Structural DNA nanotechnology: from design to applications

The exploitation of DNA for the production of nanoscale architectures presents a young yet paradigm breaking approach, which addresses many of the barriers to the self-assembly of small molecules into highly-ordered nanostructures via construct addressability. There are two major methods to construct DNA nanostructures, and in the current review we will discuss the principles and some examples of applications of both the tile-based and DNA origami methods. The tile-based approach is an older method that provides a good tool to construct small and simple structures, usually with multiply repeated domains. In contrast, the origami method, at this time, would appear to be more appropriate for the construction of bigger, more sophisticated and exactly defined structures.     

How We Make DNA Origami

DNA origami has attracted substantial attention since its invention ten years ago, due to the seemingly infinite possibilities that it affords for creating customized nanoscale objects. Although the basic concept of DNA origami is easy to understand, using custom DNA origami in practical applications requires detailed know‐how for designing and producing the particles with sufficient quality and for preparing them at appropriate concentrations with the necessary degree of purity in custom environments. Such know‐how is not readily available for newcomers to the field, thus slowing down the rate at which new applications outside the field of DNA nanotechnology may emerge. To foster faster progress, we share in this article the experience in making and preparing DNA origami that we have accumulated over recent years. We discuss design solutions for creating advanced structural motifs including corners and various types of hinges that expand the design space for the more rigid multilayer DNA origami and provide guidelines for preventing undesired aggregation and on how to induce specific oligomerization of multiple DNA origami building blocks. In addition, we provide detailed protocols and discuss the expected results for five key methods that allow efficient and damage‐free preparation of DNA origami. These methods are agarose‐gel purification, filtration through molecular cut‐off membranes, PEG precipitation, size‐exclusion chromatography, and ultracentrifugation‐based sedimentation. The guide for creating advanced design motifs and the detailed protocols with their experimental characterization that we describe here should lower the barrier for researchers to accomplish the full DNA origami production workflow.     

Flexibility of C3h‐Symmetrical Linkers in Tris‐oligonucleotide‐Based Tetrahedral Scaffolds

Flexibility of tris‐oligonucleotides is determined by the length of their connecting hydrocarbon chains. Tris‐oligonucleotides are branched DNA building blocks with three oligonucleotide arms attached to a C_3h‐symmetrical linker core at these chains. Four tris‐oligonucleotides hybridise into a tetrahedral nanocage by sequence‐determined self‐assembly. The influence of methylene, ethylene and propylene chains was studied by synthesising sets of tris‐oligonucleotides and analysing the relative stability of the hybridisation products against digestion by mung bean nuclease by using gel electrophoresis. Linkers with ethylene chains showed sufficient flexibility, whereas methylene‐chain linkers were too rigid. Tris‐oligonucleotides based on the latter still formed tetrahedral scaffolds in intermixing experiments with linkers of higher flexibility. Thus, a new generation of versatile isocyanurate‐based linkers was established.     

Construction of T‐Motif‐Based DNA Nanostructures through Enzymatic Reactions

The most common way to fabricate DNA nanostructures is to mix individually synthesized DNA oligomers in one pot. However, if DNA nanostructures could be produced through enzymatic reactions, they could be applied in various environments, including in vivo. Herein, an enzymatic method developed to construct a DNA nanostructure from a simple motif called a T‐motif is reported. A long, repeated structure was replicated from a circular template by rolling circle amplification and then cleaved into T‐motif segments by restriction enzymes. These motifs have been successfully assembled into a ladder‐like nanostructure without purification or controlled annealing. This approach is widely applicable to constructing a variety of DNA nanostructures through enzymatic reactions.     

Construction of a Holliday Junction in Small Circular DNA Molecules for Stable Motifs and Two‐Dimensional Lattices

Design rules for DNA nanotechnology have been mostly learnt from using linear single‐stranded (ss) DNA as the source material. For example, the core structure of a typical DAO (double crossover, antiparallel, odd half‐turns) tile for assembling 2D lattices is constructed from only two linear ss‐oligonucleotide scaffold strands, similar to two ropes making a square knot. Herein, a new type of coupled DAO (cDAO) tile and 2D lattices of small circular ss‐oligonucleotides as scaffold strands and linear ss‐oligonucleotides as staple strands are reported. A cDAO tile of cDAO‐c64nt (c64nt: circular 64 nucleotides), shaped as a solid parallelogram, is constructed with a Holliday junction (HJ) at the center and two HJs at both poles of a c64nt; similarly, cDAO‐c84nt, shaped as a crossed quadrilateral composed of two congruent triangles, is formed with a HJ at the center and four three‐way junctions at the corners of a c84nt. Perfect 2D lattices were assembled from cDAO tiles: infinite nanostructures of nanoribbons, nanotubes, and nanorings, and finite nanostructures. The structural relationship between the visible lattices imaged by AFM and the corresponding invisible secondary and tertiary molecular structures of HJs, inclination angle of hydrogen bonds against the double‐helix axis, and the chirality of the tile can be interpreted very well. This work could shed new light on DNA nanotechnology with unique circular tiles.     

Chaperone‐Polymer‐Assisted,Photodriven DNA Strand Displacement

Photodriven DNA strand displacement by using a 2′,6′‐dimethylazobenzene‐tethered strand and poly(l ‐lysine)‐graft‐dextran (PLL‐g‐Dex) as a chaperone is reported. Rapid strand displacement was reversibly induced by UV and visible‐light irradiation without any toehold portion. To further improve the method, the concentration of PLL‐g‐Dex and the number of equivalents of the photoresponsive strand were optimised. Optimally, 64 % strand displacement was reversibly induced by alternating UV and visible‐light irradiation.     

Exposing Differences in Monomer Exchange Rates of Multicomponent Supramolecular Polymers in Water

The formation of multicomponent and bioactive supramolecular polymers is a promising strategy for the formation of biomaterials that match the dynamic and responsive nature of biological systems. In order to fully realize the potential of this strategy, knowledge of the location and behavior of bioactive components within the system is crucial. By employing synthetic strategies to create multifunctional monomers, coupled with FRET and STORM techniques, we have investigated the formation and behavior of a bioactive and multicomponent supramolecular polymer. By creating a peptide‐dye‐monomer conjugate, we were able to measure high degrees of monomer incorporation and to visualize the equal distribution of monomers within the supramolecular polymer. Furthermore, by tracking the movement of monomers, we uncovered small differences in the dynamics of the bioactive monomers.     

阿魏酸双苄酯的合成及生物活性研究

摘要：以DMSO为溶剂,以阿魏酸与氯化苄在碱性条件下反应,合成了阿魏酸双苄酯,产率为94．32％、纯度为98．5％。通过紫外光谱、红外光谱、核磁共振氢谱、质谱及X-单晶衍射对产物结构进行了表征。用微量量热法证明了阿魏酸双苄酯对大肠杆菌具有一定的抑制作用,其最小抑茵浓度（MIC）为29．81btg·mL-1。通过紫外光谱、荧光光谱和粘度测定研究了阿魏酸双苄酯与ct-DNA的相互作用,证明其作用方式为经典插入方式,对ct-DNA的猝灭是由于形成复合物所引起的静态猝灭,与ct-DNA的结合常数为1．58×10。L·mol-1。