Large-Scale Formation of DNA Origami Lattices on Silicon

Abstract

In recent years, hierarchical nanostructures have found applications in fields like diagnostics, medicine, nano-optics, and nanoelectronics, especially in challenging applications like the creation of metasurfaces with unique optical properties. One of the promising materials to fabricate such nanostructures has been DNA due to its robust self-assembly properties and plethora of different functionalization schemes. Here, we demonstrate the assembly of a two-dimensional fishnet-type lattice on a silicon substrate using cross-shaped DNA origami as the building block, i.e., tile. The effects of different environmental and structural factors are investigated under liquid atomic force microscopy (AFM) to optimize the lattice assembly. Furthermore, the arm-to-arm binding affinity of the tiles is analyzed, revealing preferential orientations. From the liquid AFM results, we develop a methodology to produce closely-spaced DNA origami lattices on silicon substrate, which allows further nanofabrication process steps, such as metallization. This formed polycrystalline lattice has high surface coverage and is extendable to the wafer scale with an average domain size of about a micrometer. Further studies are needed to increase the domain size toward a single-crystalline large-scale lattice.

Molecular Lithography on Silicon Wafers Guided by Porous, Extended Arrays of Small DNA Tiles

“…Na + is regarded as a competitive cation with Mg 2+ by occupying the DNA backbones, which could weaken and finely tune the DNA–surface interaction strength . Compared with a recent study using large DNA origami and the optimized temperature, the DNA tiles used in this study have a relatively small molecular size and weak blunt-end inter-motif interactions, which could form single crystals by long-time isothermal incubation, rather than high temperatures and avoid multi-layer structures.…”

“…21−24 Particularly, DNA nanostructures could serve as an etchant-blocking or volatile precursor-protecting mask in surface engineering, transferring the patterns with the same shapes and dimensions as the DNA templates to surfaces. 25−31 In past decades, scientists could prepare DNA 2D crystals directly on the silicon wafer surfaces, 32,33 deposit individual DNA nanostructures on silicon wafer surfaces, and permanently transfer the pattern onto inorganic materials. 26,27,34,35 To expand DNA templates to massively modify the entire surface, the DNA pattern should be ordered, position-specific, and porous for further masking.…”

“…DNA self-assembly is a promising approach for constructing nanoscale materials with excellent shape control. − In past decades, a large variety of DNA nanostructures have been achieved. The DNA nanostructure could be designed into complex structures with atomic accuracy, facilitating the application in nanofabrication and manufacturing. − Recently, DNA nanotechnology has been applied in arranging nanoparticles, − direct metallization or mineralization on DNA nanostructures, − and electronic devices. − Particularly, DNA nanostructures could serve as an etchant-blocking or volatile precursor-protecting mask in surface engineering, transferring the patterns with the same shapes and dimensions as the DNA templates to surfaces. − In past decades, scientists could prepare DNA 2D crystals directly on the silicon wafer surfaces, , deposit individual DNA nanostructures on silicon wafer surfaces, and permanently transfer the pattern onto inorganic materials. ,,, To expand DNA templates to massively modify the entire surface, the DNA pattern should be ordered, position-specific, and porous for further masking. Here, we report a general protocol to prepare porous DNA 2D crystals with pre-designed patterns assembled from small DNA tiles on silicon wafers.…”

Ultrafast dense DNA functionalization of quantum dots and rods for scalable 2D array fabrication with nanoscale precision

“…However, without additional treatment, these assemblies may collapse upon drying due to the soft nature of the lipid substrate. More recently, longrange patterns of origamis on solid substrates have been demonstrated with the help of monovalent cations (Na + ) to promote surface diffusion and self-organization (50)(51)(52)(53)(54)(55). However, these examples only relied on either nonspecific blunt-end interactions (50,51,55) or merely surface crowding and shape matching to fit symmetrical origamis into 2D patterns (52)(53)(54).…”

Creation of ordered 3D tubes out of DNA origami lattices

“…2,3,28 Previously, different kinds of DNA origami have been used to fabricate different hierarchical 2D and 3D structures, both on surfaces and in liquid. 3,29,30,53 Both blunt-end stacking and DNA hybridization have been utilized to achieve the ordered structures, but the role of the buffer conditions on the formation of the ordered structures has not been thoroughly explored.…”