DNA Origami. Группа авторов

1.9).

1.2 Two‐Dimensional DNA Origami

DNA origami has enabled the construction of a wide variety of 2D structures approximately 100 nm in size, including rectangles, triangles, and even a smiley face and five‐pointed star (Figure 1.3) [6]. In this method, a long single‐stranded DNA (M13mp18; 7249 nucleotides) and sequence‐designed complementary strands (called “staple strands”; most of which are 32‐mer) are mixed and then annealed from 95 °C to room temperature over two hours, resulting in the formation of target structures by self‐assembly (Figure 1.3a). The structure can be imaged by AFM, and the assembled structure formed according to a design. To create 2D DNA origami structures, adjacent dsDNAs should be connected to each other via a crossover. In this design, the geometry of the double helices involved has three helical rotations for 32 base pairs (Figure 1.3b). For example, two neighboring crossovers of the central dsDNA in an arrangement of three adjacent dsDNAs should be located at the opposite sites (rotated at 180°, 0.5 turns); therefore, the crossovers should be separated by 16 base pairs (1.5 turns). This rule should be preserved to maintain stable planar structure when placing multiple staple strands on the scaffold. DNA origami structures are formed using many different staple strands, so DNA hairpins can be placed as markers at any position on the surface of the DNA structure. A hairpin DNA (dumbbell‐type) used as a topological marker was observed as a dot by AFM imaging (Figure 1.3c). In this case, hairpins are placed perpendicular to the surface of the origami; therefore, each hairpin should be placed at a position eight base pairs from the crossover (270° rotation). The distance between the centers of the adjacent staples is approximately 6 nm, so the adjacent hairpins can be observed as different spots according to the spatial resolution of AFM. Using the hairpin markers, patterns, such as the map of a hemisphere (Figure 1.3c), can be displayed precisely on the DNA origami surface.

Figure 1.2 DNA nanotechnology before the emergence of DNA origami. (a) DNA double helix structure, base pair, and double‐stranded DNA (dsDNA). (b) Holliday junction structure, four‐way junction, and conceptual diagram for construction of 2D structure.

      Source: Modified from Seeman [1].

      (c) Double crossover structure, in which two dsDNAs are connected by four‐way branched strands (crossover; arrows). Two‐dimensional periodic structure was formed by self‐assembly using two double‐crossover components (A‐tile and B‐tile* with hairpin) with sticky ends (complementary single‐stranded DNAs at the ends). AFM image of the self‐assembled 2D nanostructure.

      Source: Modified from Winfree et al. [10]

      (d) Dynamic open/close behavior of DNA tweezers operated by strand displacement using toehold containing DNA strands.

      Source: Modified from Yurke et al. [8].

      (e) PX‐JX₂ device to exchange the bottom part of by insertion and removal of the strands. The structures can be observed in AFM images.

      Source: Yan et al. [9]/with permission of Springer Nature.

Figure 1.3 DNA origami. (a) Method to prepare a DNA origami structure from the template single‐stranded DNA and staple strands. (b) Design of a self‐assembled DNA origami structure and geometry of the incorporated double‐stranded DNAs. Colored strands and a gray/black strand represent staple strands and template single‐stranded DNA, respectively. Staple strands connect the adjacent duplexes with crossovers. Inset: Structure of hairpin DNA for a topological marker. (c) Design and AFM images of self‐assembled DNA origami structures. Drawing of a hemisphere on the DNA origami with hairpin DNAs (white dots) and an AFM image of the assembled DNA origami.

      Source: Rothemund [6]/with permission of Springer Nature.

1.3 Programmed Arrangement of Multiple DNA Origami Components

      The programmed arrangement of multiple DNA origami structures is an important technique for preparing larger structures, particularly in terms of integrating complex functions. We explored techniques for arranging multiple DNA origami components and developed methods to arrange rectangular DNA origami tiles horizontally in a programmed fashion [18]. Because the ends of the helical axes align at both edges of the DNA origami rectangles, origami tiles horizontally assemble via π‐interactions at the edges in a predictable fashion [18]. Specific concave and convex connectors were introduced into DNA origami tiles to precisely align neighboring tiles in a shape‐fitting manner. DNA tiles could be correctly assembled by shape and sequence complementarity, where the complementary strands 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