Site-directed placement of three-dimensional DNA origami

Abstract

The combination of lithographic methods with two-dimensional DNA origami self-assembly has led, among others, to the development of photonic crystal cavity arrays and the exploration of sensing nanoarrays where molecular devices are patterned on the sub-micrometre scale. Here we extend this concept to the third dimension by mounting three-dimensional DNA origami onto nanopatterned substrates, followed by silicification to provide hybrid DNA-silica structures exhibiting mechanical and chemical stability and achieving feature sizes in the sub-10-nm regime. Our versatile and scalable method relying on self-assembly at ambient temperatures offers the potential to three-dimensionally position any inorganic and organic components compatible with DNA origami nanoarchitecture, demonstrated here with gold nanoparticles. This way of nanotexturing could provide a route for the low-cost production of complex and three-dimensionally patterned surfaces and integrated devices designed on the molecular level and reaching macroscopic dimensions.

Figure 1. Assembly of 3D hybrid DNA-silica nanostructured substrates.

a) Design of 3D DNA origami shapes and connection interfaces for on-surface assembly. b) Substrates are patterned by e-beam or nanosphere lithography to produce hydrophilic hydroxyl patterns on HMDS-primed hydrophobic background (Si/SiO₂ or glass). c, d) Alignment and upright positioning of 3D DNA origami structures on patterned surfaces. DNA is represented in a cylinder model. Shapes that cannot self-align in an upright position are placed in a two-step process with planar DNA origami as connectors (Fig. 1c). Other shapes are directly deposited to the patterned substrate (Fig. 1d right). e) Growing silica shells on the 3D DNA origami enables subsequent drying of the now rigidified objects.

Figure 2. Assembly of 3D hybrid nanostructured substrates by on-surface annealing of DNA origami nanotubes to a flat connector origami.

a) Design of the DNA origami tubes and triangles. Single-stranded DNA linkers extend from the center of the triangle roughly matching the circular footprint of the tube. Complementary anchor strands extend from the ends of the tubes. b-d) Uranyl-formate negative-stain TEM images of b) DNA tubes carrying 48 T₁₁ ssDNA linkers, c) a triangle, carrying 27 A₁₂ ssDNA anchors and d) a tube annealed with a triangle. e) AFM characterization of dried Si/SiO₂ chip with an array of DNA origami triangles carrying 27 A₁₂ ssDNA anchors. f) AFM and g-i) SEM characterization of dried Si/ SiO₂ chip with an array of silica-coated DNA tubes standing on top of triangles. Scale bars in g) and h): 1 μm. Scale bars in b – d, i) and in the inserts in h, i): 50 nm.

Figure 3

Pattern diversity. AFM and SEM characterization of dried Si/SiO₂ surfaces with square arrays of DNA origami prepared with e-beam lithography with periods of 400 nm (a-d) and 170 nm period (e-h). a, e) AFM characterization arrays of DNA origami triangles carrying ssDNA linkers. b, f) AFM and c, d, g, h) SEM characterization of arrays of silica-coated DNA tubes standing upright on the triangles. Scale bars in the inserts in c and g): 200 nm. All other scale bars: 400 nm.

Figure 4. Assembly of 3D hybrid nanostructured substrates by direct deposition.

a) Design of the DNA origami barrels, illustrated as a cylinder model. b, c) Uranyl formate negative-stain TEM images of b) a DNA origami barrel lying on its side, c) an upright DNA origami barrel. d, e) AFM and SEM characterization of a dried Si/SiO₂ substrate with a square array of silicified DNA origami barrels. f) Design of the DNA origami tetrapods. g) Uranyl formate negative-stain TEM images of the DNA origami tetrapod. d, e) AFM and SEM characterization of a dried Si/SiO₂ substrate with a square array of silicified DNA origami tetrapods. Scale bars in e) and i): 400 nm.

Figure 5. Assembly of hybrid silica-AuNPs-DNA nanostructures prepared via nanosphere lithography.

a) Hexagonal arrays of DNA origami tetrapods on Si/SiO₂ substrates. (b, c) SEM characterization of a dried Si/SiO₂ surface with a hexagonal pattern of tetrapods. (d - i) AuNPs-DNA nanostructures were prepared by on-surface annealing of 20 nm AuNPs to DNA origami tetrapods pre-adsorbed to their binding sites. (e, g) Scheme of DNA origami tetrapods hosting 20 nm AuNPs in two geometrical configurations. In the nanoclover configuration (e), the DNA-coated AuNPs attach to DNA handles extending from the concave, central parts of the tetrapod. In the nanoquadruped configuration (g), the AuNPs attach to handles extending from the ends of the tetrapod’s legs. d, f, h, i) SEM characterization of a dried Si/SiO₂ surface with therapods carrying AuNPs arranged as nanoclovers (d, f) and nanoquadrupeds (h, i). Scale bars in c, f, i): 1 μm. Scale bars in b, d, h) and in the insets in c, f, i): 100 nm.