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Programmable Self-assembly

Programmable self-assembly is defined as self-assembly processes whereby the information specified at the molecular sequence level can be controlled with high predictability to fold and assemble into predefined 2-D and 3-D architectures

10.7.1.1 General Principles: ''One pot'' versus "Step-wise" Assembly

Two main approaches can be distinguished for programmable self-assembly of nucleic acid architectures (Fig. 10.14). The first approach, mostly used with DNA, is a single step assembly strategy in which all the molecules encoding a specific architecture are mixed together and assembled in ''one pot'' through a slow annealing procedure [153-167, 174, 185] (Fig. 10.14a). According to the energetics of their 2° structure pairings, oligonucleotide strands form stable substructures or tiles that assemble through weaker 4° interfaces into larger nano-architectures when lower temperatures are reached. These structures can eventu-

Fig. 10.14 The four main strategies for programmable self-assembly. (a) Single step process of self-assembly whereby all the molecules are mixed together. Most DNA architectures are formed that way (adapted with permission from Ref. [193]); (b) Stepwise hierarchical self-assembly whereby specific sets of molecules are first separately assembled into small supra-molecular entities that are then mixed in a stepwise fashion to form the final architecture [35]; (c) Programmable algorithmic self-assembly:

Fig. 10.14 The four main strategies for programmable self-assembly. (a) Single step process of self-assembly whereby all the molecules are mixed together. Most DNA architectures are formed that way (adapted with permission from Ref. [193]); (b) Stepwise hierarchical self-assembly whereby specific sets of molecules are first separately assembled into small supra-molecular entities that are then mixed in a stepwise fashion to form the final architecture [35]; (c) Programmable algorithmic self-assembly:

tiles with local pairing implementing the exclusive-or function, are assembled on a template input row to form the Sierpinski triangle pattern (adapted with permission from Ref. [190]); (d) Scaffolded self-assembly where a long single stranded molecule is folded into an arbitrary shape in presence of small oligonucleotides acting as staples [174]; (e) Examples of patterns that can be generated using scaffolded DNA origami (adapted with permission from Ref. [174]). Scale bars are all 50 nm.

10.7 Self-assembly Strategies for Building Complex Nucleic Acid Nanostructures | 317

ally be ligated together to form robust covalently linked architectures [186] or networks [159].

The second approach, particularly appropriate for RNA assembly, is a stepwise hierarchical self-assembly strategy, in which various small subunits are first separately formed and then mixed together to form the final supramolecular architecture [35, 187] (Fig. 10.14b). This strategy is more time consuming, however. As exemplified by the tectosquare system [35], it can make use of the same 4° interactions and basic molecular units to build a large number of highly modular tiles that can assemble further through weaker 4° interactions. Thus, by separating tile formation from the formation of larger supramolecular assemblies, a reduced number of different connecting interfaces can be used to hierarchically build highly modular architectures [35]. In stepwise assembly, the melting temperature of the tiles and of the resulting supramolecular architecture should be kept well separated. By contrast, this is not absolutely necessary for the ''one pot'' approach, as exemplified by DNA scaffolded origami [174].

These two approaches can make use of additional self-assembly strategies that are not mutually exclusive, such as addressable self-assembly, algorithmic self-assembly, templated (or directed nucleation) self-assembly and scaffolded DNA origami.

10.7.1.2 Addressable Self-assembly

Step-wise assembly can be used to generate addressable architectures of finite size, with the position of each of the constitutive molecules being known without ambiguity within the assembly and therefore addressable within the final architecture. The first demonstration of this approach led to the fabrication of RNA nanogrids of finite size [35, 188] (Fig. 10.13). More recently, the application of this strategy to DNA led to the fabrication of nano-arrays with precisely positioned nanoparticles that form patterns of letters [187] or a pegboard [189].

10.7.1.3 Algorithmic Self-assembly

In algorithmic self-assembly, a set of nucleic acid tiles, defined as Wang tiles, is viewed as the algorithm for a particular computational task leading to the formation of 1-D, 2-D and 3-D patterns [190, 191]. This strategy was used to compute the formation of aperiodic fractal 2-D patterns based on the Sierpinski triangle pattern [190] (Fig. 10.14c). To achieve this task, a minimal set of four DNA tiles with local pairing rules designed to implement the exclusive-or (XOR) function, was assembled on a template input row to facilitate the nucleation of the directional self-assembly growth into a unique pattern [190]. The potential of algorithmic self-assembly is, however, still limited by the presence of various errors, introduced by lattice dislocation, formation of untemplated crystals and mismatched tiles.

10.7.1.4 Templated Self-assembly and Scaffolded DNA Origami

Templated or directed nucleation assembly takes advantage of a nucleic acid template that acts as a scaffold for directing the specific assembly of tiles. This strat egy led to the formation of aperiodic 2-D arrays, such as DNA barcodes [192]. The construction of a replicable DNA octahedron [102] was based on a similar scaffolded approach. In this case, a single-stranded DNA molecule that forms helical struts was assembled with the help of four small oligonucleotides into its final shape through the formation of paranemic long-range interactions (Fig. 10.3a). The generalization of these approaches led to the versatile scaffolded self-assembly strategy, also called scaffolded DNA origami [174], which can generate with a remarkable efficiency almost any type of arbitrary shape and pattern (Fig. 10.14d). In this strategy, a long single-stranded DNA scaffold is folded with complementary oligonucleotides that act as staples. The desired shape is designed by raster filling the shape with a 7-kilobase single-stranded scaffold and @200 short oligonucleotide staple strands to hold the scaffold in place (Fig. 10.14d-e). Once synthesized and mixed, the staple and scaffold strands self-assemble in one single step. The structure can be programmed into complex patterns, such as words and images (Fig. 10.14e). The success of scaffolded origami stems from several contributing factors, such as efficient strand invasion, excess of staples, cooperative effects and a design that intentionally does not rely on binding between staples [174]. A relatively good yield of defect-free DNA architectures was obtained, despite the fact that the oligonucleotides used were not purified.

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