Читать книгу DNA Origami - Группа авторов - Страница 54

In this section, we will present some example of strategies adopted for the creation of polygonal DNA nanostructures. Although the examples in this section precedes what we today call DNA origami, we think it is important to show them both from a historical perspective and for the impact they had on subsequent DNA nanostructure design strategies.

The first example of successful experimental application of structural DNA nanotechnology was the construction of a DNA cube in 1991 [39]. The design comprised 10 ssDNA strands hybridized and ligated together to form the 12 dsDNA edges of a cube (Figure 2.1a). The structure was characterized by gel electrophoresis but as no geometry characterization was possible, the authors could only claim that the structure had the right connectivity.

An alternative approach to the construction of polyhedral DNA structures was proposed in 2004 by Shih, Quispe, and Joyce [40]. Here, a single, 1.7 kb‐long strand of DNA was used to fold onto itself using only a small number of helper strands. This was achieved using five double‐crossover (DX) struts and seven paranemic‐crossover (PX) struts joined by six 4‐way junctions. The folding occurred in a one‐pot reaction in two stages: first, the DX struts would form between the scaffold and the helper strands, and in a second step the PX struts would form, creating the final octahedron (Figure 2.1c). This approach is somewhat similar to DNA origami (it even included a few short helper oligos) and brings some of the same benefits. First, since the backbone of the structure is a single‐stranded molecule, the stoichiometry of the process is not a concern, as the synthesis consists of a single cooling reaction so it can be completed in one step. In addition, the strand folds into the structure without topological or kinetic traps, so it can, in principle, be mass‐produced by simple DNA cloning. A similar technique with similar advantages was later developed and called “ssDNA origami” [41] and used to created complex 2D DNA structures. RNA structures have also been demonstrated with a similar approach [41, 42].

In 2008, He et al. [43] reported a different approach for the construction of polygonal DNA nanostructures. Building on their previous work on hexagonal 2D arrays [44], they expanded the technique to 3D nanostructures (Figure 2.1b). Their one‐pot self‐assembly process is based on sticky‐ended, three‐armed tiles, which can combine into polyhedral structures. This three‐point‐star motif consists of seven strands: a long, repetitive central strand, three identical medium strands, and three identical short peripheral strands. At the center of each motif, there are three single‐stranded loops, which length can be varied to adjust the tile flexibility. The end of each arm carries two complementary sticky ends, which are four bases long; these allow for the assembly of the tiles. Using these simple basic motifs and rules, He et al. were able to demonstrate the construction of polyhedral structures: a tetrahedron, a dodecahedron, and a truncated icosahedron (a “Buckyball”). These different structures had increasing sizes and number of tiles (3 for the tetrahedron, 20 for the dodecahedron and 60 for the Buckyball); the authors noticed how to an increased size corresponds a decrease in the yield of correctly formed nanostructures. The authors argue that the trend might be attributed to a more difficult assembly process because of the higher number of tiles required and that bigger structures are easier to deform and break.

Figure 2.1 Pre‐origami wireframe DNA structures. (a) Nadrian Seeman’s DNA cube.

Source: Chen et al. [39] / With permission of Springer Nature.

(b) Scheme for self‐assembling of three‐armed tiles into polyhedral.

Source: He et al. [43] / with permission of Springer Nature.

(c) Folding of a DNA octahedron from a single‐stranded DNA and few helper strands.

Source: Shih et al. [40] / with permission of Springer Nature.