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This section will present a series of examples of wireframe DNA origami where the routing of scaffold and staples is used to connect different subsets of monomers.

In a Festschrift paper published in 2006 [45], Paul Rothemund suggested the use of DNA origami to create planar networks out of DNA. Inspired by previous works on DNA tiles [44, 46], Paul Rothemund proposes a multi‐arm motif to create arbitrary polygonal networks. In this article, he lays down the theory for the construction of scaffolded pseudohexagonal networks based on three‐armed DNA tile‐like motifs (called by Rothemund “DNA 3‐stars”) (Figure 2.2a). They would be constituted by scaffold and by three 32‐nucleotide long helper strands. These motifs can be classified in four classes based on the number of breaks in the scaffold strand while it travels around the perimeter of the DNA 3‐star: from a “type‐0,” a single, closed‐loop network, to a “type‐3,” where all the arms are open and can link to other tiles. A polygonal network is created from the combination of these different classes of DNA 3‐stars. When the closed ends of two tiles meet, they are joined by helper strands, a structure called “helper join.” When instead two open ends meet, they are joined by the scaffold strand in a “scaffold join” structure. A simple algorithm can then be used to build molecular designs from the DNA 3‐stars. The molecular designs are arranged in a tree‐like fashion, and Rothemund argues that large 2D and 3D design seemed technically possible, as well as the creation of networks from DNA stars with more than three arms. Although Rothemund’s approach has never been tested in a laboratory, some other recent results come to a similar result from different directions [47, 48].

Figure 2.2 Hierarchical DNA origami wireframe. (a) Schematics for the strategy proposed by Paul Rothemund to create DNA polyhedra.

Source: Rothemund et al. [45] / with permission of Springer Nature.

(b) DNA origami icosahedron built by monomers binding.

Source: Douglas et al. [2] / with permission of Springer Nature.

(c) Wireframe structures based on DNA origami tripods.

Source: Linuma et al. [49] / with permission of AAAS.

(d) Gigadalton‐sized structures from building blocks kept together by shape‐complementarity.

Source: Wagenbauer et al. [3] / with permission of Springer Nature.

It was not long after the first report of the DNA origami technique by Paul Rothemund [1] that the technique was expanded to 3D shapes [2]. In this work, among other structures, a 3D wireframe icosahedron is created by the hierarchical assembly of monomers, where the struts are six‐helix‐bundle nanotubes (Figure 2.2b). The icosahedron is built through a two‐stage process. First, a scaffold is folded into one of three double triangles that act as monomers. The three monomers used in this work are built from the same design using the same scaffold and are effectively chemically different, thanks to cyclic permutation of the scaffold sequence. Every monomer displays staple sequences designed to bind to the other two monomers in a controlled fashion. These monomers are then mixed to create an icosahedron with a diameter of around 100 nm.

One of the first generalized strategies for the multimeric assembly of larger DNA nanostructures was presented by Linuma et al. [49]. In this work, the monomer is a DNA “tripod,” that is used as a three‐arm‐junction origami tile (Figure 2.2c). The tripod inter‐arm angles are controlled by supporting struts and by a vertex helix. Using different kinds of connectors on the different arms of the tripods they were able to control the self‐assembly of these monomers into six different polyhedra. The biggest structure built in this work is a hexagonal prism with an edge length of 100 nm and a diameter of 200 nm. This building technique is, theoretically, capable of creating all trivalent convex polyhedra.

Another interesting approach for the building of multimeric structures was introduced in 2015 by Gerling et al. [50]. Shape‐complementarity and short‐ranged nucleobase stacking bonds were used to stabilize multimeric assemblies. While in this work no polyhedral structures were built, the approach was used shortly after to build gigadalton‐scale structures with controlled sizes [3]. Connecting individual origami building blocks using specifically designed shapes and short‐range interactions, Wagenbuer et al. designed various structures, including impressive 3D polyhedral cages of up to 1.2 gigadaltons and 450 nm in diameter (Figure 2.3d). In this case, they first built a “reactive vertex” from three different building blocks: a triangular brick, a v‐shaped brick, and a connector brick. The reactive vertex is then formed by one central triangular brick, three v‐shaped bricks, and three connector bricks. These reactive vertices are used to create different polyhedral cages (namely, a tetrahedron, a hexahedron, and a dodecahedron) tuning the angles in the v‐shaped bricks. Upon mixing, the cages self‐assembly in a hierarchical and self‐limiting fashion.