Bottom-Up Self-Assembly Based on DNA Nanotechnology

Abstract

Manipulating materials at the atomic scale is one of the goals of the development of chemistry and materials science, as it provides the possibility to customize material properties; however, it still remains a huge challenge. Using DNA self-assembly, materials can be controlled at the nano scale to achieve atomic- or nano-scaled fabrication. The programmability and addressability of DNA molecules can be applied to realize the self-assembly of materials from the bottom-up, which is called DNA nanotechnology. DNA nanotechnology does not focus on the biological functions of DNA molecules, but combines them into motifs, and then assembles these motifs to form ordered two-dimensional (2D) or three-dimensional (3D) lattices. These lattices can serve as general templates to regulate the assembly of guest materials. In this review, we introduce three typical DNA self-assembly strategies in this field and highlight the significant progress of each. We also review the application of DNA self-assembly and propose perspectives in this field.

Keywords: DNA brick; DNA origami; DNA tile; bottom-up; nanoparticles; self-assembly.

Figure 1

Self-assembly based on DNA tiles (a) Escher’s woodcut depth (left) and the prototype of DNA nanotechnology inspired by it (right). Reproduced from [21]. (b) A schematic diagram of a two-dimensional (2D) DNA lattice assembled by four-arm holiday junctions connected by sticky ends. Reproduced with permission [22]. Copyright Materials Research Society, 2017. (c) A 2D lattice assembled by DNA double-crossover molecule (DX) and DX + J tiles. Reproduced with permission of [22]. Copyright Materials Research Society, 2017. (d) The structure of the DNA polyhedron assembled by three-pointed star DNA motifs. Reproduced with permission of [11]. Copyright Springer Nature, 2008. (e) DX-based complex DNA tile motif library and its assembly results. (I) 4 × 4 tile. Reproduced with permission of [9]. Copyright American Association for the Advancement of Science, 2003; (II) three-pointed star. Reproduced with permission of [23]. Copyright American Chemical Society, 2005; (III) six-pointed star. Reproduced with permission of [24]. Copyright American Chemical Society, 2006; cop; (IV) DX-based tensegrity triangle. Reproduced with permission of [25]. Copyright American Chemical Society, 2006; (V) a tensegrity triangle with complete triple symmetry. Reproduced from [10].

Figure 2

Single-stranded DNA tiles and single-stranded DNA bricks. (a) Rectangular 2D molecular canvas assembled by single-stranded DNA tiles. Reproduced from [42]. (b) Drawing the desired shape on the 2D molecular canvas. Reproduced from [42]. (c) LEGO model analogue of single-stranded DNA. Reproduced from [7]. (d) “Carving” the 3D canvas into any shape. Reproduced from [7].

Figure 3

Development of DNA origami. (a) The origin of DNA origami: A long DNA strand is folded into a target structure through several short DNA strands. Reproduced with permission of [8]. Copyright Springer Nature, 2006. (b) Multilayer 3D DNA origami packed into a honeycomb structure. Reproduced with permission of [46]. Copyright Springer Nature, 2009. A square. Reproduced with permission of [47]. Copyright American Chemical Society, 2009. Hexagonal lattices. Reproduced with permission of [48]. Copyright American Chemical Society, 2012. (c) 3D DNA origami framework with layered crossovers. Reproduced with permission of [49]. Copyright WILEY−VCH Verlag GmbH & Co. KGaA, Weinheim, Germany, 2016. (d) Introducing twist and curve into DNA origami by deleting and adding bases. Reproduced with permission of [50,51]. Copyright American Association for the Advancement of Science, 2011. (e) The design of 3D wireframe DNA origami. Reproduced with permission of [53]. Copyright Springer Nature, 2015. Reproduced from [52].

Figure 4

Sticky ends base pairing (a–f). (a) “Zigzag DNA origami” tiles were assembled into a one-dimensional (1D) lattice. Reproduced with permission of [55]. Copyright American Chemical Society, 2010. (b) Three different assembly methods of DNA origami monomers. Reproduced with permission of [56]. Copyright Springer Nature, 2011. (c) Assembly of a 2D DNA origami lattice using a cross-shaped origami tile. Reproduced with permission of [57]. Copyright WILEY−VCH Verlag GmbH & Co. KGaA, Weinheim, Germany, 2011. (d) Programming DNA origami honeycomb 2D lattices. Reproduced with permission of [58]. Copyright American Chemical Society, 2016. (e) A polyhedron self-assembled from DNA tripods. Reproduced from [59]. (f) Constructing different 3D DNA origami lattices using DNA-prescribed and valence-controlled material voxels. Reproduced with permission of [2]. Copyright Springer Nature, 2020. Blunt ends base stacking (g–i). (g) Recognition based on the binary sequences of blunt ends and the complementarity of the origami edge shapes of DNA nanostructures. Reproduced with permission of [60]. Copyright Springer Nature, 2011. (h) Self-assembly of 3D DNA components in a solution on the basis of shape complementarity. Reproduced from [61]. (i) Assembly of multiple DNA origami jigsaw pieces in three different ways. Reproduced with permission of [62]. Copyright American Chemical Society, 2011.