Selective transformations between nanoparticle superlattices via the reprogramming of DNA-mediated interactions

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.

Nanoparticle Superlattices Driven by Linker-Mediated Covalent Bonding Interaction

The stability of the nanoparticle superlattice (NPSL) is essential for realizing its broad spectrum of potential applications. Here, we report a linker-mediated covalent bonding interaction method for the synthesis of highly stable NPSLs. Adipic acid is used as a linker molecule which connects two Au NPs functionalized with 6-mercaptohexanol through esterification reactions in the presence of H2SO4. As-prepared NPSLs are mostly fcc Wulff polyhedra with a fairly narrow size distribution and are highly stable in solvents of different polarities and pHs (0-14) as well as in dry conditions and at temperatures as high as 175 °C. The formation of NPSLs involves random homogeneous nucleation simultaneously accompanied by growth, a gradual change of the growth mode from reaction-controlled to diffusion-controlled with time, and the oriented attachments of small crystals. The size of the NPSL can be easily tuned by the concentration of linker molecules and the reaction temperature.

Self-Assembled DNA Nanospheres Driven by Carbon Dots for MicroRNAs Imaging in Tumor via Logic Circuit

DNA nanostructures with diverse biological functions have made significant advancements in biomedical applications. However, a universal strategy for the efficient production of DNA nanostructures is still lacking. In this work, a facile and mild method is presented for self-assembling polyethylenimine-modified carbon dots (PEI-CDs) and DNA into nanospheres called CANs at room temperature. This makes CANs universally applicable to multiple biological applications involving various types of DNA. Due to the ultra-small size and strong cationic charge of PEI-CDs, CANs exhibit a dense structure with high loading capacity for encapsulated DNA while providing excellent stability by protecting DNA from enzymatic hydrolysis. Additionally, Mg2+ is incorporated into CANs to form Mg@CANs which enriches the performance of CANs and enables subsequent biological imaging applications by providing exogenous Mg2+. Especially, a DNAzyme logic gate system that contains AND and OR Mg@CANs is constructed and successfully delivered to tumor cells in vitro and in vivo. They can be specifically activated by endogenic human apurinic/apyrimidinic endonuclease 1 and recognize the expression levels of miRNA-21 and miRNA-155 at tumor sites by logic biocomputing. A versatile pattern for delivery of diverse DNA and flexible logic circuits for multiple miRNAs imaging are developed.

Programming of Supercrystals Using Replicable DNA-Functionalized Colloids

The development of self-replicating systems is of great importance in research on the origin of life. As the most iconic molecules, nucleic acids have provided prominent examples of the fabrication of self-replicating artificial nanostructures. However, it is still challenging to construct sophisticated synthetic systems that can create large-scale or three-dimensionally ordered nanomaterials using self-replicating nanostructures. By integrating a template system containing DNA-functionalized colloidal seeds with a simplified DNA strand-displacement circuit programmed subsystem to produce DNA-functionalized colloidal copies, we developed a facile enthalpy-mediated strategy to control the replication and catalytic assembly of DNA-functionalized colloids in a time-dependent manner. The replication efficiency and crystal quality of the resulting superlattice structures can be effectively increased by regulating the molar ratio of the template to the copy colloids. By constructing binary systems from two types of gold nanoparticles (or proteins), superlattice structures with different crystal symmetries can be obtained through the replication and catalytic assembly processes. This programmable enthalpy-mediated approach was easily leveraged to achieve the phase transformation and catalytic amplification of colloidal crystals starting from different initial template crystals. This work offers a potential way to construct self-replicating artificial systems that exhibit complicated phase behaviors and can produce large-scale superlattice nanomaterials.

Growth of Nanocrystal Superlattices from Liquid Crystals

The growth of superlattices (SLs) made from self-assembled nanocrystals (NCs) is a powerful method for creating new materials and gaining insight into fundamental molecular dynamics. Previous explorations of NCSL syntheses have mostly compared them to crystallization. However, NCSL synthesis has not broadly shown cooling crystallization from saturated solutions as a reversible crystallization-dissolution process. We demonstrate the reversible growth of NCSLs by dispersing NCs in liquid crystal (LC) "smart solvents," and harnessing the transitions between the isotropic and nematic phases of the LCs. The growth mode and morphology can be tuned. This process is a model platform for studying crystallization and demonstrates great potential in manufacturing NCSLs as colloidal crystals through liquid-phase epitaxy or colloidal synthesis.

Designing Superselectivity in Linker-Mediated Multivalent Nanoparticle Adsorption

Using a statistical mechanical model and numerical simulations, we provide the design principle for the bridging strength (ξ) and linker density (ρ) dependent superselectivity in linker-mediated multivalent nanoparticle adsorption. When the bridges are insufficient, the formation of multiple bridges leads to both ξ- and ρ-dependent superselectivity. When the bridges are excessive, the system becomes insensitive to bridging strength due to entropy-induced self-saturation and shows a superselective desorption with respect to the linker density. Counterintuitively, lower linker density or stronger bridging strength enhances the superselectivity. These findings help the understanding of relevant biological processes and open up opportunities for applications in biosensing, drug delivery, and programmable self-assembly.

Van der Waals Colloidal Crystals

A general guiding principle for colloidal crystallization is to tame the attractive enthalpy such that it slightly overwhelms the repulsive interaction. As-synthesized colloids are generally designed to retain a strong repulsive potential for the high stability of suspensions, encoding appropriate attractive potentials into colloids has been key to their crystallization. Despite the myriad of interparticle attractions for colloidal crystallization, the van der Waals (vdW) force remains unexplored. Here, it is shown that the implementation of gold cores into silica colloids and the resulting vdW force can reconfigure the pair potential well depth to the optimal range between -1 and -4 kB T at tens of nanometer-scale colloidal distances. As such, colloidal crystals with a distinct liquid gap can be formed, which is evidenced by photonic bandgap-based diffractive colorization.

Dynamic Nanocrystal Superlattices with Thermally Triggerable Lubricating Ligands

The size-dependent and collective physical properties of nanocrystals (NCs) and their self-assembled superlattices (SLs) enable the study of mesoscale phenomena and the design of metamaterials for a broad range of applications. However, the limited mobility of NC building blocks in dried NCSLs often hampers the potential for employing postdeposition methods to produce high-quality NCSLs. In this study, we present tailored promesogenic ligands that exhibit a lubricating property akin to thermotropic liquid crystals. The lubricating ability of ligands is thermally triggerable, allowing the dry solid NC aggregates deposited on the substrates with poor ordering to be transformed into NCSLs with high crystallinity and preferred orientations. The interplay between the dynamic behavior of NCSLs and the molecular structure of the ligands is elucidated through a comprehensive analysis of their lubricating efficacy using both experimental and simulation approaches. Coarse-grained molecular dynamic modeling suggests that a shielding layer from mesogens prevents the interdigitation of ligand tails, facilitating the sliding between outer shells and consequently enhancing the mobility of NC building blocks. The dynamic organization of NCSLs can also be triggered with high spatial resolution by laser illumination. The principles, kinetics, and utility of lubricating ligands could be generalized to unlock stimuli-responsive metamaterials from NCSLs and contribute to the fabrication of NCSLs.

Multi-Functional Applications of H-Glass Embedded with Stable Plasmonic Gold Nanoislands

Metal nanoparticles (MNPs) are synthesized using various techniques on diverse substrates that significantly impact their properties. However, among the substrate materials investigated, the major challenge is the stability of MNPs due to their poor adhesion to the substrate. Herein, it is demonstrated how a newly developed H-glass can concurrently stabilize plasmonic gold nanoislands (GNIs) and offer multifunctional applications. The GNIs on the H-glass are synthesized using a simple yet, robust thermal dewetting process. The H-glass embedded with GNIs demonstrates versatility in its applications, such as i) acting as a room temperature chemiresistive gas sensor (70% response for NO2 gas); ii) serving as substrates for surface-enhanced Raman spectroscopy for the identifications of Nile blue (dye) and picric acid (explosive) analytes down to nanomolar concentrations with enhancement factors of 4.8 × 106 and 6.1 × 105 , respectively; and iii) functioning as a nonlinear optical saturable absorber with a saturation intensity of 18.36 × 1015 W m-2 at 600 nm, and the performance characteristics are on par with those of materials reported in the existing literature. This work establishes a facile strategy to develop advanced materials by depositing metal nanoislands on glass for various functional applications.

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.

DNA-based programmable gate arrays for general-purpose DNA computing

The past decades have witnessed the evolution of electronic and photonic integrated circuits, from application specific to programmable1,2. Although liquid-phase DNA circuitry holds the potential for massive parallelism in the encoding and execution of algorithms3,4, the development of general-purpose DNA integrated circuits (DICs) has yet to be explored. Here we demonstrate a DIC system by integration of multilayer DNA-based programmable gate arrays (DPGAs). We find that the use of generic single-stranded oligonucleotides as a uniform transmission signal can reliably integrate large-scale DICs with minimal leakage and high fidelity for general-purpose computing. Reconfiguration of a single DPGA with 24 addressable dual-rail gates can be programmed with wiring instructions to implement over 100 billion distinct circuits. Furthermore, to control the intrinsically random collision of molecules, we designed DNA origami registers to provide the directionality for asynchronous execution of cascaded DPGAs. We exemplify this by a quadratic equation-solving DIC assembled with three layers of cascade DPGAs comprising 30 logic gates with around 500 DNA strands. We further show that integration of a DPGA with an analog-to-digital converter can classify disease-related microRNAs. The ability to integrate large-scale DPGA networks without apparent signal attenuation marks a key step towards general-purpose DNA computing.

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

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

DNA-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.

Catalytic-assembly of programmable atom equivalents

Escape from metastable states in self-assembly of colloids is an intractable problem. Unlike the commonly adopted approach of thermal annealing, the recently developed enthalpy-mediated strategy provided a different option to address this dilemma in a dynamically controllable manner at room temperature. However, it required a complex catalytic-assembly DNA strand-displacement circuitry to mediate interaction between multiple components. In this work, we present a simple but effective way to achieve catalytic-assembly of DNA-functionalized colloidal nanoparticles, i.e., programmable atom equivalents, in a far-from-equilibrium system. A removable molecule named "catassembler" that acts as a catalyst was employed to rectify imperfect linkages and help the system escape from metastability without affecting the assembled framework. Notably, catalytic efficiency of the catassembler can be effectively improved by changing the seesaw catassembler in toehold length design or numbers of the repeat units. Leveraging this tractable catalytic-assembly approach, different ordered architectures were easily produced by directly mixing all reactants, as in chemical reactions. By switching bonding identities, solid-solid phase transformations between different colloidal crystals were achieved. This work opens up an avenue for programming colloid assembly in a far-from-equilibrium system.

Reversible Diffusionless Phase Transitions in 3D Nanoparticle Superlattices

Nanocomposite tectons (NCTs), polymer brush-grafted nanoparticles that use supramolecular interactions to drive their assembly, form ordered nanoparticle superlattices (NPSLs) with well-defined unit cell symmetries when thermally annealed. In this work, we demonstrate that appropriate assembly and processing conditions can also enable control over the microstructure of NCT lattices by balancing the enthalpic and entropic factors associated with ligand packing and supramolecular bonding during crystallization. Unary systems of NCTs are assembled via the addition of a small molecule capable of binding to multiple nanoparticle ligands; these NCTs initially form face-centered-cubic (FCC) structures in solvents that are favorable for the particles' polymer brushes. However, the FCC lattices undergo a reversible, diffusionless phase transition to body-centered-cubic (BCC) lattices when transferred to a solvent that induces polymer brush collapse. The BCC superlattices maintain the same crystal habit as the parent FCC phase but exhibit significant transformation twinning similar to that seen in martensitic alloys. This previously unseen diffusionless phase transformation in NPSLs enables unique microstructural features in the resulting assemblies, suggesting that NPSLs could serve as models for the investigation of microstructural evolution in crystalline systems and extend our understanding of NPSLs as atomic material analogues.

Dynamically Reconfigurable DNA Origami Crystals Driven by a Designated Path Diagram

Constructing adaptable and switchable crystal structures renders it possible to dynamically control the properties and functions of adaptive materials, thereby expanding the potential application of these structures in fields such as optics, biology, and catalysis. Recently, researchers have developed various dynamic crystals possessing phase transition abilities. However, manufacturing switchable crystals with multiple-phase-transition ability by integrating various responsive behaviors into different dimensions of a single lattice remains considerably challenging. Herein, we built a set of dynamically reconfigurable DNA origami crystals by orthogonally integrating multiple dynamic effectors into the prescribed dimensions of the octahedral DNA origami frames. Further, we independently manipulated and logically combined the dynamic behaviors of the effectors in different dimensions. The initial mother phase and three derived daughter phases were interconnected into a path diagram by six elementary paths. Furthermore, these paths could be superimposed under multiple stimulus instructions by design to obtain the desired intricate transition routes. Moreover, finer manipulations were also applied to these paths to obtain extra new phase stations for the path diagram. To conveniently detect these phase transitions, a color-based visualization strategy was developed that converted the microscopic symmetry transformation of the lattices into macroscopic color changes that could be observed via a fluorescence microscope. Hence, this strategy lays the foundation for artificially constructing biomimetic functional crystals.

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.

Effective Hard-Sphere Repulsions between Oleate-Capped Colloidal Metal Oxide Nanocrystals

Nanocrystal interactions in solvent influence colloidal stability and dictate self-assembly outcomes. Small-angle X-ray scattering is used to study how dilute oleate-capped In₂O₃ nanocrystals with 7-19 nm core diameters interact when dispersed in a series of nonpolar solvents. Osmotic second virial coefficient analysis finds toluene-dispersed nanocrystals in this size range interact like effective hard spheres with diameters comprising the inorganic core and a ligand-solvent corona with a core-size independent thickness. Hard-sphere-like structure factors are similarly observed for nanocrystals with a 9.7 nm core diameter dispersed in all the solvents investigated. Nanocrystal hydrodynamic diameters from dynamic light scattering measurements correlate with thermodynamic diameters obtained from the osmotic second virial coefficient analysis for all samples. The ability to prepare nanoscale building blocks of different sizes, and dispersed in a variety of solvents, with effective hard-sphere repulsions provides a foundation for assembly, where secondary linking or depletant molecules can be deliberately added to customize interactions to form superstructures such as gel networks or superlattices.

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

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

Self-Assembly of DNA-Grafted Colloids: A Review of Challenges

DNA-mediated self-assembly of colloids has emerged as a powerful tool to assemble the materials of prescribed structure and properties. The uniqueness of the approach lies in the sequence-specific, thermo-reversible hybridization of the DNA-strands based on Watson–Crick base pairing. Grafting particles with DNA strands, thus, results into building blocks that are fully programmable, and can, in principle, be assembled into any desired structure. There are, however, impediments that hinder the DNA-grafted particles from realizing their full potential, as building blocks, for programmable self-assembly. In this short review, we focus on these challenges and highlight the research around tackling these challenges.

Programming Directed Motion with DNA-Grafted Particles

Colloidal particles can be programmed to interact in complex ways by functionalizing them with DNA oligonucleotides. Adding DNA strand-displacement reactions to the system allows these interparticle interactions to respond to specific changes in temperature. We present the requirements for thermally driven directed motion of colloidal particles, and we explore how these conditions can be realized experimentally using strand-displacement reactions. To evaluate the concept, we build and test a colloidal "dancer": a single particle that can be driven to move through a programmed sequence of steps along a one-dimensional track composed of other particles. The results of these tests reveal the capabilities and limitations of using DNA-mediated interactions for applications in dynamic systems. Specifically, we discuss how to design the substrate to limit complexity while permitting full control of the motile component, how to ratchet the interactions to move over many substrate positions with a limited regime of control parameters, and how to use technological developments to reduce the probability of detachment without sacrificing speed.

The emergence of valency in colloidal crystals through electron equivalents

Colloidal crystal engineering of complex, low-symmetry architectures is challenging when isotropic building blocks are assembled. Here we describe an approach to generating such structures based upon programmable atom equivalents (nanoparticles functionalized with many DNA strands) and mobile electron equivalents (small particles functionalized with a low number of DNA strands complementary to the programmable atom equivalents). Under appropriate conditions, the spatial distribution of the electron equivalents breaks the symmetry of isotropic programmable atom equivalents, akin to the anisotropic distribution of valence electrons or coordination sites around a metal atom, leading to a set of well-defined coordination geometries and access to three new low-symmetry crystalline phases. All three phases represent the first examples of colloidal crystals, with two of them having elemental analogues (body-centred tetragonal and high-pressure gallium), while the third (triple double-gyroid structure) has no known natural equivalent. This approach enables the creation of complex, low-symmetry colloidal crystals that might find use in various technologies.

Nanocomposite tectons as unifying systems for nanoparticle assembly

Nanocomposite tectons (NCTs) are nanocomposite building blocks consisting of nanoparticle cores functionalized with a polymer brush, where each polymer chain terminates in a supramolecular recognition group capable of driving particle assembly. Like other ligand-driven nanoparticle assembly schemes (for example those using DNA-hybridization or solvent evaporation), NCTs are able to make colloidal crystal structures with precise particle organization in three dimensions. However, despite the similarity of NCT assembly to other methods of engineering ordered particle arrays, the crystallographic symmetries of assembled NCTs are significantly different. In this study, we provide a detailed characterization of the dynamics of hybridizations through universal (independent of microscopic details) parameters. We perform rigorous free energy calculations and identify the persistence length of the ligand as the critical parameter accounting for the differences in the phase diagrams of NCTs and other assembly methods driven by hydrogen bond hybridizations. We also report new experiments to provide direct verification for the predictions. We conclude by discussing the role of non-equilibrium effects and illustrating how NCTs provide a unification of the two most successful strategies for nanoparticle assembly: solvent evaporation and DNA programmable assembly.

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.

Temperature-Selective Self-Assembled Superlattices of Gold Nanoparticles Driven by Block Copolymer Template Guidance

Self-assembly of nanoparticles (NPs) into highly ordered structure can enhance their electronic and optical properties that provide great potential applications such as nanoelectronics and nanophotonics. However, the self-assembly of NPs upon external stimuli was still mainly continuous and irreversible, making various potential applications of NPs difficult. Herein, the self-assembled superlattices of gold nanoparticles (AuNPs) with a temperature-selective response had been investigated by using the amphiphilic block copolymer as a template. The AuNPs in the block copolymer template, which has the closed looplike phase behavior upon heating, self-assembled into the highly ordered body centered cubic (BCC) or face centered cubic (FCC) structures at a specific temperature region that means a temperature-selective responsiveness. The formation of highly ordered self-assembled superlattices (BCC or FCC symmetries) of AuNPs with the closed looplike phase behavior was controlled by the additive and temperature. This study is the first demonstration for temperature-selective response of the cooperative self-assembly of AuNPs in the block copolymer template.

Chemically modified nucleic acids and DNA intercalators as tools for nanoparticle assembly

The self-assembly of inorganic nanoparticles to larger structures is of great research interest as it allows the fabrication of novel materials with collective properties correlated to the nanoparticles' individual characteristics. Recently developed methods for controlling nanoparticle organisation have enabled the fabrication of a range of new materials. Amongst these, the assembly of nanoparticles using DNA has attracted significant attention due to the highly selective recognition between complementary DNA strands, DNA nanostructure versatility, and ease of DNA chemical modification. In this review we discuss the application of various chemical DNA modifications and molecular intercalators as tools for the manipulation of DNA-nanoparticle structures. In detail, we discuss how DNA modifications and small molecule intercalators have been employed in the chemical and photochemical DNA ligation in nanostructures; DNA rotaxanes and catenanes associated with reconfigurable nanoparticle assemblies; and DNA backbone modifications including locked nucleic acids, peptide nucleic acids and borane nucleic acids, which affect the stability of nanostructures in complex environments. We conclude by highlighting the importance of maximising the synergy between the communities of DNA chemistry and nanoparticle self-assembly with the aim to enrich the library of tools available for the manipulation of nanostructures.

Colloidal Self-Assembly Approaches to Smart Nanostructured Materials

Colloidal self-assembly refers to a solution-processed assembly of nanometer-/micrometer-sized, well-dispersed particles into secondary structures, whose collective properties are controlled by not only nanoparticle property but also the superstructure symmetry, orientation, phase, and dimension. This combination of characteristics makes colloidal superstructures highly susceptible to remote stimuli or local environmental changes, representing a prominent platform for developing stimuli-responsive materials and smart devices. Chemists are achieving even more delicate control over their active responses to various practical stimuli, setting the stage ready for fully exploiting the potential of this unique set of materials. This review addresses the assembly of colloids into stimuli-responsive or smart nanostructured materials. We first delineate the colloidal self-assembly driven by forces of different length scales. A set of concepts and equations are outlined for controlling the colloidal crystal growth, appreciating the importance of particle connectivity in creating responsive superstructures. We then present working mechanisms and practical strategies for engineering smart colloidal assemblies. The concepts underpinning separation and connectivity control are systematically introduced, allowing active tuning and precise prediction of the colloidal crystal properties in response to external stimuli. Various exciting applications of these unique materials are summarized with a specific focus on the structure-property correlation in smart materials and functional devices. We conclude this review with a summary of existing challenges in colloidal self-assembly of smart materials and provide a perspective on their further advances to the next generation.

Nanoparticle Superlattices through Template-Encoded DNA Dendrimers

The chemical interactions that lead to the emergence of hierarchical structures are often highly complex and difficult to program. Herein, the synthesis of a series of superlattices based upon 30 different structurally reconfigurable DNA dendrimers is reported, each of which presents a well-defined number of single-stranded oligonucleotides (i.e., sticky ends) on its surface. Such building blocks assemble with complementary DNA-functionalized gold nanoparticles (AuNPs) to yield five distinct crystal structures, depending upon choice of dendrimer and defined by phase symmetry. These DNA dendrimers can associate to form micelle-dendrimers, whereby the extent of association can be modulated based upon surfactant concentration and dendrimer length to produce a low-symmetry Ti5Ga4-type phase that has yet to be reported in the field of colloidal crystal engineering. Taken together, colloidal crystals that feature three different types of particle bonding interactions-template-dendron, dendrimer-dendrimer, and DNA-modified AuNP-dendrimer-are reported, illustrating how sequence-defined recognition and dynamic association can be combined to yield complex hierarchical materials.

Multifarious colloidal structures: new insight into ternary and quadripartite ordered assemblies

DNA-mediated assembly of colloidal particles can be utilized to produce a variety of structures which may have desirable phononic, photonic, or electronic transport properties. Recent developments in linker-mediated assembly processes allow for interactions to be coordinated between many different types of colloidal particles more easily and with fewer unique sequences than direct hybridization. However, the dynamics of colloidal self-assembly becomes increasingly more complex when coordinating interactions between three or more distinct interacting elements. In such cases particle pairs with similar binding energies are allowed to interact unpredictably, and enthalpically degenerate binding sites will be noticeably more present while numerous secondary phases may also result from the self-assembly process. Therefore, it is necessary to develop procedures for predicting feasible superstructure geometries for these systems before they can be implemented in material design. Here we investigate the formation of multifarious ordered structures through self-assembly of multiple types of spherically symmetrical colloidal particles with a variety of interaction matrices. We utilize Molecular Dynamics (MD) simulations to study the growth behavior of systems with different types of interacting elements and different particle sizes, and also predict the formation and stability of the target structures. We also study the phononic spectra of various ternary structures in order to identify the influence of key structural parameters on phonon bandgap frequencies and ranges. Our results provide direct guidelines for designing ternary and quadripartite multifarious colloidal structures, and motivate new directions for future experimental work to target formation of multi-component colloidal superstructures beyond the well-established binary symmetries studied in the past.

Optimizing the dynamic and thermodynamic properties of hybridization in DNA-mediated nanoparticle self-assembly

DNA-directed nanoparticle (DNA-NP) systems provide various applications in sensing, medical diagnosis, data storage, plasmonics and photovoltaics. Bonding probability and melting properties are helpful to evaluate the selectivity, thermostability and thermosensitivity of these applications. We investigated the influence of temperature, nanoparticle size, DNA chain length and surface grafting density of DNA on one nanoparticle on the DNA dynamic hybridization percentage and melting properties of DNA-NP assembly systems by molecular dynamics simulation. The high degree of consistency of free energy estimations for DNA hybridization via our theoretical deduction and the nearest-neighbor rule generally used in experiments validates reasonably our DNA model. The melting temperature and thermosensitivity parameter are determined by the sigmoidal melting curves based on hybridization percentage versus temperature. The results indicated that the hybridization percentage presents a downward trend with increasing temperature and nanoparticle size. Applications based on DNA-NP systems with bigger nanoparticle size, such as DNA probes, have better selectivity, thermostability and thermosensitivity. There exist optimal DNA chain length and surface grafting density where the hybridization percentage reaches the maximal value. The melting temperature reaches a maximum at the point of optimal grafting density, while the thermosensitivity parameter presents an upward trend with the increase of grafting density. Several physical quantities consisting of the radial density function, root mean square end-to-end distance, contact distance parameter and effective volume fraction are used to analyse DNA chain conformations and DNA-NP packing in the assembly process. Our findings provide the theoretical basis for the improvement and optimization of applications based on DNA-NP systems.

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.

Unconventional-Phase Crystalline Materials Constructed from Multiscale Building Blocks

Crystal phase, an intrinsic characteristic of crystalline materials, is one of the key parameters to determine their physicochemical properties. Recently, great progress has been made in the synthesis of nanomaterials with unconventional phases that are different from their thermodynamically stable bulk counterparts via various synthetic methods. A nanocrystalline material can also be viewed as an assembly of atoms with long-range order. When larger entities, such as nanoclusters, nanoparticles, and microparticles, are used as building blocks, supercrystalline materials with rich phases are obtained, some of which even have no analogues in the atomic and molecular crystals. The unconventional phases of nanocrystalline and supercrystalline materials endow them with distinctive properties as compared to their conventional counterparts. This Review highlights the state-of-the-art progress of nanocrystalline and supercrystalline materials with unconventional phases constructed from multiscale building blocks, including atoms, nanoclusters, spherical and anisotropic nanoparticles, and microparticles. Emerging strategies for engineering their crystal phases are introduced, with highlights on the governing parameters that are essential for the formation of unconventional phases. Phase-dependent properties and applications of nanocrystalline and supercrystalline materials are summarized. Finally, major challenges and opportunities in future research directions are proposed.

Temperature-Controlled Reconfigurable Nanoparticle Binary Superlattices

The presence of diffusionless transformations during the assembly of DNA-functionalized particles (DFPs) is highly significant in designing reconfigurable materials whose structure and functional properties are tunable with controllable variables. In this paper, we first use a variety of computational models and techniques (including free energy methods) to address the nature of such transformations between face-centered cubic (FCC) and body-centered cubic (BCC) structures in a three-dimensional binary system of multiflavored DFPs. We find that the structural rearrangements between BCC and FCC structures are thermodynamically reversible and dependent on crystallite size. Smaller nuclei favor nonclose-packed BCC structures, whereas close-packed FCC structures are observed during the growth stage once the crystallite size exceeds a threshold value. Importantly, we show that a similar reversible transformation between BCC/FCC structures can be driven by changing temperature without introducing additional solution components, highlighting the feasibility of creating reconfigurable crystalline materials. Lastly, we validate this thermally responsive switching behavior in a DFP system with explicit DNA (un)hybridization, demonstrating our findings' applicability to experimentally realizable systems.

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.

Single-strand DNA-nanorod conjugates - tunable anisotropic colloids for on-demand self-assembly

Directed self-assembly uses different stimuli to initiate and control the interaction between nanocrystals. Protonation at reduced pH represents a convenient stimulus for initiating self-assembly. Prior work has focused on protonation-induced hydrogen bonding between peptide or amino acid functionalized nanocrystals for reversible cycling between dispersed and aggregated states. Here, we discuss a fundamentally different approach, in which changes in pH modify the nonspecific interparticle interaction between Au nanorods conjugated with single-stranded (ss) DNA. While electrostatic repulsion stabilizes dispersed suspensions at neutral pH, protonation in acidic solution modifies the DNA corona, turning the interaction between the rods attractive and triggering their self-assembly. Analysis of in-situ electron microscopy of ssDNA-Au nanorods in solution is consistent with a van der Waals attraction of charge-neutral monomers at acidic pH. The results demonstrate ssDNA-conjugated anisotropic nanostructures as versatile building blocks with stimuli-programmable interactions for on-demand self-assembly.

In Situ Constructing the Kinetic Roadmap of Octahedral Nanocrystal Assembly Toward Controlled Superlattice Fabrication

Crystallization and growth of anisotropic nanocrystals (NCs) into distinct superlattices were studied in real time, yielding kinetic details and designer parameters for scale-up fabrication of functional materials. Using octahedral PbS NC blocks, we discovered that NC assembly involves a primary lamellar ordering of NC-detached Pb(OA)₂ molecules on the front-spreading solvent surfaces. Upon a spontaneous increase of NC concentration during solvent processing, PbS NCs preferentially self-assembled into an orientation-disordered face-centered cubic (fcc) superlattice, which subsequently transformed into a body-centered cubic (bcc) superlattice with single NC-orientational ordering across individual domains. Unlike the deformation-based transformation route claimed previously, this solid-solid phase transformation involved a hidden intermediate formation of a lamellar-confined liquid interface at cost of the disassembly (melting) of small fcc grains. Such highly condensed and liquidized NCs recrystallized into the stable bcc phase with an energy reduction of 1.16 k_BT. This energy-favorable and high NC-fraction-driven bcc phase grew as a 2D film at a propagation rate of 0.74 μm/min, smaller than the 1.23 μm/min observed in the early nucleated fcc phase under a dilute NC environment. Taking such insights and defined parameters, we designed experiments to manipulate the NC assembly pathway and achieved scalable fabrication of a large/single bcc supercrystal with coherent ordering of NC translation and atomic plane orientation. This study not only provides a design avenue for controllable fabrication of a large supercrystal with desired superlattices for application but also sheds new light on the nature of crystal nucleation/growth and phase transformation by extending the lengths from the nanoscale into the atomic scale, molecular scale, and microscale levels.

Microfluidic synthesis of high-valence programmable atom-like nanoparticles for reliable sensing

Synthesis of programmable atom-like nanoparticles (PANs) with high valences and high yields remains a grand challenge. Here, a novel synthetic strategy of microfluidic galvanic displacement (μ-GD) coupled with microfluidic DNA nanoassembly is advanced for synthesis of single-stranded DNA encoder (SSE)-encoded PANs for reliable surface-enhanced Raman scattering (SERS) sensing. Notably, PANs with high valences (e.g., n-valence, n = 12) are synthesized with high yields (e.g., >80%) owing to the effective control of interfacial reactions sequentially occurring in the microfluidic system. On the basis of this, we present the first demonstration of a PAN-based automatic analytical platform, in which sensor construction, sample loading and on-line monitoring are carried out in the microfluidic system, thus guaranteeing reliable quantitative measurement. In the proof-of-concept demonstration, accurate determination of tetracycline (TET) in serum and milk samples with a high recovery close to 100% and a low relative standard deviation (RSD) less than 5.0% is achieved by using this integrated analytical platform.

Programming nanoparticle valence bonds with single-stranded DNA encoders

Nature has evolved strategies to encode information within a single biopolymer to program biomolecular interactions with characteristic stoichiometry, orthogonality and reconfigurability. Nevertheless, synthetic approaches for programming molecular reactions or assembly generally rely on the use of multiple polymer chains (for example, patchy particles). Here we demonstrate a method for patterning colloidal gold nanoparticles with valence bond analogues using single-stranded DNA encoders containing polyadenine (polyA). By programming the order, length and sequence of each encoder with alternating polyA/non-polyA domains, we synthesize programmable atom-like nanoparticles (PANs) with n-valence that can be used to assemble a spectrum of low-coordination colloidal molecules with different composition, size, chirality and linearity. Moreover, by exploiting the reconfigurability of PANs, we demonstrate dynamic colloidal bond-breaking and bond-formation reactions, structural rearrangement and even the implementation of Boolean logic operations. This approach may be useful for generating responsive functional materials for distinct technological applications.

sasPDF: pair distribution function analysis of nanoparticle assemblies from small-angle scattering data

sasPDF, a method for characterizing the structure of nanoparticle assemblies (NPAs), is presented. The method is an extension of the atomic pair distribution function (PDF) analysis to the small-angle scattering (SAS) regime. The PDFgetS3 software package for computing the PDF from SAS data is also presented. An application of the sasPDF method to characterize structures of representative NPA samples with different levels of structural order is then demonstrated. The sasPDF method quantitatively yields information such as structure, disorder and crystallite sizes of ordered NPA samples. The method was also used to successfully model the data from a disordered NPA sample. The sasPDF method offers the possibility of more quantitative characterizations of NPA structures for a wide class of samples.

Combinatorial-Entropy-Driven Aggregation in DNA-Grafted Nanoparticles

We use computer simulations and experiments to study the interactions between nanoparticles (NPs) grafted with self-complementary DNA strands. Each strand ends with a sticky palindromic single-stranded sequence, allowing it to associate equally favorably with strands grafted on the same particle or on different NPs. Surprisingly we find an attractive interaction between a pair of NPs, and we demonstrate that at low temperature it arises purely from a combinatorial-entropy contribution. We evaluate theoretically and verify numerically this entropic contribution originating from the number of distinct bonding patterns associated with intra- and interparticle binding. This entropic attraction becomes more favorable with decreasing inter-NP distance because more sticky ends can participate in making this choice.

Hydrodynamic and frictional modulation of deformations in switchable colloidal crystallites

Displacive transformations in colloidal crystals may offer a pathway for increasing the diversity of accessible configurations without the need to engineer particle shape or interaction complexity. To date, binary crystals composed of spherically symmetric particles at specific size ratios have been formed that exhibit floppiness and facile routes for transformation into more rigid structures that are otherwise not accessible by direct nucleation and growth. There is evidence that such transformations, at least at the micrometer scale, are kinetically influenced by concomitant solvent motion that effectively induces hydrodynamic correlations between particles. Here, we study quantitatively the impact of such interactions on the transformation of binary bcc-CsCl analog crystals into close-packed configurations. We first employ principal-component analysis to stratify the explorations of a bcc-CsCl crystallite into orthogonal directions according to displacement. We then compute diffusion coefficients along the different directions using several dynamical models and find that hydrodynamic correlations, depending on their range, can either enhance or dampen collective particle motions. These two distinct effects work synergistically to bias crystallite deformations toward a subset of the available outcomes.

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.

Linker-mediated self-assembly of mobile DNA-coated colloids

Developing construction methods of materials tailored for given applications with absolute control over building block placement poses an immense challenge. DNA-coated colloids offer the possibility of realising programmable self-assembly, which, in principle, can assemble almost any structure in equilibrium, but remains challenging experimentally. Here, we propose an innovative system of linker-mediated mobile DNA-coated colloids (mDNACCs), in which mDNACCs are bridged by the free DNA linkers in solution, whose two single-stranded DNA tails can bind with specific single-stranded DNA receptors of complementary sequence coated on colloids. We formulate a mean-field theory efficiently calculating the effective interaction between mDNACCs, where the entropy of DNA linkers plays a nontrivial role. Particularly, when the binding between free DNA linkers in solution and the corresponding receptors on mDNACCs is strong, the linker-mediated colloidal interaction is determined by the linker entropy depending on the linker concentration.

Reconfigurable Self-Assembly and Kinetic Control of Multiprogrammed DNA-Coated Particles

DNA is a unique molecule for storing information, which is used to provide particular biological instructions. Its function is primarily determined by the sequence of its four nucleobases, which have highly specific base-pairing interactions. This unique feature can be applied to direct the self-assembly of colloids by grafting DNA onto them. Due to the sequence-specific interactions, colloids can be programmed with multiple instructions. Here, we show that particles having multiple DNA strands with different melting profiles can undergo multiple phase transitions and reassemble into different crystalline structures in response to temperature. We include free DNA strands in the medium to selectively switch on and off DNA hybridization depending on temperature. We also demonstrate that DNA hybridization kinetics can be used as a means to achieve targeted assembling structure of colloids. These transitions impart a reconfigurability to colloids in which systems can be transformed an arbitrary number of times using thermal and kinetic control.

DNA-Programmed Chemical Synthesis of Polymers and Inorganic Nanomaterials

DNA nanotechnology, based on sequence-specific DNA recognition, could allow programmed self-assembly of sophisticated nanostructures with molecular precision. Extension of this technique to the preparation of broader types of nanomaterials would significantly improve nanofabrication technique to lower nanometer scale and even achieve single molecule operation. Using such exquisite DNA nanostructures as templates, chemical synthesis of polymer and inorganic nanomaterials could also be programmed with unprecedented accuracy and flexibility. This review summarizes recent advances in the synthesis and assembly of polymer and inorganic nanomaterials using DNA nanostructures as templates, and discusses the current challenges and future outlook of DNA templated nanotechnology.

Programming colloidal bonding using DNA strand-displacement circuitry

As a strategy for regulating entropy, thermal annealing is a commonly adopted approach for controlling dynamic pathways in colloid assembly. By coupling DNA strand-displacement circuits with DNA-functionalized colloid assembly, we developed an enthalpy-mediated strategy for achieving the same goal while working at a constant temperature. Using this tractable approach allows colloidal bonding to be programmed for synchronization with colloid assembly, thereby realizing the optimal programmability of DNA-functionalized colloids. We applied this strategy to conditionally activate colloid assembly and dynamically switch colloid identities by reconfiguring DNA molecular architectures, thereby achieving orderly structural transformations; leveraging the advantage of room-temperature assembly, we used this method to prepare a lattice of temperature-sensitive proteins and gold nanoparticles. This approach bridges two subfields: dynamic DNA nanotechnology and DNA-functionalized colloid programming.