A 3D chiral nanoporous coordination framework consisting of homochiral nanotubes assembled from octuple helices

A 3D chiral nanoporous coordination framework consisting of homochiral nanotubes assembled from octuple helices with a 19.4 A by 22.4 A aperture is formed by the parallel alignment of eight infinite helical chains.     

Double cohesion in structural DNA nanotechnology

Double cohesion has proved to be a useful tool to assemble robust 2D arrays of large tiles. Here we present a variety of examples showing the utility of this approach. We apply this principle to the 3 types of 2D lattice sections of arrays whose individual tiles are inherently 3 dimensional, because they contain three vectors that span 3-space. This application includes motifs which are based on the tensegrity triangle, the six-helix bundle motif and on three skewed triple crossover molecules. All of these designs have the potential to form 3 dimensional structures if all three directions of propagation are allowed. If one direction is blunted, 2D arrays form, and all 3 combinations are presented here. In addition, a large parallelogram array that was not attainable previously using single duplex cohesion was also constructed using double cohesion. For comparison, arrays which use another type of double cohesion, double paranemic (PX) cohesion are also presented. Double cohesion of sticky ends proved to be the more effective tool to assemble large motifs into arrays.     

Self‐Assembly of a 3D DNA Crystal Structure with Rationally Designed Six‐Fold Symmetry

Programming self‐assembled designer DNA crystals with various lattices and functions is one of the most important goals for nanofabrication using nucleic acids. The resulting porous materials possess atomic precision for several potential applications that rely on crystalline lattices and cavities. Herein, we present a rationally designed and self‐assembled 3D DNA crystal lattice with hexagonal symmetry. In our design, two 21‐base oligonucleotides are used to form a duplex motif that further assembles into a 3D array. The interactions between the strands are programmed using Watson–Crick base‐pairing. The six‐fold symmetry, as well as the chirality, is directed by the Holliday junctions formed between the duplex motifs. The rationally designed DNA crystal provides a new avenue that could create self‐assembled macromolecular 3D crystalline lattices with atomic precision. In addition, the structure contains a highly organized array of well‐defined cavities that are suitable for future applications with immobilized guests.     

Large-scale synthesis of uniform nanotubes of a nickel complex by a solution chemical route

Novel layer-rolled nanotubes of a nickel complex have been successfully synthesized by a simple wet chemical method. The nanotubes are assembled by rolling the (111) sheets of [Ni(NH3)6]Cl2 with the assistance of a polymer. The remarkable uniformity and high yields of the nickel complex nanotubes point to future applications in various fields of nanotechnology.     

Folding and unfolding of helix-turn-helix motifs in the gas phase

Ion mobility measurements and molecular dynamic simulations have been performed for a series of peptides designed to have helix-turn-helix motifs. For peptides with two helical sections linked by a short loop region: AcA(14)KG(3)A(14)K+2H(+), AcA(14)KG(5)A(14)K+2H(+), AcA(14)KG(7)A(14)K+2H(+), and AcA(14)KSar(3)A(14)K+2H(+) (Ac = acetyl, A = alanine, G = glycine, Sar = sarcosine and K = lysine); a coiled-coil geometry with two anti-parallel helices is the lowest energy conformation. The helices uncouple and the coiled-coil unfolds as the temperature is raised. Equilibrium constants determined as a function of temperature yield enthalpy and entropy changes for the unfolding of the coiled-coil. The enthalpy and entropy changes depend on the length and nature of the loop region. For a peptide with three helical sections: protonated AcA(14)KG(3)A(14)KG(3)A(14)K; a coiled-coil bundle with three helices side-by-side is substantially less stable than a geometry with two helices in an antiparallel coiled-coil and the third helix collinear with one of the other two.     

At the crossroads of chemistry, biology, and materials: structural DNA nanotechnology

Structural DNA nanotechnology consists of combining unusual DNA motifs by specific structurally well-defined cohesive interactions (primarily sticky ends) to produce target materials with predictable 3D structures. This effort has generated DNA polyhedral catenanes, robust nanomechanical devices, and a variety of periodic arrays in two dimensions. The system has been used to produce specific patterns on the mesoscale through designing and combining specific DNA strands, which are then examined by atomic force microscopy. The combination of these constructions with other chemical components is expected to contribute to the development of nanoelectronics, nanorobotics, and smart materials. The organizational capabilities of structural DNA nanotechnology are just beginning to be explored, and the field is expected ultimately to be able to organize a variety of species that will lead to exciting and possibly revolutionary materials.     

DNA-directed artificial light-harvesting antenna

Designing and constructing multichromophoric, artificial light-harvesting antennas with controlled interchromophore distances, orientations, and defined donor-acceptor ratios to facilitate efficient unidirectional energy transfer is extremely challenging. Here, we demonstrate the assembly of a series of structurally well-defined artificial light-harvesting triads based on the principles of structural DNA nanotechnology. DNA nanotechnology offers addressable scaffolds for the organization of various functional molecules with nanometer scale spatial resolution. The triads are organized by a self-assembled seven-helix DNA bundle (7HB) into cyclic arrays of three distinct chromophores, reminiscent of natural photosynthetic systems. The scaffold accommodates a primary donor array (Py), secondary donor array (Cy3) and an acceptor (AF) with defined interchromophore distances. Steady-state fluorescence analyses of the triads revealed an efficient, stepwise funneling of the excitation energy from the primary donor array to the acceptor core through the intermediate donor. The efficiency of excitation energy transfer and the light-harvesting ability (antenna effect) of the triads was greatly affected by the relative ratio of the primary to the intermediate donors, as well as on the interchromophore distance. Time-resolved fluorescence analyses by time-correlated single-photon counting (TCSPC) and streak camera techniques further confirmed the cascading energy transfer processes on the picosecond time scale. Our results clearly show that DNA nanoscaffolds are promising templates for the design of artificial photonic antennas with structural characteristics that are ideal for the efficient harvesting and transport of energy.     

Characterization of 3D DNA Assemblies Using Cryogenic Electron Microscopy

DNA nanotechnology utilizes DNA double strands as building units for self-assembly of DNA nanostructures.The specific base-pairing interaction between DNA molecules is the basis of these assemblies.After decades of development,this technology has been able to construct complex and programmable structures.With the increase in delicate nature and complexity of the synthesized nanostructures,a characterization technology that can observe these structures in three dimensions has become necessary,and developing such a technology is considerably challenging.DNA assemblies have been studied using different characterization methods including atomic force microscopy(AFM),scanning electron microscopy(SEM),and transmission electron microscopy(TEM).However,the three-dimensional(3D)DNA assemblies always collapse locally due to the dehydration during the drying process.Cryogenic electron microscopy(cryo-EM)can overcome the challenge by maintaining three-dimensional morphologies of the cryogenic samples and reconstruct the 3D models from cryogenic samples accordingly by collecting thousands of two-dimensional(2D)projection images,which can restore their original morphologies in solution.Here,we have reviewed several typical cases of 3D DNA-assemblies and highlighted the applications of cryo-EM in characterization of these assemblies.By comparing with some other characterization methods,we have shown how cryo-EM promoted the development of structural characterization in the field of DNA nanotechnology.     

Hierarchical assembly of SnO2 nanorod arrays on alpha-Fe2O3 nanotubes: a case of interfacial lattice compatibility

SnO2 nanorod arrays were hierarchically assembled onto the surface of alpha-Fe2O3 nanotubes via a facile solution method. Determined by the hexagonal geometrical nature of the alpha-Fe2O3 nanotubes, the heterostructures were of 6-fold symmetry. HRTEM characterizations demonstrated that the lattice mismatch at the interface was an important factor in determining the growth direction of the secondary nanorod arrays.     

Biomimetic DNA Nanotubes: Nanoscale Channel Design and Applications

Biomacromolecular nanotubes play important physiological roles in transmembrane ion/molecule channeling, intracellular transport, and inter‐cellular communications. While genetically encoded protein nanotubes are prevalent in vivo, the in vitro construction of biomimetic DNA nanotubes has attracted intense interest with the rise of structural DNA nanotechnology. The abiotic use of DNA assembly provides a powerful bottom‐up approach for the rational construction of complex materials with arbitrary size and shape at the nanoscale. More specifically, a typical DNA nanotube can be assembled either with parallel‐aligned DNA duplexes or by closing DNA tile lattices. These artificial DNA nanotubes can be tailored and site‐specifically modified to realize biomimetic functions including ionic or molecular channeling, bioreactors, drug delivery, and biomolecular sensing. In this Minireview, we aim to summarize recent advances in design strategies, including the characterization and applications of biomimetic DNA nanotubes.     

Sequence Decoding of 1D to 2D Self-Assembling Cyclic Peptides

The inherent ability of peptides to self-assemble with directional and rationally predictable interactions has fostered a plethora of synthetic two-dimensional (2D) supramolecular biomaterials. However, the design of peptides with hierarchical assembly in different dimensions across mesoscopic lengths remains a challenging task. We here describe the structural exploration of a d /l -alternating cyclic octapeptide capable of assembling one-dimensional (1D) nanotubes in water, which subsequently pack laterally to form giant 2D nanosheets up to 500 μm long with a constant 3.2 nm thickness. Specific amino acid mutations allowed the mapping of structure–assembly relationships that determine 2D self-assembly. Nine peptide modifications were studied, revealing key features in the peptide sequence that nanosheets tolerated, while a total of three peptide variants included modifications that compromised their 2D arrangement. These lessons will serve as guide and inspiration for new 2D supramolecular peptide designs.     

Programmable 3D Hexagonal Geometry of DNA Tensegrity Triangles

Non-canonical interactions in DNA remain under-explored in DNA nanotechnology. Recently, many structures with non-canonical motifs have been discovered, notably a hexagonal arrangement of typically rhombohedral DNA tensegrity triangles that forms through non-canonical sticky end interactions. Here, we find a series of mechanisms to program a hexagonal arrangement using: the sticky end sequence; triangle edge torsional stress; and crystallization condition. We showcase cross-talking between Watson–Crick and non-canonical sticky ends in which the ratio between the two dictates segregation by crystal forms or combination into composite crystals. Finally, we develop a method for reconfiguring the long-range geometry of formed crystals from rhombohedral to hexagonal and vice versa. These data demonstrate fine control over non-canonical motifs and their topological self-assembly. This will vastly increase the programmability, functionality, and versatility of rationally designed DNA constructs.     

Assembly of one dimensional inorganic nanostructures into functional 2D and 3D architectures. Synthesis, arrangement and functionality

This review will focus on the synthesis, arrangement, structural assembly, for current and future applications, of 1D nanomaterials (tubes, wires, rods) in 2D and 3D ordered arrangements. The ability to synthesize and arrange one dimensional nanomaterials into ordered 2D or 3D micro or macro sized structures is of utmost importance in developing new devices and applications of these materials. Micro and macro sized architectures based on such 1D nanomaterials (e.g. tubes, wires, rods) provide a platform to integrate nanostructures at a larger and thus manageable scale into high performance electronic devices like field effect transistors, as chemo- and biosensors, catalysts, or in energy material applications. Carbon based, metal oxide and metal based 1D arranged materials as well as hybrid or composite 1D materials of the latter provide a broad materials platform, offering a perspective for new entries into fascinating structures and future applications of such assembled architectures. These architectures allow bridging the gap between 1D nanostructures and the micro and macro world and are the basis for an assembly of 1D materials into higher hierarchy domains. This critical review is intended to provide an interesting starting point to view the current state of the art and show perspectives for future developments in this field. The emphasis is on selected nanomaterials and the possibilities for building three dimensional arrays starting from one dimensional building blocks. Carbon nanotubes, metal oxide nanotubes and nanowires (e.g. ZnO, TiO(2), V(2)O(5), Cu(2)O, NiO, Fe(2)O(3)), silicon and germanium nanowires, and group III-V or II-VI based 1D semiconductor nanostructures like GaS and GaN, pure metals as well as 1D hybrid materials and their higher organized architectures (foremost in 3D) will be focussed. These materials have been the most intensively studied within the last 5-10 years with respect to nano-micro integration aspects and their functional and application oriented properties. The critical review should be interesting for a broader scientific community (chemists, physicists, material scientists) interested in synthetic and functional material aspects of 1D materials as well as their integration into next higher organized architectures.     

Charge Neutralization Drives the Shape Reconfiguration of DNA Nanotubes

Reconfiguration of membrane protein channels for gated transport is highly regulated under physiological conditions. However, a mechanistic understanding of such channels remains challenging owing to the difficulty in probing subtle gating‐associated structural changes. Herein, we show that charge neutralization can drive the shape reconfiguration of a biomimetic 6‐helix bundle DNA nanotube (6HB). Specifically, 6HB adopts a compact state when its charge is neutralized by Mg²⁺; whereas Na⁺ switches it to the expanded state, as revealed by MD simulations, small‐angle X‐ray scattering (SAXS), and FRET characterization. Furthermore, partial neutralization of the DNA backbone charges by chemical modification renders 6HB compact and insensitive to ions, suggesting an interplay between electrostatic and hydrophobic forces in the channels. This system provides a platform for understanding the structure–function relationship of biological channels and designing rules for the shape control of DNA nanostructures in biomedical applications.     

Synthesis of two mirror image 4-helix junctions derived from glycerol nucleic acid

Structural DNA nanotechnology relies on Watson-Crick base pairing rules to assemble DNA motifs into diverse arrangements of geometric shapes and patterns. While substantial effort has been devoted to expanding the programmability of natural DNA, considerably less attention has been given to the development of nucleic acid structures based on non-natural DNA polymers. Here we describe the use of glycerol nucleic acid (GNA), a simple polymer based on an acyclic repeating unit, as an alternative genetic material for assembling nucleic acid nanostructures independent of RNA or DNA recognition. We synthesized two 4-helix junctions based entirely on GNA self-pairing and showed that GNA provides easy access to highly stable nanostructures with left- and right-handed helical configurations.     

Template-directed synthesis of ordered iron pyrite (FeS2) nanowires and nanotubes arrays

Highly ordered iron pyrite (FeS₂) nanowires and nanotubes arrays have been fabricated by using sol–gel method with AAO templates. The prepared nanowires and nanotubes have uniform lengths and 200 nm diameters. Their crystal phase was identified as cubic FeS₂ by using X-ray diffraction, Raman spectroscopy, high-resolution transmission electron microscopy and selected-area electron diffraction pattern. The direct optical band gaps of the as-prepared FeS₂ nanowires were 0.98 and 1.23 eV, respectively, indicating their suitability for photovoltaic application.     

Complexing DNA Origami Frameworks through Sequential Self‐Assembly Based on Directed Docking

Ordered DNA origami arrays have the potential to compartmentalize space into distinct periodic domains that can incorporate a variety of nanoscale objects. Herein, we used the cavities of a preassembled 2D DNA origami framework to incorporate square‐shaped DNA origami structures (SQ‐origamis). The framework was self‐assembled on a lipid bilayer membrane from cross‐shaped DNA origami structures (CR‐origamis) and subsequently exposed to the SQ‐origamis. High‐speed AFM revealed the dynamic adsorption/desorption behavior of the SQ‐origamis, which resulted in continuous changing of their arrangements in the framework. These dynamic SQ‐origamis were trapped in the cavities by increasing the Mg²⁺ concentration or by introducing sticky‐ended cohesions between extended staples, both from the SQ‐ and CR‐origamis, which enabled the directed docking of the SQ‐origamis. Our study offers a platform to create supramolecular structures or systems consisting of multiple DNA origami components.     

2D Crystal Engineering of Nanosheets Assembled from Helical Peptide Building Blocks

The successful integration of 2D nanomaterials into functional devices hinges on developing fabrication methods that afford hierarchical control across length scales of the entire assembly. We demonstrate structural control over a class of crystalline 2D nanosheets assembled from collagen triple helices. By lengthening the triple helix unit through sequential additions of Pro‐Hyp‐Gly triads, we achieved sub‐angstrom tuning over the 2D lattice. These subtle changes influence the overall nanosheet size, which can be adjusted across the mesoscale size regime. The internal structure was observed by cryo‐TEM with direct electron detection, which provides real‐space high‐resolution images, in which individual triple helices comprising the lattice can be clearly discerned. These results establish a general strategy for tuning the structural hierarchy of 2D nanomaterials that employ rigid, cylindrical structural units.     

Pseudohexagonal 2D DNA crystals from double crossover cohesion

Two-dimensional pseudohexagonal trigonal arrays have been constructed by self-assembly from DNA. The motif used is a bulged-junction DNA triangle whose edges and extensions are DNA double crossover (DX) molecules, rather than conventional DNA double helices. Experiments were performed to establish whether the success of this system results from the added stiffness of DX molecules or the presence of two sticky ends at the terminus of each edge. Removal of one sticky end precludes lattice formation, suggesting that it is the double sticky end that is the primary factor enabling lattice formation.