Interconnecting gold islands with DNA origami nanotubes

Abstract

Scaffolded DNA origami has recently emerged as a versatile, programmable method to fold DNA into arbitrarily shaped nanostructures that are spatially addressable, with sub-10-nm resolution. Toward functional DNA nanotechnology, one of the key challenges is to integrate the bottom-up self-assembly of DNA origami with the top-down lithographic methods used to generate surface patterning. In this report we demonstrate that fixed length DNA origami nanotubes, modified with multiple thiol groups near both ends, can be used to connect surface patterned gold islands (tens of nanometers in diameter) fabricated by electron beam lithography (EBL). Atomic force microscopic imaging verified that the DNA origami nanotubes can be efficiently aligned between gold islands with various interisland distances and relative locations. This development represents progress toward the goal of bridging bottom-up and top-down assembly approaches.

Figure 1

a) Schematic drawing of gold islands connected by DNA origami tubes on the substrate surface. Thiolated DNA strands (shown in red) are extended from each end of DNA origami tube and the thiol-gold bonds align the tubes along the gold islands. The distance between the thiolated groups is designed so the tube will only connect gold islands that match its length. b) The fabrication of gold islands and binding of DNA origami tubes. An HMDS and PMMA resist layer were spin coated on a clean Si or SiO₂ substrate. E-Beam exposure was performed with a designed pattern. After O₂ plasma treatment was used to eliminate the exposed HMDS, 2 nm Cr and 7 nm Au were deposited through evaporation. After lift-off with acetone, patterns of gold surface islands with the background covered by HMDS, were fabricated on the substrate. Gold patterned substrate was cut into ~ 5 × 20 mm sections and incubated with freshly purified and reduced DNA origami tube solution to facilitate the specific attachment of the DNA tubes to the gold islands.

Figure 2

AFM images of gold islands connected by DNA origami tubes. The gold islands in the images are 60 nm in diameter. For each pair, the distance between the gold islands is 300 nm, while the distance between neighboring pairs of gold islands is 600 nm. Interconnection can be observed for most gold island pairs. DNA origami tubes were aligned along the pairs of the gold islands with either 0° or 180° orientation. Scale bar is 500 nm.

Figure 3

Graph showing how the binding efficiency depends on both the number of thiol groups at each end of the DNA tube and the diameter of the gold islands. The average interconnection number was calculated by dividing the total number of observed connections by the total number of gold pairs in the image area. The incubation time for all the samples represented in the graph was 20 hours; DNA tube concentration was 2 nM. Note the flat square corresponding to the 40 nm island indicates zero because we observed no DNA nanotube binding in this case.

Figure 4

a) AFM image of a hexagonal gold island lattice with by DNA origami tube connections. Scale bar is 500 nm. b) Corresponding histogram of the number of DNA nanotubes attached to each gold island, with a wide distribution from 0 to 8, with 4 tubes the most frequent number observed (22%). Only a small fraction of the gold islands (~11.5%) have 6 or more tubes attached.

Figure 5

Various structures formed by connecting gold islands with DNA origami tubes. a) triangle, b) hexagon, c) square, d) “z” shape. All scale bars are 300 nm.