DNA Origami. Группа авторов

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СКАЧАТЬ were introduced into the concavity and the convex connectors. After self‐assembly of three, four, and five tiles, the DNA tiles were aligned and oriented in the same direction in a designed manner. For identification of the DNA tiles, hairpin markers were introduced onto individual tiles. After self‐assembly, judging from the order of the markers, the five tiles were aligned correctly. This method was further expanded vertically to form 2D assemblies.

      Rothemund and coworker created a programmed assembly system by controlling the positions of adhesive π‐stacking terminals for selective connection between rectangular tiles [19]. They showed that a relaxed edge with blunt ends can form a stable connection, as opposed to a stressed edge with the usual loop ends, which induces structural distortions. Multiple dsDNA terminals with blunt ends were introduced to assemble complementary edges of the counterpart tiles as a binary code. In addition, the complementarity of the edge shape effectively aligned the different tiles for one‐dimensional assemblies. The results indicate that the π‐stacking interactions between the complementary edges can control the programmed assembly of multiple different origami tiles.

The method described above was applied for the preparation of a 2D assembly system [20]. The shape and sequence selectivity were introduced to both lateral edges for extension in the vertical direction (Figure 1.4a). Nine DNA tiles were designed and prepared. Three tiles were then programmed to be connected vertically or horizontally, and three sets of vertical or horizontal trimers were finally assembled into a 3 × 3 assembly in ~30% yield. This assembly was confirmed by hairpin markers on the individual origami tiles. Using a different approach, we explored novel 2D assemblies. Four connection sites of the four‐way DNA origami connector were designed and prepared to facilitate connection between the edges of neighboring DNA jigsaw tiles via π–stacking interactions [24]. Using this four‐way connector, five and eight origami monomers were assembled to form a cruciform and a hollow square structure, respectively. Thus, we successfully created DNA origami‐based 2D assembly systems. The method can be expanded to assemble multiple DNA origami structures in a programmed fashion.

Yan and coworkers presented the template‐assisted assembly of DNA origami structures (Figure 1.4b) [21]. In this method, scaffold frames prepared from the single‐stranded template DNA, and staple strands were used to direct the positioning of six to ten predesigned DNA origami structures including triangles, squares, and hexagons (Figure 1.4b). By annealing the origami structures with connection strands and a scaffold frame, the target assemblies were obtained in a predesigned fashion in relatively high yields. This strategy can be used to produce larger structures when applied to origami assembly, and the positioning of the origami units can be programmed by using the origami sequence design. The variety of available 2D origami structures can be expanded by introducing predesigned and template‐assisted strategies.

      Seeman and coworkers created a strategy for lattice formation by the self‐assembly of cross‐shaped DNA origami structures [22]. Using the sticky ends of four edges from two different cross‐shaped DNA origamis, a large lattice structure was formed by self‐assembly, generating an array with dimensions of about 2 μm × 3 μm (Figure 1.4c). We examined the formation of a lattice using a lipid bilayer surface to assemble DNA origami structures into large‐sized assemblies. A lipid‐bilayer‐assisted assembly was performed to assemble various DNA origami monomers into 2D lattices (Figure 1.4d) [23]. Due to π–π interaction of the blunt ends of DNA, four edges of a cross‐shaped DNA origami monomer were connected to form a lattice. DNA origami structures were electrostatically adsorbed onto the lipid bilayer surface in the presence of divalent cations. The origami structures were mobile on the lipid bilayer surface and assembled into large 2D lattices in the range of micrometers. We also visualized the dynamic processes including attachment and detachment of monomers and reorganization of lattices using high‐speed AFM (HS‐AFM). Other monomers, including the triangular and hexagonal monomers, were also assembled into packed micrometer‐sized assemblies.

      

Figure 1.4 Programmed self‐assembly of DNA origami. (a) Structure of DNA origami having concavity and a convex connector; the structure is called a “DNA jigsaw piece” for 2D assembly. A 3 × 3 assembly of nine origami tiles and the AFM image of the assembly.

      Source: Rajendran et al. [20]/with permission of American Chemical Society.

      (b) Programmed assembly of multiple DNA origami structures using the assistance of scaffold frames. Target assemblies and their AFM images are shown.

      Source: Zhao et al. [21]/with permission of American Chemical Society.

      (c) Lattice formation by self‐assembly of cross‐shaped DNA origami.

      Source: Liu et al. [22]/with permission of John Wiley & Sons, Inc.

      (d) Surface‐assisted lattice formation on the lipid bilayer.

      Source: Suzuki et al. [23]/Springer Nature/CC BY 4.0.

1.4 Three‐Dimensional DNA Origami Structures

The geometry of double‐helical DNA allows for the design of 3D DNA origami structures by extending the 2D DNA origami system. Two strategies for preparing 3D DNA origami structures have been developed. One is the bundling of dsDNAs, where the relative positioning between adjacent dsDNAs is controlled by crossovers, and the other is the folding of 2D origami domains into 3D structures using interconnection strands. In the former method, developed by Shih and coworkers, the relative positioning of adjacent dsDNAs is geometrically controlled by the crossovers. By arranging the positions of the crossovers, tubular and multilayered structures were constructed (Figure 1.5a) [25]. By increasing or decreasing the number of base pairs between crossovers (in this case, 21 base pairs for two helical turns), the relative positional relationship between adjacent dsDNAs can be controlled. Using a rotational angle of 240° for seven base pairs, three adjacent dsDNAs are placed at a relative angle of ±120° with crossovers every 7 or 14 base pairs. By alternating this relative positioning between adjacent dsDNAs, duplexes form a pleated structure. When adjacent dsDNAs are placed to rotate in one direction, the contiguous duplexes finally form a six‐helix bundled tubular structure. Therefore, when some parts of the pleated structures are turned backward by the introduction of one‐directional rotation of adjacent dsDNAs, the structures fold to become a stacked layer structure (Figure 1.5a). In this case, to stabilize the 3D structures, adjacent layers of dsDNAs are further connected by crossovers of staple strands. Because of the complexity and high density of the introduced crossovers, accurate folding into the target 3D structure requires a long folding time. When the pleated structures were integrated as multilayered structures, the repeating units of the six‐helix bundled tubular structures formed a honeycomb lattice, which was viewed from the axial direction of the double helices. It was also possible to create more complex structures by perpendicularly joining these 3D structures (Figure 1.5b). In addition, a wireframe icosahedron structure was assembled from three double‐triangle monomers made СКАЧАТЬ