二维DNA晶体的程序化设计与自组装的研究进展

按照Watson-Crick的碱基配对原则，在理论上能够人工设计与合成DNA碱基序列并自组装成任何一维和二维结构的DNA晶体。DNA分子这种底端向上(bottom-up)的自组装模式为我们提供了一种精确合成纳米材料的方法。本文将从程序化设计、合成刚性的DNA分子瓦(DNA tile)、分子瓦自组装成二维DNA晶体以及二维DNA晶体作为模板在纳米技术中的应用等方面展开，简述这一新奇的并且有着潜在应用前景的研究领域的最新进展。     

Self-assembled nanostructures of oligopyridine molecules

The high potential of self-assembly processes of molecular building blocks is reflected in the vast variety of different functional nanostructures reported in the literature. The constituting units must fulfill several requirements like synthetic accessibility, presence of functional groups for appropriate intermolecular interactions and depending on the type of self-assembly processsignificant chemical and thermal stability. It is shown that oligopyridines are versatile building blocks for two- and three-dimensional (2D and 3D) self-assembly. They can be employed for building up different architectures like gridlike metal complexes in solution. By the appropriate tailoring of the heterocycles, further metal coordinating and/or hydrogen bonding capabilities to the heteroaromatic molecules can be added. Thus, the above-mentioned architectures can be extended in one-step processes to larger entities, or in a hierarchical fashion to infinite assemblies in the solid state, respectively. Besides the organizational properties of small molecules in solution, 2D assemblies on surfaces offer certain advantages over 3D arrays. By precise tailoring of the molecular structures, the intermolecular interactions can be fine-tuned expressed by a large variety of resulting 2D patterns. Oligopyridines prove to be ideal candidates for 2D assemblies on graphite and metal sufaces, respectively, expressing highly ordered structures. A slight structural variation in the periphery of the molecules leads to strongly changed 2D packing motifs based on weak hydrogen bonding interactions. Such 2D assemblies can be exploited for building up host-guest networks which are attractive candidates for manipulation experiments on the single-molecule level. Thus, "erasing" and "writing" processes by the scanning tunneling microscopy (STM) tip at the liquid/solid interface are shown. The 2D networks are also employed for performing coordination chemistry experiments at surfaces.     

DNA-templated photonic arrays and assemblies: design principles and future opportunities

Molecular photonics is a rapidly developing and multi-disciplinary field of research involving the construction of molecular assemblies comprising photoactive building blocks that are responsive to a light stimulus. A salient challenge in this field is the controlled assembly of these building blocks with nanoscale precision. DNA exhibits considerable promise as an architecture for the templated assembly of photoactive materials. In this Concept Article we describe the progress that has been made in the area of DNA photonics, in which DNA acts as a platform for the construction of optoelectronic assemblies, thin films and devices.     

Rational design of DNA nanoarchitectures

DNA has many physical and chemical properties that make it a powerful material for molecular constructions at the nanometer length scale. In particular, its ability to form duplexes and other secondary structures through predictable nucleotide-sequence-directed hybridization allows for the design of programmable structural motifs which can self-assemble to form large supramolecular arrays, scaffolds, and even mechanical and logical nanodevices. Despite the large variety of structural motifs used as building blocks in the programmed assembly of supramolecular DNA nanoarchitectures, the various modules share underlying principles in terms of the design of their hierarchical configuration and the implemented nucleotide sequences. This Review is intended to provide an overview of this fascinating and rapidly growing field of research from the structural design point of view.     

Surface‐Assisted Large‐Scale Ordering of DNA Origami Tiles

The arrangement of DNA‐based nanostructures into extended higher order assemblies is an important step towards their utilization as functional molecular materials. We herein demonstrate that by electrostatically controlling the adhesion and mobility of DNA origami structures on mica surfaces by the simple addition of monovalent cations, large ordered 2D arrays of origami tiles can be generated. The lattices can be formed either by close‐packing of symmetric, non‐interacting DNA origami structures, or by utilizing blunt‐end stacking interactions between the origami units. The resulting crystalline lattices can be readily utilized as templates for the ordered arrangement of proteins.     

DNA tile based self-assembly: building complex nanoarchitectures.

DNA tile based self-assembly provides an attractive route to create nanoarchitectures of programmable patterns. It also offers excellent scaffolds for directed self-assembly of nanometer-scale materials, ranging from nanoparticles to proteins, with potential applications in constructing nanoelectronic/nanophotonic devices and protein/ligand nanoarrays. This Review first summarizes the currently available DNA tile toolboxes and further emphasizes recent developments toward self-assembling DNA nanostructures with increasing complexity. Exciting progress using DNA tiles for directed self-assembly of other nanometer scale components is also discussed.     

Simultaneous targeted immobilization of anti-human IgG-coated nanotubes and anti-mouse IgG-coated nanotubes on the complementary antigen-patterned surfaces via biological molecular recognition

Introduction of self-assembly in nanometer-sized building blocks is expected to accomplish bottom-up fabrications in a more reproducible, efficient, and economic manner; however, it is necessary to selectively place multiple types of nano-building blocks (e.g., metal nanotubes and semiconductor nanotubes) at specific locations on surfaces with high precision and reproducibility for more complex nanometer-scale device assemblies. Biological molecular recognition such as antibody-antigen bindings may be suitable to use in the building-block assembly since nature always assembles materials with complex functions and structures at room temperature reproducibly. Our approach is to immobilize antibody-coated nanotubes at specific complementary binding positions patterned on surfaces. To demonstrate this hypothesis, two types of nanotubes coated with different antibodies were anchored selectively onto their complementary antigen areas, patterned by tips of atomic force microscope (AFM). Because those nanotubes can be coated by various metals and semiconductors with controlled morphologies, this outcome opens the possibility to accomplish the proposed unconventional device fabrication methodology that antibody nanotubes coated with different types of metals/semiconductors can be self-assembled on antigen-patterned surfaces via biological molecular recognition.     

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.     

Precise Macroscopic Supramolecular Assemblies: Strategies and Applications

Macroscopic supramolecular assembly (MSA) is a new concept in supramolecular science with a focus on interfacial assembly of macroscopic building blocks, which has largely extended the applicable materials of supramolecular assembly and provided new solutions to fabricating tissue scaffolds, soft devices, etc. The precision of the assembled structures is of great interest; unlike molecular assemblies, MSA precision is highly dependent on the matching degree of assembled surfaces because of the large interactive area and group number, which result in remarkably increased kinetic possibilities and metastable assemblies. This Concept introduces the principle, history, and development of MSA, elaborates the low-precision challenge in MSA, summarizes the strategies for precise MSA based on the different thermodynamic stability of precise/imprecise structures and control over assembly kinetics, and finally demonstrates the applications of precise MSA structures in advanced manufacture such as tissue scaffolds.     

Precise Assembly of Polyoxometalates at Single-cluster Levels

Polyoxometalate (POM) clusters with atomic precision structures are promising candidates construct functional nanomaterials via self-assembly. Non-covalent interactions at molecular levels can govern the self-assembly of POM clusters, for which the precise control of POM-based assemblies can be realized at single-cluster levels. This mini-review focuses on the synthesis and properties of POM-based nanostructures, including amphiphilic POM assemblies and co-assemblies of POM clusters and other subnanometer building blocks. Several synthetic strategies have been developed for rational control of POM-based assemblies in terms of morphologies, compositions and properties. 1D subnanometer POM assemblies demonstrate remarkable enhanced mechanical properties due to the topological interactions between nanowires and surroundings. The in-depth understanding of POM-based assemblies may help in the design of functional nanomaterials in fundamental perspectives and applications.     

Self-assembly of organic molecules at metal surfaces

Self-assembly represents a promising strategy for surface functionalisation as well as creating nanostructures with well-controlled, tailor-made properties and functionality. Molecular self-assembly at solid surfaces is governed by the subtle interplay between molecule–molecule and molecule–substrate interactions that can be tuned by varying molecular building blocks, surface chemistry and structure as well as substrate temperature.In this review, basic principles behind molecular self-assembly of organic molecules on metal surfaces will be discussed. Controlling these formation principles allows for creating a wide variety of different molecular surface structures ranging from well-defined clusters, quasi one-dimensional rows to ordered, two-dimensional overlayers. An impressive number of studies exist, demonstrating the ability of molecular self-assembly to create these different structural motifs in a predictable manner by tuning the molecular building blocks as well as the metallic substrate.Here, the multitude of different surface structures of the natural amino acid cysteine on two different gold surfaces observed with scanning tunnelling microscopy will be reviewed. Cysteine on Au(110)-(1×2) represents a model system illustrating the formation of all the above mentioned structural motifs without changing the molecular building blocks or the substrate surface. The only parameters in this system are substrate temperature and molecular coverage, controlling both the molecular adsorption state (physisorption versus chemisorption) and molecular surface mobility. By tuning the adsorption state and the molecular mobility, distinctly different molecular structures are formed, exemplifying the variety of structural motifs that can be achieved by molecular self-assembly.     

Colloidal assembly: the road from particles to colloidal molecules and crystals

Colloidal particles may be considered as building blocks for materials, just like atoms are the bricks of molecules, macromolecules, and crystals. Periodic arrays of colloids (colloidal crystals) have attracted much interest over the last two decades, largely because of their unique photonic properties. The archetype opal structures are based on close-packed arrays of spheres of submicrometer diameter. Interest in structuring materials at this length scale, but with more complex features and ideally by self-assembly processes, has led to much progress in controlling features of both building blocks and assemblies. The necessary ingredients include colloids, colloidal clusters, and colloidal "molecules" which have special shapes and the ability to bind directionally, the control over short-range and long-range interactions, and the capability to place and orientate these bricks. This Review highlights recent experimental and theoretical progress in the assembly of colloids larger than 50 nm.     

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.     

Macroscopic Supramolecular Assembly and Its Applications

Macroscopic supramolecular assembly (MSA) has been a recent progress in supramolecular chemistry.MSA mainly focuses on studies of the building blocks with a size beyond ten micrometers and the non-covalent interactions between these interactive building blocks to form ordered structures.MSA is essential to realize the concept of"self-assembly at all scales" by bridging most supramolecular researches at molecular level and at macroscopic scale.This review summaries the development of MSA,the basic design principle and related strategies to achieve MSA and potential applications.Correspondingly,we try to elucidate the correlations and differences between "macroscopic assembly" and MSA based on intermolecular interactions;the design principle and the underlying assembly mechanism of MSA are proposed to understand the reported MSA behaviors;to demonstrate further applications of MSA,we introduce some methods to improve the ordered degree of the assembled structures from the point of precise assembly and thus envision some possible fields for the use of MSA.     

Enhancing the melting properties of small molecule-DNA hybrids through designed hydrophobic interactions: an experimental-computational study

Detailed experimental and computational studies revealed the important role that hydrophobic interactions play in the aqueous assembly of rigid small molecule-DNA hybrid (rSMDH) building blocks into nanoscale cage and face-to-face (ff) dimeric structures. In aqueous environments, the hydrophobic surfaces of the organic cores in these nanostructures are minimized by interactions with the core in another rSMDHs, with the bases in the attached DNA strands, and/or with the base pairs in the final assembled structures. In the case that the hydrophobic surfaces of the cores could not be properly isolated in the assembly process, an ill-defined network results instead of dimers, even at low concentration of DNA. In contrast, if ff dimers can be formed with good minimization of the exposed hydrophobic surfaces of the cores, they are highly stable structures with enhanced melting temperatures and cooperative melting behavior.     

Variations in Complementary Hydrogen Bonds Direct Assembly Patterns of Isosteric Polyheteroaromatics at Surfaces

Intermolecular interactions guide self-assembly on the surface. Precise control over these interactions by rational design of the molecule should allow fine control over the self-assembly patterns. Functional groups installed for electronic modulation often induce significant changes in the molecular dimensions, thereby disrupting the original assembly pattern. To overcome this challenge, we have employed a family of isosteric phenazine derivatives, DHP , DAP , and DBQD , to investigate the impacts of hydrogen bonding on two-dimensional molecular self-assembly. While these molecules are similar in size and chemical composition, the strength and directionality of hydrogen bonding differ significantly depending on the chemical structure of donor-acceptor pairs and prototropic tautomerization from positional isomerism. Scanning tunneling microscopy (STM) characterization of the assembled structures on Ag(111), Au(111), and Cu(100) surfaces revealed that minimal changes in molecular structure have a profound impact on the self-assembly patterns. While DHP exhibits highly ordered and robust assemblies, DAP and DBQD show either spatially confined or ill-defined assemblies. In conjunction with hydrogen bonding, prototropic tautomerism is a potent strategy to modulate molecular 2D lattices on surfaces.     

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.     

Recent advances in biocompatible supramolecular assemblies for biomolecular detection and delivery

Inspired by sophisticated biological structures and their physiological processes,supramolecular chemistry has been developed for understanding and mimicking the behaviors of natural species. Through spontaneous self-assembly of functional building blocks,we are able to control the structures and regulate the functions of resulting supramolecular assemblies.Up to now,numerous functional supramolecular assemblies have been constructed and successfully employed as molecular devices, machines and biological diagnostic platforms.This review will focus on molecular structures of functional molecular building blocks and their assembled superstructures for biological detection and delivery.