Design and characterization of 1D nanotubes and 2D periodic arrays self-assembled from DNA multi-helix bundles

Among the key goals of structural DNA nanotechnology are to build highly ordered structures self-assembled from individual DNA motifs in 1D, 2D, and finally 3D. All three of these goals have been achieved with a variety of motifs. Here, we report the design and characterization of 1D nanotubes and 2D arrays assembled from three novel DNA motifs, the 6-helix bundle (6HB), the 6-helix bundle flanked by two helices in the same plane (6HB+2), and the 6-helix bundle flanked by three helices in a trigonal arrangement (6HB+3). Long DNA nanotubes have been assembled from all three motifs. Such nanotubes are likely to have applications in structural DNA nanotechnology, so it is important to characterize their physical properties. Prominent among these are their rigidities, described by their persistence lengths, which we report here. We find large persistence lengths in all species, around 1-5 μm. The magnitudes of the persistence lengths are clearly related to the designs of the linkages between the unit motifs. Both the 6HB+2 and the 6HB+3 motifs have been successfully used to produce well-ordered 2D periodic arrays via sticky-ended cohesion.     

Geometric self-sorting in DNA self-assembly

Two types of DNA star motifs (tiles) can recognize and associate with like tiles to form 2D arrays but exclude unlike tiles even though the local interactions between any two tiles are exactly the same.     

Formation of Discrete Ladders and a Macroporous Xerogel Film by the Zipperlike Dimerization of Meso–Meso‐Linked Zinc(II) Porphyrin Arrays with Di(pyrid‐3‐yl)acetylene

Metal porphyrins assemble to form a supramolecular architecture with a characteristic structure and characteristic properties and functions upon complexation with appropriate ligands. However, there are few applications of these assembly processes to the construction of polymeric porphyrin arrays with useful functionalities. In this study, we found that meso–meso‐linked Zn^II porphyrin arrays underwent zipperlike dimerization upon complexation with di(pyrid‐3‐yl)acetylene (DPA) in chloroform to form discrete double‐stranded porphyrin ladders. Similarly, the assembly of poly(zinc(II) porphyrinylene) with DPA gave a thermoresponsive gel, whose three‐dimensional network structure was so strong that a macroporous xerogel film was obtained.     

Self-assembly of chiral DNA nanotubes

A system of DNA "tiles" that is designed to assemble to form two-dimensional arrays is observed to form narrow ribbons several micrometers in length. The uniform width of the ribbons and lack of frayed edges lead us to propose that they are arrays that have curled and closed on themselves to form tubes. This proposal is confirmed by the observation of tubes with helical order.     

Divergent Chemistry Paths for 3D and 1D Metallo‐Covalent Organic Frameworks (COFs)

The marriage of dynamic covalent chemistry (DCC) and coordination chemistry is a powerful tool for assembling complex architectures from simple building units. Recently, the synthesis of woven covalent organic frameworks (COFs) with topologically fascinating structures has been achieved using this approach. However, the scope is highly limited and there is a need to discover new pathways that can assemble covalently linked organic threads into crystalline frameworks. Herein, we have identified branching pathways leading to the assembly of three‐dimensional (3D) woven COFs or one‐dimensional (1D) metallo‐COFs (mCOFs), where the mechanism is underpinned by the absence or presence of ligand exchange.     

An Adamantane‐Based Building Block for DNA Networks

DNA governs the storage and transfer of genetic information through generations in all living systems with the exception of some viruses. Its physicochemical nature and the Watson–Crick base pairing properties allow molecular constructions at nanometer length, thereby enabling the design of desired structural motifs, which can self‐assemble to form large supramolecular arrays and scaffolds. The tailor‐made DNAs have been an interesting material for such designed nanoscale constructions. However, the synthesis of specific structures with a desired molecular function is still in its infancy and therefore has to be further explored. To add a new dimension to this approach, we have synthesized a rigid three‐way branched adamantane motif, which is capable of forming highly stable DNA networks. The moiety generated could serve as a useful building block for DNA‐based nanoconstructions.     

A study of DNA tube formation mechanisms using 4-, 8-, and 12-helix DNA nanostructures

This paper describes the design and characterization of a new family of rectangular-shaped DNA nanostructures (DNA tiles) containing 4, 8, and 12 helices. The self-assembled morphologies of the three tiles were also investigated. The motivation for designing this set of DNA nanostructures originated from the desire to produce DNA lattices containing periodic cavities of programmable dimensions and to investigate the mechanism of DNA tube formation. Nine assembly scenarios have been investigated through the combination of the three different tiles and three sticky end association strategies. Imaging by atomic force microscopy (AFM) revealed self-assembled structures with varied cavity sizes, lattice morphologies, and orientations. Six samples show only tube formation, two samples show both 2D lattices (>2 microm) and tubes, and one sample shows only 2D lattices without tubes. We found that a lower tile dimensional anisotropy, weaker connection, and corrugated design favor the large 2D array formation, while the opposite (higher tile anisotropy, stronger connection, and uncorrugated design) favors tube formation. We discuss these observations in terms of an energy balance at equilibrium and the kinetic competition between diffusion-limited lateral lattice growth versus fluctuation of the lattice to form tubes at an early stage of the assembly. The DNA nanostructures and their self-assembly demonstrated herein not only provide a new repertoire of scaffolds to template the organization of nanoscale materials, but may also provide useful information for investigating other self-assembly systems.     

Paranemic cohesion of topologically-closed DNA molecules

Specific cohesion of DNA molecules is key to the success of work in biotechnology, DNA nanotechnology and DNA-based computation. The most common form of intermolecular cohesion between double helices is by sticky ends, but sticky ends generated by naturally occurring restriction enzymes may often be too short to bind large constructs together. An alternative form of binding is available through the paranemic crossover (PX) motif. Each of the two components of a PX motif can be a DNA dumbbell or other topologically closed species. Alternate half-turns of the dumbbell are paired intramolecularly. The intervening half-turns are paired with those of the opposite component. We demonstrate the efficacy of PX cohesion by showing that it can result in the 1:1 binding of two triangle motifs, each containing nearly 500 nucleotides. The cohesion goes to completion, demonstrating an alternative to binding nucleic acid molecules through sticky ends.     

Polysulfonylamine. CLXIII [1] Kristallstrukturen von Metall‐di(methansulfonyl)amiden. 12 [1] Das orthorhombische Doppelsalz Na2Cs2[(CH3SO2)2N]4·3H2O: Ein dreidimensionales Koordinationspolymer aus (Caesium‐Anion‐Wasser)‐Schichten und intercalierten Natriumionen

Polysulfonylamines. CLXIII. Crystal Structures of Metal Di(methanesulfonyl)amides. 12. The Orthorhombic Double Salt Na₂Cs₂[(CH₃SO₂)₂N]₄·3H₂O: A Three‐Dimensional Coordination Polymer Built up from Cesium‐Anion‐Water Layers and Intercalated Sodium Ions The packing arrangement of the three‐dimensional coordination polymer Na₂Cs₂[(MeSO₂)₂N]₄·3H₂O (orthorhombic, space group Pna2₁, Z′ = 1) is in some respects similar to that of the previously reported sodium‐potassium double salt Na₂K₂[(MeSO₂)₂N]₄·4H₂O (tetragonal, P4₃2₁2, Z′ = 1/2). In the present structure, four multidentately coordinating independent anions, three independent aquo ligands and two types of cesium cation form monolayer substructures that are associated in pairs to form double layers via a Cs(1)—H₂O—Cs(2) motif, thus conferring upon each Cs⁺ an irregular O₈N₂ environment drawn from two N, O‐chelating anions, two O, O‐chelating anions and two water molecules. Half of the sodium ions occupy pseudo‐inversion centres situated between the double layers and have an octahedral O₆ coordination built up from four anions and two water molecules, whereas the remaining Na⁺ are intercalated within the double layers in a square‐pyramidal and pseudo‐C₂ symmetric O₅ environment provided by four anions and the water molecule of the Cs—H₂O—Cs motif. The net effect is that each of the four independent anions forms bonds to two Cs⁺ and two Na⁺, two independent water molecules are involved in Cs—H₂O—Na motifs, and the third water molecule acts as a μ₃‐bridging ligand for two Cs⁺ and one Na⁺. The crystal cohesion is reinforced by a three‐dimensional network of conventional O—H···O=S and weak C—H···O=S/N hydrogen bonds.     

Photon Counting Histogram Analysis for Two‐Dimensional Systems

Photon counting statistics in 3D photon counting histogram analysis for one‐photon excitation is a function of the number of molecules of particular brightness in the excitation‐detection volume of a confocal microscope. In mathematical form that volume is approximated by a three‐dimensional Gaussian function which is embedded in the PCH theoretical equations. PCH theory assumes that a molecule can be found anywhere inside the excitation‐detection volume with equal probability. However, one can easily imagine systems in which this assumption is violated because molecules are constrained by the geometry of the sample. For example, molecules on a surface or in a membrane would be constrained to two dimensions. To enable the analysis of such systems by PCH, the theoretical framework requires modification. Herein, we present an extension of the PCH analysis to systems where molecules exist in thin structures that are effectively two‐dimensional. The method, aptly called two‐dimensional photon counting histogram (2D PCH), recovers the number of fluorescent particles per unit area and their molecular brightness. Both theoretical background and experimental results are presented. The theory was tested using computer‐simulated and experimental 2D PCHs obtained from confocal experiments. We demonstrate that this modification of the theoretical framework provides a tool to extract data that reveal states of aggregation, surface photophysics, and reactivity.     

Directing the Self-Assembly of Aromatic Foldamer Helices using Acridine Appendages and Metal Coordination

Folded molecules provide complex interaction interfaces amenable to sophisticated self-assembly motifs. Because of their high conformational stability, aromatic foldamers constitute suitable candidates for the rational elaboration of self-assembled architectures. Several multiturn helical aromatic oligoamides have been synthesized that possess arrays of acridine appendages pointing in one or two directions. The acridine units were shown to direct self-assembly in the solid state via aromatic stacking leading to recurrent helix-helix association patterns under the form of discrete dimers or extended arrays. In the presence of Pd(II), metal coordination of the acridine units overwhelms other forces and generates new metal-mediated multihelical self-assemblies, including macrocycles. These observations demonstrate simple access to different types of foldamer-containing architectures, ranging from discrete objects to 1D and, by extension, 2D and 3D arrays.     

Homomeric Inclusion and Hydrogen‐Bonding Cooperatively Directed Crystalline Assembly of a Cyclotriguaiacylene Derivative with Different Aromatic Acids

Five organic complexes are prepared by cocrystallization of tri‐[(N‐methyl‐2‐imidazoly)methoxy]cyclotriguiacylene (TMIM‐CTG) with corresponding acids. While hydrogen bonds are the basic interactions in the five complexes, the homo‐included motifs with C? H···π interactions also control the molecular arrangement except for complex 5 . In complex 1 , the two dimensional networks contain 1D zigzag chains formed by hydrogen bonding and 1D chains of homo‐included CTG motifs. Complex 2 has 2D 4·8² hydrogen bonding networks, and the chains of homomeric inclusion extend the 2D structure to a 3D framework. Complex 3 contains four‐membered rings through hydrogen bonds, and the chains of homo‐inclusion link the rings to a novel 2D network. In complex 4 , hydrogen bonds construct a novel double‐layer 2D network, which is extended to a 3D framework by "hand‐shake" dimeric homomeric inclusion interactions. Interestingly, there is no homomeric inclusion phenomenon in complex 5 and hydrogen bonds solely connect two components to a chiral (6,3) 2D network.     

Self‐Assembly of a Tripod Aromatic Rod into Stacked Planar Networks

Threefold symmetric rigid‐core molecules with an internally grafted poly(ethylene oxide) (PEO) chain were synthesized, and their self‐assembled structures were characterized using differential scanning calorimetry, TEM, and 1D and 2D X‐ray scatterings in the solid state. The tripod compounds based on short PEO chains (n=8, 13, 17, 21), self‐assemble into 2D channel‐like network structures, whereas the compound with the longest PEO chain (n=34) forms a lamellar liquid crystalline phase. The interiors of the channel structures are filled with flexible PEO chains along the double‐walled aromatic circumference. In these channel‐like networks, three aromatic rods connected in the meta‐position to each other are superimposed in parallel to other adjacent molecules to form the double‐walled aromatic frameworks stacked perpendicular to the resulting channels. These are novel examples of supramolecular channel‐like structures developed using amphiphilic diblock molecules based on a threefold symmetric rigid scaffold.     

Self-assembly of symmetric finite-size DNA nanoarrays

We report a novel and cost-effective strategy to self-assemble finite-size DNA nanoarrays. This strategy takes advantage of the geometric symmetry of the DNA nanostructures. In general, to construct a 2D array with a total of N tiles containing Cm symmetry, where m = 2, 3, 4, or 6, the number of unique tiles the fixed-size array requires is N/m, if N/m is an integral number, or Int(N/m) + 1, if N/m is an nonintegral number. We herein demonstrate two examples of fixed-size arrays with C2 and C4-fold symmetry.dagger     

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。     

陶瓷泡沫空气过滤器涂覆中孔TiO2薄膜用于室内空气净化中高效光催化降解NO

由于人们80%的时间呆在室内,室内空气的质量直接影响人类健康,因此近年来室内空气质量越来越受到人们的关注.室内污染物包括CO氮氧化物(NOx)和挥发性有机化合物(VOCs),它们给人体健康带来众多负面影响.更为重要的是,考虑到节能,现代建筑的空气密闭性大都较高,但这种减少吸入新鲜空气的设计直接导致室内各种污染物的累积.有些家用电器,如燃气灶和热水器,在使用的时候会涉及到煤、油和天然气的燃烧,特别是通风较差的情况下会成为室内主要的污染源.常规的治理技术,包括吸附和过滤,其成本相对较高,也不适用于低浓度污染物的治理.尤其是更换不及时的过滤器在排风系统中可能会成为VOCs的一个来源.因此,很有必要开发一种新型的技术以降低室内污染物的浓度和保持一个清洁的室内空气环境,从而保障人们的身体健康.光催化是去除室内空气污染物的有效方法.例如, TiO2、钛酸铋和钛酸锶等具有强氧化能力和稳定的光催化活性,因而是高效的光催化剂.一般而言,通常报道的TiO2光催化剂是高度分散的、或悬浮于液体介质中的细小颗粒或粉末.然而,粉末状的TiO2光催化剂不适宜于室内空气净化,因为它变得可吸入而对人体健康造成不利的影响.因此,人们尝试将TiO2颗粒作为薄膜固定在不同的刚性载体上,如玻璃、不锈钢和铝合金板.对基体进行涂覆可显著影响光催化时反应物的表面吸附行为.一般而言,光催化薄膜通常涂覆在平面上,如蜂窝空气过滤器.三维(3D)多孔的陶瓷泡沫对气体通过具有非常好的流体性质,因此本文以它作为涂覆的基体.这种陶瓷泡沫具有3D多孔结构,多种孔密度、比表面积和化学性质.3D多孔陶瓷泡沫空气过滤器的床层空隙率较高,因此使用时压降较低,且不像蜂窝空气过滤器,它具有复杂多变的孔结构,可增强流体的扰动和混合.另外,3D多孔陶瓷泡沫空气过滤器的开发多孔和网状的结构使得在催化体系具有非常好的气体动力学性质,催化剂表面和气体反应物有充分的接触.多孔材料在液相或气相催化反应中具有独特的优势,因此,陶瓷泡沫、多孔的氧化铝、多孔硅胶.分子筛和活性炭经常被用作催化剂载体.在固体基体上TiO2膜的形成可能使得TiO2光催化剂的有效比表面积降低,从而导致其光催化活性下降.然而,由于具有中孔结构的TiO2薄膜的比表面积大,其用于催化反应的活性位也更多,因此使用时仍然具有较高的活性.前期研究表明,涂覆在平面玻璃、不锈钢和氧化铝基体上的中孔TiO2薄膜用于环境净化时表现出增强的光催化效率.另外,室内环境中NO和NO2的浓度一般分别为几百个ppb之内和100 ppb以下.可见, NO是主要的室内空气污染物,对人体健康危害较大.基于此,本文首次采用反胶束法将中孔锐钛矿TiO2薄膜均匀一地涂覆在3D多孔高比表面积的泡沫过滤器上,采用X射线衍射、扫描电镜、X射线光电子能谱、N2吸附-脱附、紫外-可见光光谱和原子力显微镜对所制样品进行了表征,并将样品用于紫外光下催化降解NO,以揭示所制的中孔TiO2涂层具有高的比表面积和高的光催化活性,从而克服使用TiO2粉末所带来的不足.结果表明,由于中孔TiO2薄膜涂层具有较大的有效比表面积,其表面存在很多吸附活性位,用于吸附在反应过程中形成的水蒸汽、气相反应物和产物,因而具有更高的光催化活性,因此在陶瓷泡沫空气净化系统中可以高效地光催化NO降解：在所考察的不同孔密度的陶瓷泡沫过滤器涂覆的TiO2上400 ppb的NO单程转化率均在92.5%以上,高于涂覆在平面陶瓷砖上的TiO2.该陶瓷过滤器的3D多孔特性可增强流体的扰动和混合,使得气相反应物与光催化剂表面有着充分的接触;其大的孔密度也导致高的光催化速率.另外,本文所制样品在所有反应过程中均保持较高且稳定的NO降解速率,这表明其在NO降解反应中没有失活.     

Design and construction of double-decker tile as a route to three-dimensional periodic assembly of DNA

DNA is a useful material for nanoscale construction. Due to highly specific Watson-Crick base pairing, the DNA sequences can be designed to form small tiles or origami. Adjacent helices in such nanostructures are connected via Holliday junction-like crossovers. DNA tiles can have sticky ends which can then be programmed to form large one-dimensional and two-dimensional periodic lattices. Recently, a three-dimensional DNA lattice has also been constructed. Here we report the design and construction of a novel DNA cross tile, called the double-decker tile. Its arms are symmetric and have four double helices each. Using its sticky ends, large two-dimensional square lattices have been constructed which are on the order of tens of micrometers. Furthermore, it is proposed that the sticky ends of the double-decker tile can be programmed to form a three-dimensional periodic lattice with large cavities that could be used as a scaffold for precise positioning of molecules in space.     

DNA: beyond the double helix

Reciprocal exchange can be used to produce DNA motifs based on branching at the level of secondary structure. These motifs can be combined by sticky-ended cohesion to produce a variety of structures. Stick polyhedra and nanomechanical devices have been produced by self-assembly from motifs based on branched DNA. Periodic arrays with tunable surface features has also been produced; aperiodic arrangements have been used for DNA-based computation.     

Three‐Dimensional Ordered Antibody Arrays Through Self‐Assembly of Antibody–Polymer Conjugates

Three‐dimensional (3D) ordered arrays of human immunoglobulin G (IgG) were fabricated using well‐defined full‐length antibody–polymer conjugates (APCs). The conjugates were prepared through a two‐step sequential click approach with a combination of oxime ligation and strain promoted alkyne–azide cycloaddition. They were able to self‐assemble into lamellar nanostructures with alternating IgG and poly(N ‐isopropylacrylamide) (PNIPAM) nanodomains. As a proof‐of‐concept, these materials were fabricated into thin films and their specific binding ability was tested. The nanostructure not only improves the packing density and the proper orientation of the IgG, but also provides nanochannels to facilitate substrate transport.     

Two‐Dimensional Crystals from Reduced Symmetry Analogues of Trimesic Acid

The two‐dimensional assembly of multicarboxylated arenes is explored at the liquid–graphite interface using scanning tunneling microscopy. Symmetry variations were introduced via phenylene spacer addition and the influence of these perturbations on the formation of hydrogen‐bonded motifs from an alkanoic acid solvent is observed. This work demonstrates the importance of symmetry in 2D crystal formation and draws possible links of this behavior to prediction of coordination modes in three‐dimensional coordination polymers.