DNA Origami Meets Bottom-Up Nanopatterning

Abstract

DNA origami has emerged as a powerful molecular breadboard with nanometer resolution that can integrate the world of bottom-up (bio)chemistry with large-scale, macroscopic devices created by top-down lithography. Substituting the top-down patterning with self-assembled colloidal nanoparticles now takes the manufacturing complexity of top-down lithography out of the equation. As a result, the deterministic positioning of single molecules or nanoscale objects on macroscopic arrays is benchtop ready and easily accessible.

Figure 1

Schematic drawing of bottom-up fabrication of integrated macroscopic devices: Self-assembled nanostructures featuring molecular addressability are deposited on a prepatterned substrate, creating a complex functional material of macroscopic dimensions.

Figure 2

(A) Gigadalton-scale DNA brick structures made from 10,000 individual DNA oligonucleotides. The black arrow points to a conventional DNA origami structure as size comparison. Adapted with permission from ref (16). Copyright 2017 Springer Nature. (B) Hybrid λ/M13 phage-based DNA origami structure. The black arrow points to a conventional DNA origami structure lying on top as size comparison. Adapted with permission from ref (17). Copyright 2014 American Chemical Society. (C) DNA origami jigsaw 3 × 3 assembly. Reprinted from ref (18). Copyright 2011 American Chemical Society. (D) DNA origami and nanoparticle planet-satellite clusters. Reprinted with permission from ref (19). Copyright 2014 Springer Nature. (E) DNA origami dodecahedron. Reprinted with permission from ref (20). Copyright 2017 Springer Nature. Scale bars are 100 nm.

Figure 3

(A) Two-dimensional DNA-origami array. Reprinted with permission from ref (24). Copyright 2011 Wiley-VCH. (B) Surface-assisted ordering of DNA origami. Reprinted with permission from ref (25). Copyright 2014 Wiley-VCH. (C) Crystalline three-dimensional structure made purely from DNA origami motifs. Scale bar is 100 nm. Reprinted with permission from ref (26). Copyright 2018 Wiley-VCH. (D) Nanoparticle-mediated assembly of a three-dimensional DNA origami lattice. Reprinted with permission from ref (27). Reprinted under a CC BY-NC 4.0 license. Copyright 2021 AAAS.

Figure 4

(A) Controlled placement of DNA origami triangles via patterning with electron-beam lithography. Reprinted from ref (5). Copyright 2014 American Chemical Society. (B) Approximation of Van Gogh’s The Starry Night with 65,536 cavities each having a DNA origami triangle placed inside. Reprinted with permission from ref (9). Copyright 2016 Springer Nature. (C) 3456 individual DNA origami structures placed with precise orientation make up this two-dimensional polarimeter. Reprinted with permission from ref (32). Copyright 2021 AAAS.

Figure 5

(A) Illustration of the bottom-up nanopatterning: the close-packed nanospheres create a mask for the background passivation of the glass substrate. After lift-off, DNA origami structures are placed on the reactive patches. (B and C) Atomic force microscopy images of the resulting hexagonal close-packed (HCP) array. (A–C) Reprinted from ref (33). Copyright 2021 American Chemical Society. (D) Replication of the bottom-up nanopatterning in our own lab: Our undergraduate student Veronika was able to replicate the method on her first attempt (left) and achieved a similar success of placement (with triangular DNA origami structures in this case) as Shetty et al. after only 5 days of practice/optimization. Scale bars are 1 μm. The insets show zoom-in images of 1 μm × 1 μm of individual hexagons.