence-controlled material voxels. These material voxels consist of 3D DNA frames that integrate nano-objects within their scaffold, thus enabling the object's valence and coordination to be determined by the frame's vertices, which can bind to each other through hybridization. Such DNA material voxels define the lattice symmetry through the spatially prescribed valence decoupling the 3D assembly process from the nature of the nanocomponents, such as their intrinsic properties and shapes. We show this by assembling metallic and semiconductor nanoparticles and also protein superlattices. We support the technological potential of such an assembly approach by fabricating light-emitting 3D arrays with diffraction-limited spectral purity and 3D enzymatic arrays with increased activity.

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.

Publisher Correction: Regioselective surface encoding of nanoparticles for programmable self-assembly.

In the version of this Article originally published, the diblock copolymer structure in Fig. 2a showed a single bond between the carbon and the oxygen atoms; it should have been a double bond. This has been corrected in all versions of the Article.

Regioselective surface encoding of nanoparticles for programmable self-assembly.

Surface encoding of colloidal nanoparticles with DNA is fundamental for fields where recognition interaction is required, particularly controllable material self-assembly. However, regioselective surface encoding of nanoparticles is still challenging because of the difficulty associated with breaking the identical chemical environment on nanoparticle surfaces. Here we demonstrate the selective blocking of nanoparticle surfaces with a diblock copolymer (polystyrene-b-polyacrylic acid). By tuning the interfacial free energies of a ternary system involving the nanoparticles, solvent and copolymer, controllable accessibilities to the nanoparticles' surfaces are obtained. Through the modification of the polymer-free surface region with single-stranded DNA, regioselective and programmable surface encoding is realized. The resultant interparticle binding potential is selective and directional, allowing for an increased degree of complexity of potential self-assemblies. The versatility of this regioselective surface encoding strategy is demonstrated on various nanoparticles of isotropic or anisotropic shape and a total of 24 distinct complex nanoassemblies are fabricated.

Controllable Covalent-Bound Nanoarchitectures from DNA Frames.

Could one manipulate nanoscale building blocks using chemical reactions like molecular synthesis to yield new supra-nanoscale objects? The precise control over the final architecture might be challenging due to the size mismatch of molecularly scaled reactive functional groups and nanoscale building blocks, which limits a control over the valence and specific locations of reaction spots. Taking advantage of programmable octahedral DNA frame, we report a facile approach of engineering chemical reactions between nanoscale building blocks toward formation of controlled nanoarchitectures. Azide and alkyne moieties were specifically anchored onto desired vertices of DNA frames, providing chemically reactive nanoconstructs with directionally defined valence. Akin to the conventional molecular reactions, the formation of a variety of nanoscale architectures was readily achieved upon mixing of the frames with the different reactive valence and at different stoichiometric ratios. This strategy may open a door for a programmable synthesis of supra-nanoscale structures with complex architectures and diversified functions.

Liquid interfaces with pH-switchable nanoparticle arrays.

Stimuli-responsive 2D nanoscale systems offer intriguing opportunities for creating switchable interfaces. At liquid interfaces, such systems can provide control over interfacial energies, surface structure, and rheological and transport characteristics, which is relevant, for example, to bio- and chemical reactors, microfluidic devices, and soft robotics. Here, we explore the formation of a pH-responsive membrane formed from gold nanoparticles grafted with DNA (DNA-NPs) at a liquid-vapor interface. A DNA-NP 2D hexagonal lattice can be reversibly switched by pH modulation between an expanded state of non-connected nanoparticles at neutral pH and a contracted state of linked nanoparticles at acidic pH due to the AH+-H+A base pairing between A-motifs. Our in situ surface X-ray scattering studies reveal that the reversible lattice contraction can be tuned by the length of pH-activated linkers, with up to ∼71% change in surface area.

Stoichiometric control of DNA-grafted colloid self-assembly.

There has been considerable interest in understanding the self-assembly of DNA-grafted nanoparticles into different crystal structures, e.g., CsCl, AlB2, and Cr3Si. Although there are important exceptions, a generally accepted view is that the right stoichiometry of the two building block colloids needs to be mixed to form the desired crystal structure. To incisively probe this issue, we combine experiments and theory on a series of DNA-grafted nanoparticles at varying stoichiometries, including noninteger values. We show that stoichiometry can couple with the geometries of the building blocks to tune the resulting equilibrium crystal morphology. As a concrete example, a stoichiometric ratio of 3:1 typically results in the Cr3Si structure. However, AlB2 can form when appropriate building blocks are used so that the AlB2 standard-state free energy is low enough to overcome the entropic preference for Cr3Si. These situations can also lead to an undesirable phase coexistence between crystal polymorphs. Thus, whereas stoichiometry can be a powerful handle for direct control of lattice formation, care must be taken in its design and selection to avoid polymorph coexistence.

Surface Proton Transfer Promotes Four-Electron Oxygen Reduction on Gold Nanocrystal Surfaces in Alkaline Solution.

Four-electron oxygen reduction reaction (4e-ORR), a key pathway in energy conversion, is preferred over the two-electron reduction pathway that falls short in dissociating dioxygen molecules. Gold surfaces exhibit high sensitivity of the ORR pathway to its atomic structures. A long-standing puzzle remains unsolved: why the Au surfaces with {100} sub-facets were exceptionally capable to catalyze the 4e-ORR in alkaline solution, though limited within a narrow potential window. Herein we report the discovery of a dominant 4e-ORR over the whole potential range on {310} surface of Au nanocrystal shaped as truncated ditetragonal prism (TDP). In contrast, ORR pathways on single-crystalline facets of shaped nanoparticles, including {111} on nano-octahedra and {100} on nanocubes, are similar to their single-crystal counterparts. Combining our experimental results with density functional theory calculations, we elucidate the key role of surface proton transfers from co-adsorbed H2O molecules in activating the facet- and potential-dependent 4e-ORR on Au in alkaline solutions. These results elucidate how surface atomic structures determine the reaction pathways via bond scission and formation among weakly adsorbed water and reaction intermediates. The new insight helps in developing facet-specific nanocatalysts for various reactions.

Lattice engineering through nanoparticle-DNA frameworks.

Advances in self-assembly over the past decade have demonstrated that nano- and microscale particles can be organized into a large diversity of ordered three-dimensional (3D) lattices. However, the ability to generate different desired lattice types from the same set of particles remains challenging. Here, we show that nanoparticles can be assembled into crystalline and open 3D frameworks by connecting them through designed DNA-based polyhedral frames. The geometrical shapes of the frames, combined with the DNA-assisted binding properties of their vertices, facilitate the well-defined topological connections between particles in accordance with frame geometry. With this strategy, different crystallographic lattices using the same particles can be assembled by introduction of the corresponding DNA polyhedral frames. This approach should facilitate the rational assembly of nanoscale lattices through the design of the unit cell.