Stepwise surface encoding for high-throughput assembly of nanoclusters

Nucleic acid-responsive smart systems for controlled cargo delivery

Stimulus-responsive delivery systems allow controlled, highly regulated, and efficient delivery of various cargos while minimizing side effects. Owing to the unique properties of nucleic acids, including the ability to adopt complex structures by base pairing, their easy synthesis, high specificity, shape memory, and configurability, they have been employed in autonomous molecular motors, logic circuits, reconfigurable nanoplatforms, and catalytic amplifiers. Moreover, the development of nucleic acid (NA)-responsive intelligent delivery vehicles is a rapidly growing field. These vehicles have attracted much attention in recent years due to their programmable, controllable, and reversible properties. In this work, we review several types of NA-responsive controlled delivery vehicles based on locks and keys, including DNA/RNA-responsive, aptamer-responsive, and CRISPR-responsive, and summarize their advantages and limitations.

Welded Gold Nanoparticle Assemblies Defined Plasmonic Coupling

Nanoparticle assemblies with interparticle ohmic contacts are crucial for nanodevice fabrication. Despite tremendous progress in DNA-programmable nanoparticle assemblies, seamlessly welding discrete components into welded continuous three-dimensional (3D) configurations remains challenging. Here, we introduce a single-stranded DNA-encoded strategy to customize welded metal nanostructures with tunable morphologies and plasmonic properties. We demonstrate the precise welding of gold nanoparticle assemblies into continuous metal nanostructures with interparticle ohmic contacts through chemical welding in solution. We find that the welded gold nanoparticle assemblies show a consistent morphology with welded efficiency over 90%, such as the rod-like, triangular, and tetrahedral metal nanostructures. Next, we show the versatility of this strategy by welding gold nanoparticle assemblies of varied sizes and shapes. Furthermore, the experiment and simulation show that the welded gold nanoparticle assemblies exhibit defined plasmonic coupling. This single-stranded DNA encoded welding system may provide a new route for accurately building functional plasmonic nanomaterials and devices.

Structural Control of Plasmon Resonance in Molecularly Linked Metal Oxide Nanocrystal Gel Assemblies

Nanocrystal gels exhibit collective optical phenomena based on interactions among their constituent building blocks. However, their inherently disordered structures have made it challenging to understand, predict, or design properties such as optical absorption spectra that are sensitive to the coupling between the plasmon resonances of the individual nanocrystals. Here, we bring indium tin oxide nanocrystal gels under chemical control and show that their infrared absorption can be predicted and systematically tuned by selecting the nanocrystal sizes and compositions and molecular structures of the link-mediating surface ligands. Thermoreversible assemblies with metal-terpyridine links form reproducible gel architectures, enabling us to derive a plasmon ruler that governs the spectral shifts upon gelation, predicated on the nanocrystal and ligand compositions. This empirical guide is validated using large-scale, many-bodied simulations to compute the optical spectra of gels with varied structural parameters. Based on the derived plasmon ruler, we design and demonstrate a nanocrystal mixture whose spectrum exhibits distinctive line narrowing upon assembly.

Relating the length of a magnetic filament with solvophobic, superparamagnetic colloids to its properties in applied magnetic fields

The idea of creating polymer-like structures by crosslinking magnetic nanoparticles (MNPs) opened an alternative perspective on controlling the rheological properties of magnetoresponsive systems, because unlike suspensions of self-assembled MNPs, whose cluster sizes are sensitive to temperature, magnetic filaments (MFs) preserve their initial topology. Considering the length scales characteristic of single-domain nanoparticles used to create MFs, the MNPs can be both ferro- and superparamagnetic. Moreover, steric or electrostatic stabilization might not fully screen van der Waals interactions. In this paper, using coarse-grained molecular dynamics simulations, we investigate the influence of susceptibility of superparamagnetic MNPs-their number and central attraction forces between them-on the polymeric, structural, and magnetic properties of MFs with varied backbone rigidity. We find that, due to the general tendency of MFs with superparamagnetic monomers to bend, reinforced for colloids with a high susceptibility, properties of MFs vary greatly with chain length.

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.

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.

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.

Mechanical Janus Structures by Soft-Hard Material Integration

Engineering Janus structures that possess anisotropic features in functions have attracted growing attention for a wide range of applications in sensors, catalysis, and biomedicine, and are yet usually designed at the nanoscale with distinct physical or chemical functionalities in their opposite sides. Inspired by the seamless integration of soft and hard materials in biological structures, here a mechanical Janus structure composed of soft and hard materials with a dramatic difference in mechanical properties at an additively manufacturable macroscale is presented. In the combination of extensive experimental, theoretical, and computational studies, the design principle of soft-hard materials integrated mechanical Janus structures is established and their unique rotation mechanism is addressed. The systematic studies of assembling the Janus structure units into superstructures with well-ordered organizations by programming the local rotations are further shown, providing a direct route of designing superstructures by leveraging mechanical Janus structures with unique soft-hard material integration. Applications are conducted to demonstrate the features and functionalities of assembled superstructures with local ordered organizations in regulating and filtering acoustic wave propagations, thereby providing exemplification applications of mechanical Janus design in functional structures and devices.

Sorting Nanoparticles by Valency with DNA Barcoding

Self-assembly of DNA-labeled nanoparticles is an effective strategy to fabricate new nanocomposite materials and nanoscale devices from the bottom-up. To tailor the properties of the resulting material or device, one requires access to a wide range of nanoparticle sizes and shapes, as well as control over the number (valency) of DNA molecules on the nanoparticle surface. Currently, nanoparticles with a defined DNA valency can only be obtained in a narrow range of sizes, and in small quantities, limiting the properties of the resulting composite structures and their applications. Here, we leverage the digital information encoded in the number and sequence of short DNA barcodes to generate preparatory amounts of nanoparticles bearing a specific number of DNA molecules, irrespective of the identity of the nanocomponent. We show that this DNA valency sorting chromatography, which is driven by the selective affinity of Watson-Crick base pairs, is applicable to arbitrary DNA sequences and a broad range of nanoparticle sizes, shapes, and material compositions. To further demonstrate this fact, we use valency-sorted large gold nanospheres directly in self-assembly schemes to create, in one synthesis step, large amounts of several previously inaccessible molecule-like dimer and trimer nanostructures with unique optical properties. We anticipate that the expanded scope of DNA valency-defined nanoparticle reagents, and the increased scale at which they can be produced, will open new avenues for the molecularly precise manipulation of nanoscale matter.

Self-Assembled Metal Nanoclusters: Driving Forces and Structural Correlation with Optical Properties

Studies on self-assembly of metal nanoclusters (MNCs) are an emerging field of research owing to their significant optical properties and potential applications in many areas. Fabricating the desired self-assembly structure for specific implementation has always been challenging in nanotechnology. The building blocks organize themselves into a hierarchical structure with a high order of directional control in the self-assembly process. An overview of the recent achievements in the self-assembly chemistry of MNCs is summarized in this review article. Here, we investigate the underlying mechanism for the self-assembly structures, and analysis reveals that van der Waals forces, electrostatic interaction, metallophilic interaction, and amphiphilicity are the crucial parameters. In addition, we discuss the principles of template-mediated interaction and the effect of external stimuli on assembly formation in detail. We also focus on the structural correlation of the assemblies with their photophysical properties. A deep perception of the self-assembly mechanism and the degree of interactions on the excited state dynamics is provided for the future synthesis of customizable MNCs with promising applications.

Low-entropy lattices engineered through bridged DNA origami frames

The transformation from disorder to order in self-assembly is an autonomous entropy-decreasing process. The spatial organization of nanoscale anisotropic building blocks involves the intrinsic heterogeneity in three dimensions and requires sufficiently precise control to coordinate intricate interactions. Only a few approaches have been shown to achieve the anisotropic extension from components to assemblies. Here, we demonstrate the ability to engineer three-dimensional low-entropy lattices at the nucleotide level from modular DNA origami frames. Through the programmable DNA bridging strategy, DNA domains of the same composition are periodically arranged in the crystal growth directions. We combine the site-specific positioning of guest nanoparticles to reflect the anisotropy control, which is validated by small-angle X-ray scattering and electron microscopy. We expect that our DNA origami-mediated crystallization method will facilitate both the exploration of refined self-assembly platforms and the creation of anisotropic metamaterials.

Through the bridging principle, DNA origami building blocks are integrated into ordered self-assembled structures. Periodically arranged DNA domains can locate the nanoparticles in a uniform site to achieve precise control of the contents.

Synthesis, Assembly, Optical Properties, and Sensing Applications of Plasmonic Gap Nanostructures

Plasmonic gap nanostructures (PGNs) have been extensively investigated mainly because of their strongly enhanced optical responses, which stem from the high intensity of the localized field in the nanogap. The recently developed methods for the preparation of versatile nanogap structures open new avenues for the exploration of unprecedented optical properties and development of sensing applications relying on the amplification of various optical signals. However, the reproducible and controlled preparation of highly uniform plasmonic nanogaps and the prediction, understanding, and control of their optical properties, especially for nanogaps in the nanometer or sub-nanometer range, remain challenging. This is because subtle changes in the nanogap significantly affect the plasmonic response and are of paramount importance to the desired optical performance and further applications. Here, recent advances in the synthesis, assembly, and fabrication strategies, prediction and control of optical properties, and sensing applications of PGNs are discussed, and perspectives toward addressing these challenging issues and the future research directions are presented.

Janus Nanoparticles: From Fabrication to (Bio)Applications

Janus nanoparticles (JNPs) refer to the integration of two or more chemically discrepant composites into one structure system. Studies into JNPs have been of significant interest due to their interesting characteristics stemming from their asymmetric structures, which can integrate different functional properties and perform more synergetic functions simultaneously. Herein, we present recent progress of Janus particles, comprehensively detailing fabrication strategies and applications. First, the classification of JNPs is divided into three blocks, consisting of polymeric composites, inorganic composites, and hybrid polymeric/inorganic JNPs composites. Then, the fabrication strategies are alternately summarized, examining self-assembly strategy, phase separation strategy, seed-mediated polymerization, microfluidic preparation strategy, nucleation growth methods, and masking methods. Finally, various intriguing applications of JNPs are presented, including solid surfactants agents, micro/nanomotors, and biomedical applications such as biosensing, controlled drug delivery, bioimaging, cancer therapy, and combined theranostics. Furthermore, challenges and future works in this field are provided.

One-Step Synthesis of Single-Stranded DNA-Bridged Iron Oxide Supraparticles as MRI Contrast Agents

Despite progress on DNA-assembled nanoparticle (NP) superstructures, their complicated synthesis procedures hamper their potential biomedical applications. Here, we present an exceptionally simple strategy for the synthesis of single-stranded DNA (ssDNA) assembled Fe₃O₄ supraparticles (DFe-SPs) as magnetic resonance contrast agents. Unlike traditional approaches that assemble DNA-conjugated NPs via Watson-Crick hybridization, our DFe-SPs are formed with a high yield through one-step synthesis and assembly of ultrasmall Fe₃O₄ NPs via ssDNA-metal coordination bridges. We demonstrate that the DFe-SPs can efficiently accumulate into tumors for sensitive MR imaging. By virtue of reversible DNA-metal coordination bridges, the DFe-SPs could be disassembled into isolated small NPs in vivo, facilitating their elimination from the body. This work opens a new avenue for the ssDNA-mediated synthesis of superstructures, which expands the repertoire of DNA-directed NP assembly for biomedical applications.

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.

Local Environment Affects the Activity of Enzymes on a 3D Molecular Scaffold

The ability to coordinate and confine enzymes presents an opportunity to affect their performance and to create chemically active materials. Recent studies show that polymers and biopolymers can be used to scaffold enzymes, and that can lead to the modulated biocatalytic efficiency. Here, we investigated the role of microenvironments on enzyme activity using a well-defined molecular scaffold. An enzyme, glucose oxidase (GOx), was positioned at different locations of a three-dimensional (3D) octahedral DNA scaffold (OS), allowing the enzyme's polyanionic environments to be altered. Using electrical sensing, based on a bipolar junction transistor, we measured directly and in real-time the enzyme's proton generation at these different microenvironments. We found a 200% enhancement of immobilized enzyme over free GOx and about a 30% increase in catalytic rates when the enzyme was moved on the same molecular scaffold to a microenvironment with a higher local concentration of polyanions, which suggests a role of local pH on the enzymatic activity.

Self-limiting directional nanoparticle bonding governed by reaction stoichiometry

Nanoparticle clusters with molecular-like configurations are an emerging class of colloidal materials. Particles decorated with attractive surface patches acting as analogs of functional groups are used to assemble colloidal molecules (CMs); however, high-yield generation of patchy nanoparticles remains a challenge. We show that for nanoparticles capped with complementary reactive polymers, a stoichiometric reaction leads to reorganization of the uniform ligand shell and self-limiting nanoparticle bonding, whereas electrostatic repulsion between colloidal bonds governs CM symmetry. This mechanism enables high-yield CM generation and their programmable organization in hierarchical nanostructures. Our work bridges the gap between covalent bonding taking place at an atomic level and colloidal bonding occurring at the length scale two orders of magnitude larger and broadens the methods for nanomaterial fabrication.

Characterisation of the magnetic response of nanoscale magnetic filaments in applied fields

Incorporating magnetic nanoparticles (MNPs) within permanently crosslinked polymer-like structures opens up the possibility for synthesis of complex, highly magneto-responsive systems. Among such structures are chains of prealigned magnetic (ferro- or super-paramagnetic) monomers, permanently crosslinked by means of macromolecules, which we refer to as magnetic filaments (MFs). In this paper, using molecular dynamics simulations, we encompass filament synthesis scenarios, with a compact set of easily tuneable computational models, where we consider two distinct crosslinking approaches, for both ferromagnetic and super-paramagnetic monomers. We characterise the equilibrium structure, correlations and magnetic properties of MFs in static magnetic fields. Calculations show that MFs with ferromagnetic MNPs in crosslinking scenarios where the dipole moment orientations are decoupled from the filament backbone, have similar properties to MFs with super-paramagnetic monomers. At the same time, magnetic properties of MFs with ferromagnetic MNPs are more dependent on the crosslinking approach than they are for ones with super-paramagnetic monomers. Our results show that, in a strong applied field, MFs with super-paramagnetic MNPs have similar magnetic properties to ferromagnetic ones, while exhibiting higher susceptibility in low fields. We find that MFs with super-paramagnetic MNPs have a tendency to bend the backbone locally rather than to fully stretch along the field. We explain this behaviour by supplementing Flory theory with an explicit dipole-dipole interaction potential, with which we can take in to account folded filament configurations. It turns out that the entropy gain obtained through bending compensates an insignificant loss in dipolar energy for the filament lengths considered in the manuscript.

Stepwise assembly of nanoclusters guided by DNA origami frames with high-throughput

We contrive two strategies to assemble well-defined nanoclusters with high-throughput guided by DNA origami frames either by (1) introducing a micro-sized surface to fabricate patchy particles for binding with DNA structures or (2) restricting the assembly process of free nanoparticles and DNA origami frames on the fixed sites. Both the strategies can omit the process of gel purification of the final products.

Self-assembly and phase behavior of mixed patchy colloids with any bonding site geometry: theory and simulation

Patchy colloids and associating fluids have attracted continued interest due to the interesting phase behavior and self-assembly in solution. The ability to fabricate patchy colloids with multiple attractive surface patches of different number, size, shape, and relative location makes patchy colloids a good candidate as building blocks to form complex advanced materials. However, a theory that clearly relates the self-assembled structures that form based on the anisotropic interactions has been missing. Although Wertheim's theory in the form of the SAFT model is widely used to predict self-assembly and phase behavior in solution, SAFT does not include multibody correlations necessary to model any shape of association site or sites that can form multiple bonds. We have recently developed a new theory for associating colloids that naturally incorporates multibody correlations based on a cluster distribution approach due to Bansal, Asthagiri, Marshall, and Chapman (BAMC). In this paper, we extended the cluster distribution theory to predict the thermodynamic properties and phase behavior of binary systems consisting of anisotropic particles with any geometry of bonding site. In particular, we consider self-assembly of Janus particles, Saturn particles, and ternary particles mixed with solvent colloids that have two directional patchy sites. Good agreement between theoretical predictions and molecular simulation is shown for self-assembly, thermodynamic properties in this system. Re-entrant phase behavior has been investigated and low density gels is predicted.

Programmable dynamic covalent nanoparticle building blocks with complementary reactivity

A toolkit of two complementary dynamic covalent nanoparticles enables programmable and reversible nanoparticle functionalization and construction of adaptive binary assemblies.

Nanoparticle-based devices, materials and technologies will demand a new era of synthetic chemistry where predictive principles familiar in the molecular regime are extended to nanoscale building blocks. Typical covalent strategies for modifying nanoparticle-bound species rely on kinetically controlled reactions optimised for efficiency but with limited capacity for selective and divergent access to a range of product constitutions. In this work, monolayer-stabilized nanoparticles displaying complementary dynamic covalent hydrazone exchange reactivity undergo distinct chemospecific transformations by selecting appropriate combinations of ‘nucleophilic’ or ‘electrophilic’ nanoparticle-bound monolayers with nucleophilic or electrophilic molecular modifiers. Thermodynamically governed reactions allow modulation of product compositions, spanning mixed-ligand monolayers to exhaustive exchange. High-density nanoparticle-stabilizing monolayers facilitate in situ reaction monitoring by quantitative ¹⁹F NMR spectroscopy. Kinetic analysis reveals that hydrazone exchange rates are moderately diminished by surface confinement, and that the magnitude of this effect is dependent on mechanistic details: surface-bound electrophiles react intrinsically faster, but are more significantly affected by surface immobilization than nucleophiles. Complementary nanoparticles react with each other to form robust covalently connected binary aggregates. Endowed with the adaptive characteristics of the dynamic covalent linking process, the nanoscale assemblies can be tuned from extended aggregates to colloidally stable clusters of equilibrium sizes that depend on the concentration of a monofunctional capping agent. Just two ‘dynamic covalent nanoparticles’ with complementary thermodynamically governed reactivities therefore institute a programmable toolkit offering flexible control over nanoparticle surface functionalization, and construction of adaptive assemblies that selectively combine several nanoscale building blocks.

Reversible Polymerization-like Kinetics for Programmable Self-Assembly of DNA-Encoded Nanoparticles with Limited Valence

A similarity between the polymerization reaction of molecules and the self-assembly of nanoparticles provides a unique way to reliably predict structural characteristics of nanoparticle ensembles. However, the quantitative elucidation of programmable self-assembly kinetics of DNA-encoded nanoparticles is still challenging due to the existence of hybridization and dehybridization of DNA strands. Herein, a joint theoretical-computational method is developed to explicate the mechanism and kinetics of programmable self-assembly of limited-valence nanoparticles with surface encoding of complementary DNA strands. It is revealed that the DNA-encoded nanoparticles are programmed to form a diverse range of self-assembled superstructures with complex architecture, such as linear chains, sols, and gels of nanoparticles. It is theoretically demonstrated that the programmable self-assembly of DNA-encoded nanoparticles with limited valence generally obeys the kinetics and statistics of reversible step-growth polymerization originally proposed in polymer science. Furthermore, the theoretical-computational method is applied to capture the programmable self-assembly behavior of bivalent DNA-protein conjugates. The obtained results not only provide fundamental insights into the programmable self-assembly of DNA-encoded nanoparticles but also offer design rules for the DNA-programmed superstructures with elaborate architecture.

Three-Dimensional Molecular Transfer from DNA Nanocages to Inner Gold Nanoparticle Surfaces

It is of great interest to construct DNA-functionalized gold nanoparticles (DNA-AuNPs) with a controllable number of DNA strands and relative orientations. Herein, we describe a three-dimensional (3D) molecular transfer strategy, in which a pattern of DNA strands can be transferred from a DNA icosahedron cage (I-Cage) to the wrapped AuNP surface. The results show that DNA-AuNPs produced by this method inherit DNA pattern information encoded in the transient I-Cage template with high fidelity. Controllable numbers and positions of DNA on the surface of AuNPs can be simultaneously realized by direct "printing" of a DNA pattern from the nanoshell (I-Cage) to the nanocore (AuNP), further expanding the applications of DNA nanotechnology to nanolithography. Prospectively, the customized DNA-printed nanoparticles possess great potential for constructing programmable architectures for optoelectronic devices as well as smart biosensors for biomedical applications.

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.

Redox Engineering of Cytochrome c using DNA Nanostructure-Based Charged Encapsulation and Spatial Control

Three-dimensional (3D) DNA nanostructures facilitate the directed self-assembly of various objects with designed patterns with nanometer scale addressability. Here, we report the enhancement of cytochrome c (cyt c) redox activity by using a designed 3D DNA nanostructure attached to a gold electrode to spatially control the position of cyt c within the tetrahedral framework. Charged encapsulation and spatial control result in the significantly increased redox potential and enhanced electron transfer of this redox protein when compared to cyt c directly adsorbed on the gold surface. Two different protein attachment sites on one double stranded edge of a DNA tetrahedron were used to position cyt c inside and outside of the cage. Cyt c at both binding sites show similar redox potential shift and only slight difference in the electron transfer rate, both orders of magnitude faster than the cases when the protein was directly deposited on the gold electrode, likely due to an effective electron transfer pathway provided by the stabilization effect of the protein created by the DNA framework. This study shows great potential of using structural DNA nanotechnology for spatial control of protein positioning on electrode, which opens new routes to engineer redox proteins and interface microelectronic devices with biological function.

Stepwise Ligand-induced Self-assembly for Facile Fabrication of Nanodiamond-Gold Nanoparticle Dimers via Noncovalent Biotin-Streptavidin Interactions

Nanodiamond-gold nanoparticle (ND-AuNP) dimers constitute a potent tool for controlled thermal heating of biological systems on the nanoscale, by combining a local light-induced heat source with a sensitive local thermometer. Unfortunately, previous solution-based strategies to build ND-AuNP conjugates resulted in large nanoclusters or a broad population of multimers with limited separation efficiency. Here, we describe a new strategy to synthesize discrete ND-AuNP dimers via the synthesis of biotin-labeled DNA-AuNPs through thiol chemistry and its immobilization onto the magnetic bead (MB) surface, followed by reacting with streptavidin-labeled NDs. The dimers can be easily released from MB via a strand displacement reaction and separated magnetically. Our method is facile, convenient, and scalable, ensuring high-throughput formation of very stable dimer structures. This ligand-induced self-assembly approach enables the preparation of a wide variety of dimers of designated sizes and compositions, thus opening up the possibility that they can be deployed in many biological actuation and sensing applications.

Multivalent Traptavidin-DNA Conjugates for the Programmable Assembly of Nanostructures

Here, we explore the extended utility of two important functional biomolecules, DNA and protein, by hybridizing them through avidin-biotin conjugation. We report a simple yet scalable technique of successive magnetic separations to synthesize traptavidin-DNA conjugates with four distinct DNA binding sites that can be used as a supramolecular building block for programmable assembly of nanostructures. Using this nanoassembly platform, we fabricate several different plasmonic nanostructures with various metallic as well as semiconductor nanoparticles in predetermined ways. We also use the platform to construct dendrimer nanostructures using valency-controlled traptavidin-DNA conjugates in a programmable manner. These results suggest that our protein-DNA supramolecular building blocks would make a significant contribution to the assembly of multicomponent and complex nanostructures for numerous contemporary and future applications from molecular imaging to drug delivery.

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.

Self-assembly and structural manipulation of diblock-copolymer grafted nanoparticles in a homopolymer matrix

Detailed coarse-grained molecular dynamics simulations are performed to investigate the structural and mechanical properties of nanoparticles (NPs) grafted with an amphiphilic AB diblock copolymer, with the A-block being compatible with NPs and the B-block being miscible with a homopolymer matrix.

Hierarchical Crystals Formed from DNA-Functionalized Janus Nanoparticles

Harnessing anisotropic interactions in a DNA-mediated nanoparticle assembly holds great promise as a rational strategy to advance this important area. Here, using molecular dynamics simulations, we report the formation of novel hierarchical crystalline assemblies of Janus nanoparticles functionalized with two types of DNA chains (DNA-JNPs). We find that in addition to the primary nanoparticle crystallization into face-centered cubic (FCC) structure, sequence-specific DNA hybridization events further direct the rotational orientation of the DNA-JNPs to diverse secondary crystalline phases including simple cubic (SC), tetragonally ordered cylinder (P4), and lamella (L) structures, which are mapped in the phase diagrams relating to various asymmetric parameters. The crystallization dynamics of such hierarchical crystals is featured by two consequent processes: entropy-dominated translational order for the primary crystalline structure and enthalpy-dominated rotational order for the secondary crystalline structure. For DNA-JNPs with high asymmetry in DNA sequence length, tetrahedral nanoclusters tend to be favored, which is revealed to be governed by the conformational entropy penalty caused by bounded DNA chains. This work might bear important consequences for constructing new classes of nanoparticle crystals with designed structures and properties at multiple levels and in a predictable manner.

Supraparticles: Functionality from Uniform Structural Motifs

Under the right process conditions, nanoparticles can cluster together to form defined, dispersed structures, which can be termed supraparticles. Controlling the size, shape, and morphology of such entities is a central step in various fields of science and technology, ranging from colloid chemistry and soft matter physics to powder technology and pharmaceutical and food sciences. These diverse scientific communities have been investigating formation processes and structure/property relations of such supraparticles under completely different boundary conditions. On the fundamental side, the field is driven by the desire to gain maximum control of the assembly structures using very defined and tailored colloidal building blocks, whereas more applied disciplines focus on optimizing the functional properties from rather ill-defined starting materials. With this review article, we aim to provide a connecting perspective by outlining fundamental principles that govern the formation and functionality of supraparticles. We discuss the formation of supraparticles as a result of colloidal properties interplaying with external process parameters. We then outline how the structure of the supraparticles gives rise to diverse functional properties. They can be a result of the structure itself (emergent properties), of the colocalization of different, functional building blocks, or of coupling between individual particles in close proximity. Taken together, we aim to establish structure-property and process-structure relationships that provide unifying guidelines for the rational design of functional supraparticles with optimized properties. Finally, we aspire to connect the different disciplines by providing a categorized overview of the existing, diverging nomenclature of seemingly similar supraparticle structures.

Aptamer based SERS detection of Salmonella typhimurium using DNA-assembled gold nanodimers

The authors describe a surface-enhanced Raman scattering (SERS) based aptasensor for Salmonella typhimurium (S. typhimurium). Gold nanoparticles (AuNPs; 35 nm i.d.) were functionalized with the aptamer (ssDNA 1) and used as the capture probe, while smaller (15 nm) AuNPs were modified with a Cy3-labeled complementary sequence (ssDNA 2) and used as the signalling probe. The asymmetric gold nanodimers (AuNDs) were assemblied with the Raman signal probe and the capture probe via hybridization of the complementary ssDNAs. The gap between two nanoparticles is a "hot spot" in which the Raman reporter Cy3 is localized. It experiences a strong enhancement of the electromagnetic field around the particle. After addition of S. typhimurium, it will be bound by the aptamer which therefore is partially dehybridized from its complementary sequence. Hence, Raman intensity drops. Under the optimal experimental conditions, the SERS signal at 1203 cm^-1 increases linearly with the logarithm of the number of colonies in the 10² to 10⁷ cfu·mL^-1 concentration range, and the limit of detection is 35 cfu·mL^-1. The method can be performed within 1 h and was successfully applied to the analysis of spiked milk samples and performed very well and with high specificity. Graphical abstract DNA-assembled asymmetric gold nanodimers (AuNDs) were synthesized and appllied in a SERS-based aptasensor for S. typhimurium. Capture probe was preferentially combined with S. typhimurium and the structure of the AuNDs was destroyed. The "hot spot" vanished partly, this resulting in the decreased Raman intensity of Cy3.

DNA Nanotechnology-Enabled Drug Delivery Systems

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

Encapsulation of Gold Nanoparticles into DNA Minimal Cages for 3D-Anisotropic Functionalization and Assembly

Gold nanoparticles (AuNPs) endowed with anisotropic DNA valency are an important class of materials, as they can assemble into complex structures with a minimal number of DNA strands. However, methods to encode 3D DNA strand patterns on AuNPs with a controlled number of unique DNA strands in a predesigned spatial arrangement remain elusive. In this work, a simple one-step method to yield such DNA-decorated AuNPs is demonstrated, through encapsulating AuNPs into DNA minimal nanocages. The AuNP@DNA cage encapsulation complex inherits the 3D anisotropic molecular information from the DNA nanocage with enhanced structural stability. The DNA nanocage can be further functionalized and used as a building block for the self-assembly of complex architectures, such as dimers and trimers, programmed assemblies with sequential growth DNA backbones and DNA origami.

Intracellular localization of nanoparticle dimers by chirality reversal

The intra- and extracellular positioning of plasmonic nanoparticles (NPs) can dramatically alter their curative/diagnostic abilities and medical outcomes. However, the inability of common spectroscopic identifiers to register the events of transmembrane transport denies their intracellular vs. extracellular localization even for cell cultures. Here we show that the chiroptical activity of DNA-bridged NP dimers allows one to follow the process of internalization of the particles by the mammalian cells and to distinguish their extra- vs intra-cellular localizations by real-time spectroscopy in ensemble. Circular dichroism peaks in the visible range change from negative to positive during transmembrane transport. The chirality reversal is associated with a spontaneous twisting motion around the DNA bridge caused by the large change in electrostatic repulsion between NPs when the dimers move from interstitial fluid to cytosol. This finding opens the door for spectroscopic targeting of plasmonic nanodrugs and quantitative assessment of nanoscale interactions. The efficacy of dichroic targeting of chiral nanostructures for biomedical applications is exemplified here as photodynamic therapy of malignancies. The efficacy of cervical cancer cell elimination was drastically increased when circular polarization of incident photons matched to the preferential absorption of dimers localized inside the cancer cells, which is associated with the increased generation of reactive oxygen species and their preferential intracellular localization.

The ability to spectroscopically pinpoint whether nanoparticles are located inside or outside of cells represents an overarching need in biology and medicine. Here, the authors show that the chirality of DNA-bridged particle dimers reverses when they cross the cell membrane, providing a real-time chiroptical signature of their intra- or extracellular location.

Heterodimers Made of Upconversion Nanoparticles and Metal-Organic Frameworks

Creating nanoparticle dimers has attracted extensive interest. However, it still remains a great challenge to synthesize heterodimers with asymmetric compositions and synergistically enhanced functions. In this work, we report the synthesis of high quality heterodimers composed of porphyrinic nanoscale metal-organic frameworks (nMOF) and lanthanide-doped upconversion nanoparticles (UCNPs). Due to the dual optical properties inherited from individual nanoparticles and their interactions, absorption of low energy photons by the UCNPs is followed by energy transfer to the nMOFs, which then undergo activation of porphyrins to generate singlet oxygen. Furthermore, the strategy enables the synthesis of heterodimers with tunable UCNP size and dual NIR light harvesting functionality. We demonstrated that the hybrid architectures represent a promising platform to combine NIR-induced photodynamic therapy and chemotherapy for efficient cancer treatment. We believe that such heterodimers are capable of expanding their potential for applications in solar cells, photocatalysis, and nanomedicine.