Catalytic Hairpin Assembly‐Programmed DNA Three‐Way Junction for Enzyme‐Free and Amplified Electrochemical Detection of Target DNA

DNA three‐way junctions (DNA 3WJ) have been widely used as important building blocks for the construction of DNA architectures and dynamic assemblies. Herein, we describe for the first time a catalytic hairpin assembly‐programmed DNA three‐way junction (CHA‐3WJ) strategy for the enzyme‐free and amplified electrochemical detection of target DNA. It takes full advantage of the target‐catalyzed hairpin assembly‐induced proximity effect of toehold and branch‐migration domains for the ingenious execution of the strand displacement reaction to form the DNA 3WJ on the electrode surface. A low detection limit of 0.5 pM with an excellent selectivity was achieved for target DNA detection. The developed CHA‐3WJ strategy also offers distinct advantages of simplicity in probe design and biosensor fabrication, as well as enzyme‐free operation. Thus, it opens a promising avenue for applications in bioanalysis, design of DNA‐responsive devices, and dynamic DNA assemblies.     

Constructing Large 2D Lattices Out of DNA-Tiles

The predictable nature of deoxyribonucleic acid (DNA) interactions enables assembly of DNA into almost any arbitrary shape with programmable features of nanometer precision. The recent progress of DNA nanotechnology has allowed production of an even wider gamut of possible shapes with high-yield and error-free assembly processes. Most of these structures are, however, limited in size to a nanometer scale. To overcome this limitation, a plethora of studies has been carried out to form larger structures using DNA assemblies as building blocks or tiles. Therefore, DNA tiles have become one of the most widely used building blocks for engineering large, intricate structures with nanometer precision. To create even larger assemblies with highly organized patterns, scientists have developed a variety of structural design principles and assembly methods. This review first summarizes currently available DNA tile toolboxes and the basic principles of lattice formation and hierarchical self-assembly using DNA tiles. Special emphasis is given to the forces involved in the assembly process in liquid-liquid and at solid-liquid interfaces, and how to master them to reach the optimum balance between the involved interactions for successful self-assembly. In addition, we focus on the recent approaches that have shown great potential for the controlled immobilization and positioning of DNA nanostructures on different surfaces. The ability to position DNA objects in a controllable manner on technologically relevant surfaces is one step forward towards the integration of DNA-based materials into nanoelectronic and sensor devices.     

Reciprocal Self‐Assembly of Peptide–DNA Conjugates into a Programmable Sub‐10‐nm Supramolecular Deoxyribonucleoprotein

To overcome the limitations of molecular assemblies, the development of novel supramolecular building blocks and self‐assembly modes is essential to create more sophisticated, complex, and controllable aggregates. The self‐assembly of peptide–DNA conjugates (PDCs), in which two orthogonal self‐assembly modes, that is, β‐sheet formation and Watson–Crick base pairing, are covalently combined in one supramolecular system, is reported. Despite extensive research, most self‐assembly studies have focused on using only one type of building block, which restricts structural and functional diversity compared to multicomponent systems. Multicomponent systems, however, suffer from poor control of self‐assembly behaviors. Covalently conjugated PDC building blocks are shown to assemble into well‐defined and controllable nanostructures. This controllability likely results from the decrease in entropy associated with the restriction of the molecular degrees of freedom by the covalent constraints. Using this strategy, the possibility to thermodynamically program nano‐assemblies to exert gene regulation activity with low cytotoxicity is demonstrated.     

Hybridization chain reaction triggered controllable one-dimensional assembly of gold nanoparticles

Assembling and ordering nanomaterials into desirable patterns are considerably significant, since the properties of nanomaterials depend not only on the size and shape, but also on the spatial arrangement among the collective building blocks. In this work, the DNA self-assembly technology of hybridization chain reaction (HCR) provided a convenient method to yield long double-strand DNA (dsDNA) to install gold nanoparticles (AuNPs) into one dimensional assembly along the skeleton of dsDNA. Interestingly, the tunable length of AuNPs assemblies along dsDNA chain could be achieved by adjusting the reaction time of HCR, which is based on the formation of covalent bond between Au and the -SH group of DNA. Compared with weak light scattering of single AuNP, these AuNPs assemblies could be clearly imaged under the dark field microscopy, indicating that the light scattering was greatly improved after assembling.     

DNA Origami Rotaxanes: Tailored Synthesis and Controlled Structure Switching

Mechanically interlocked supramolecular assemblies are appealing building blocks for creating functional nanodevices. Herein, we describe the multistep assembly of large DNA origami rotaxanes that are capable of programmable structural switching. We validated the topology and structural integrity of these rotaxanes by analyzing the intermediate and final products of various assembly routes by electrophoresis and electron microscopy. We further analyzed two structure‐switching behaviors of our rotaxanes, which are both mediated by DNA hybridization. In the first mechanism, the translational motion of the macrocycle can be triggered or halted at either terminus. In the second mechanism, the macrocycle can be elongated after completion of the rotaxane assembly, giving rise to a unique structure that is otherwise difficult to access.     

Super crystal structures of octahedral c-In2O3 nanocrystals

The three-dimensional self-assembly of a nanocrystal superlattice, i.e., a super crystal, has attracted increasing attention. The small building blocks for assemblies are usually spherical nanocrystals. Recent progress indicates that it is possible to achieve a super crystal using cubic nanocrystals. We further analyze and describe two-dimensional and some three-dimensional assemblies of uniform cubic-phase In2O3 nanocrystals with an octahedral shape. In this article, we demonstrate our amazing observations on these kinds of super crystals (or superlattices) as a model system, report their scale in at least tens of microns, and show other interesting features such as steps, terraces, kinks, and vacancies which are similar to those from a single crystal. Based on electron microscopy observations, three types of well-defined octahedral nanocrystal packed structures in such super crystal systems are also identified. The investigation of octahedral super crystal systems provides an alternate direction in research that may extend the interest of superlattice study to a broad spectrum by enriching and varying the shape of elemental building blocks. This may potentially result in new concepts and more challenging applications such as soft X-ray photonics.     

Playing with Structures at the Nanoscale: Designing Catalysts by Manipulation of Clusters and Nanocrystals as Building Blocks

The purpose of this Concept is to highlight some of the most recent and promising methods for the preparation of tailored catalysts by designing and preparing the component building blocks and by assembling them in a controlled fashion. We want to emphasize how rational design and synthesis of catalysts must be coupled to precise catalytic and structural characterization of the systems in an ideal feedback loop. New catalyst design and preparation techniques, dictated by information about the active sites that the specific application requires, are frequently available. The building blocks for developing these novel catalysts include colloidal methods for the preparation of uniform nanostructures, physical methods for rational assembly of the building blocks (Langmuir–Blodgett, liquid–air self‐assembly), and development of rational interactions between the building blocks for enhanced activity of the assemblies. These methods, which apply techniques normally used in other fields of nanotechnology to catalysis, offer exciting opportunities to help improve currently available catalytic systems in terms of activity, stability and selectivity.     

Cover Picture

The cover picture shows a rhodium catalyst (green) that is encapsulated by three porphyrin molecules (black; the van der Waals radii are shown in yellow). The hemispherical assembly is obtained by a self‐assembly process using readily available pyridylphosphane and zinc‐porphyrin building blocks. Its exclusive formation is based on selective coordination of the nitrogen atom to the zinc atom and the phosphane group to the rhodium center. The catalyst assemblies show a higher activity than the free rhodium catalyst in the rhodium‐catalyzed hydroformylation of 1‐octene, and the branched product is now the main product. In a similar way, the assembly of porphyrin building blocks to pyridylphosphane can regulate the performance of palladium catalysts in the Heck reaction. Further details about these catalyst assemblies can be found in the article by Reek et al. on p. 4271ff.     

Stepwise construction of a cross-shaped covalent assembly of dendrimers

A methodology for the stepwise construction of shape-persistent assemblies using snowflake-shaped dendrimers as the key modular building blocks was described. The Sonogashira coupling reaction of A₃B-type Zn-porphyrin with A₄-type free-base porphyrin afforded a cross-shaped covalent assembly. Intramolecular singlet energy transfer from peripheral Zn-porphyrin core to a free-base porphyrin core was observed.     

Host–Guest Binding‐Site‐Tunable Self‐Assembly of Stimuli‐Responsive Supramolecular Polymers

Despite the remarkable progress made in controllable self‐assembly of stimuli‐responsive supramolecular polymers (SSPs), a basic issue that has not been consideration to date is the essential binding site. The noncovalent binding sites, which connect the building blocks and endow supramolecular polymers with their ability to respond to stimuli, are expected to strongly affect the self‐assembly of SSPs. Herein, the design and synthesis of a dual‐stimuli thermo‐ and photoresponsive Y‐shaped supramolecular polymer (SSP2) with two adjacent β‐cyclodextrin/azobenzene (β‐CD/Azo) binding sites, and another SSP (SSP1) with similar building blocks, but only one β‐CD/Azo binding site as a control, are described. Upon gradually increasing the polymer solution temperature or irradiating with UV light, SSP2 self‐assemblies with a higher binding‐site distribution density; exhibits a flower‐like morphology, smaller size, and more stable dynamic aggregation process; and greater controllability for drug‐release behavior than those observed with SSP1 self‐assemblies. The host–guest binding‐site‐tunable self‐assembly was attributed to the positive cooperativity generated among adjacent binding sites on the surfaces of SSP2 self‐assemblies. This work is beneficial for precisely controlling the structural parameters and controlled release function of SSP self‐assemblies.     

Bolaform superamphiphile based on a dynamic covalent bond and its self-assembly in water

We have employed a dynamic covalent bond to fabricate a bolaform superamphiphile, which can be used as building blocks for controlled assembly and disassembly. In alkaline environment, one building block bearing a benzoic aldehyde group can react with the other building block bearing an amino group to form a bolaform superamphiphile. It is found that the bolaform superamphiphiles can self-assemble in water to form micellar aggregates. When the pH is tuned down to slightly acidic values, the benzoic imine bond can be hydrolyzed, leading to the dissociation of the superamphiphile. The micellar aggregates will also disassemble, and the loaded guest molecules are released subsequently. This line of research has enriched the family of bolaform amphiphiles, and the resulting assemblies may find application in the field of controlled and targetable drug-delivery in a biological environment.     

Fluorescent assemblies: Synergistic of amphiphilic molecules and fluorescent elements

In recent years, fluorescent assemblies based amphiphilic molecules have gained attention as unique and powerful materials for multiple applications that cover sensors, optoelectronics and bioimaging because of amphiphilic molecules self-assembly with outstanding flexibility and diversity spanning assembly structure from micelles, vesicles and nano-assemblies to gels. Weak and noncovalent interactions are important driving force for assemblies. The combination of the structural characteristics of self-assembly and the fluorescent properties of the fluorescent building element render the fluorescent material versatility and their easy-to-tune properties. Amphiphilic molecules can be used as building elements to co-assemble with dye molecules, aggregation-induced emission (AIE) gens, fluorescent nanoparticles and new amphiphilic molecules containing fluorescent groups can also be designed and prepared with self-assembly capability. Concomitantly, the improvement of fluorescence performance including fluorescence intensity, quantum yield, stability and controllability during assembly proved outstanding properties of fluorescence assemblies. These promising fluorescent assemblies are by far not exhaustive in construction method and mechanism explanation but foreshadow their more potential applications. Here, we will understand deeper the fluorescent assemblies and inspire future developments and applications employing this emerging fluorescence soft materials.     

Nanoparticle-DNA conjugates bearing a specific number of short DNA strands by enzymatic manipulation of nanoparticle-bound DNA

Self-assembling of metallic nanoparticles to form well-defined nanostructured structures is a field that has been receiving considerable research interest in recent years. In this field, DNA is a commonly used linker molecule to direct the assembly of the nanoscale building blocks because of its unique recognition capabilities, mechanical rigidity, and physicochemical stability. This study reported our novel approach to generate gold nanoparticle-DNA conjugates bearing specially designed DNA linker molecules that can be used as building blocks to construct nanoassemblies with precisely controlled structure or as nanoprobes for quantitative DNA sequence detection analysis. In our approach, gold nanoparticle-DNA conjugates bearing a specific number of long double-stranded DNA strands were prepared by gel electrophoresis. A restriction endonuclease enzyme was then used to manipulate the length of the nanoparticle-bound DNA. This enzymatic cleavage was confirmed by gel electrophoresis, and digestion efficiency of 90% or more was achieved. With this approach, nanoparticle conjugates bearing a specific number of strands of short DNA with less than 20-base can be achieved.     

Bilayer Molecular Assembly at a Solid/Liquid Interface as Triggered by a Mild Electric Field

The construction of a spatially defined assembly of molecular building blocks, especially in the vertical direction, presents a great challenge for surface molecular engineering. Herein, we demonstrate that an electric field applied between an STM tip and a substrate triggered the formation of a bilayer structure at the solid–liquid interface. In contrast to the typical high electric‐field strength (10⁹ V m^?1) used to induce structural transitions in supramolecular assemblies, a mild electric field (10⁵ V m^?1) triggered the formation of a bilayer structure of a polar molecule on top of a nanoporous network of trimesic acid on graphite. The bilayer structure was transformed into a monolayer kagome structure by changing the polarity of the electric field. This tailored formation and large‐scale phase transformation of a molecular assembly in the perpendicular dimension by a mild electric field opens perspectives for the manipulation of surface molecular nanoarchitectures.     

Precise Macroscopic Supramolecular Assembly by Combining Spontaneous Locomotion Driven by the Marangoni Effect and Molecular Recognition

Macroscopic supramolecular assembly bridges fundamental research on molecular recognition and the potential applications as bulk supramolecular materials. However, challenges remain to realize stable precise assembly, which is significant for further functions. To handle this issue, the Marangoni effect is applied to achieve spontaneous locomotion of macroscopic building blocks to reach interactive distance, thus contributing to formation of ordered structures. By increasing the density of the building blocks, the driving force for assembly transforms from a hydrophobic–hydrophobic interaction to hydrophilic–hydrophilic interaction, which is favorable for introducing hydrophilic coatings with supramolecular interactive groups on matched surfaces, consequently realizing the fabrication of stable precise macroscopic supramolecular assemblies.     

Inorganic semiconductor nanowires: rational growth, assembly, and novel properties

Rationally controlled growth of inorganic semiconductor nanowires is important for their applications in nanoscale electronics and photonics. In this article, we discuss the rational growth, physical properties, and integration of nanowires based on the results from the authors' laboratory. The composition, diameter, growth position, and orientation of the nanowires are controlled based on the vapor-solid-liquid (VLS) crystal growth mechanism. The thermal stability and optical properties of these semiconductor nanowires are investigated. Particularly, ZnO nanowires with well-defined end surfaces can function as room-temperature ultraviolet nanolasers. In addition, a novel microfluidic-assisted nanowire integration (MANI) process was developed for the hierarchical assembly of nanowire building blocks into functional devices and systems.     

Molecular dipole engineering: new aspects of molecular dipoles in molecular architecture and their functions

The assembly of molecular architectures on the basis of molecular dipoles is proposed here to be a promising tool for construction of nanomaterials and nanodevices. Three kinds of building blocks having dipoles are discussed; helical peptides, cyclic beta-peptides, and oligo(phenylene ethynylene)s having donor and acceptor substituents. Secondary interactions involving molecular dipoles are shown to be effective to control precise molecular shapes and to assemble the building blocks in a regular manner. Furthermore, molecular dipoles can generate a strong electric field at the nanoscale, which is useful for the promotion or suppression of electron transfer processes. Organic molecules with strong dipoles will therefore be applicable to various fields, such as molecular electronics and medical chemistry, as functional nanomaterials. It is expected that the chemistry of dipolar molecules will lay a firm foundation for a new interdisciplinary field, that of "molecular dipole engineering".     

Zn(II)-salphen complexes as versatile building blocks for the construction of supramolecular box assemblies

Zn(II)-salphen complexes are readily accessible and interesting supramolecular building blocks with a large structural diversity. Higher-order supramolecular assemblies, such as molecular boxes based on a bis-Zn(II)-salphen building block and various ditopic bipyridine ligands, have been constructed by means of supramolecular, coordinative Zn(II)-N(pyr) interactions. The use of bipyridine ligands of differing sizes enables the construction of structures with predefined box diameters. The features of the 2:2 box assemblies were investigated in detail by (variable temperature) NMR spectroscopy, UV-visible spectroscopy, NMR titrations, and X-ray crystallographic studies. The spectroscopic studies reveal a high association constant for the Zn(II)-salphen-pyridyl motif, which lies in the range 10(5)-10(6) M(-1). The strong interaction between the Zn(II) center and pyridine donors was supported by PM3 calculations that showed a relatively high Lewis acid character of the metal center in the salphen complex. Titration curves monitored by UV-visible show a cooperative effect between the two bipyridine ligands upon complexation to the bis-Zn(II) template, suggesting the formation of 2:2 complexes. The crystal structures of two supramolecular boxes have been determined. In both examples such a 2:2 assembly is present in the solid state, and the box size is different because they consist of different building blocks. Interestingly, the box assemblies line up in the solid state to form porous channels that are potentially useful in a number of applications.     

Insights into the Structure and Energy of DNA Nanoassemblies

Since the pioneering work of Ned Seeman in the early 1980s, the use of the DNA molecule as a construction material experienced a rapid growth and led to the establishment of a new field of science, nowadays called structural DNA nanotechnology. Here, the self-recognition properties of DNA are employed to build micrometer-large molecular objects with nanometer-sized features, thus bridging the nano- to the microscopic world in a programmable fashion. Distinct design strategies and experimental procedures have been developed over the years, enabling the realization of extremely sophisticated structures with a level of control that approaches that of natural macromolecular assemblies. Nevertheless, our understanding of the building process, i.e., what defines the route that goes from the initial mixture of DNA strands to the final intertwined superstructure, is, in some cases, still limited. In this review, we describe the main structural and energetic features of DNA nanoconstructs, from the simple Holliday junction to more complicated DNA architectures, and present the theoretical frameworks that have been formulated until now to explain their self-assembly. Deeper insights into the underlying principles of DNA self-assembly may certainly help us to overcome current experimental challenges and foster the development of original strategies inspired to dissipative and evolutive assembly processes occurring in nature.     

Programming supramolecular peptide materials by modulating the intermediate steps in the complex assembly pathway: Implications for biomedical applications

Self-assembling peptides form a prominent class of supramolecular materials with in general good biocompatibility. To afford better control over the material properties, tremendous progress has been made in studying the supramolecular organization of the peptide assemblies. This knowledge has helped us to understand the correlation between the molecular structure of the peptide building blocks and the properties of the supramolecular products. However, peptide self-assembly consists of a complex pathway rather than a spontaneous thermodynamic process. This implies that the outcome of the self-assembly is critically governed by the assembly pathway. Here, we are going to discuss how peptide self-assembly can be modulated at the intermediate steps in the self-assembly pathway. The focus will be to demonstrate this engineering approach on the example of zero-dimensional/one-dimensional nanostructure selectivity over the β-sheet assembly pathway. In addition, we provide examples of biomedical applications of such steered peptide assemblies in the field of drug delivery and tissue engineering.