Macroscale-area patterning of three-dimensional DNA-programmable frameworks

Abstract

DNA, owing to its adaptable structure and sequence-prescribed interactions, provides a versatile molecular tool to program the assembly of organized three-dimensional (3D) nanostructures with precisely incorporated inorganic and biomolecular nanoscale components. While such programmability allows for self-assembly of lattices with diverse symmetries, there is an increasing need to integrate them onto planar substrates for their translation into applications. In this study, we develop an approach for the growth of 3D DNA-programmable frameworks on arbitrarily patterned silicon wafers and metal oxide surfaces, as well as study the leading effects controlling these processes. We achieve the selective growth of DNA origami superlattices into customized surface patterns with feature sizes in the tens of microns across macroscale areas using polymer templates patterned by electron-beam lithography. We uncover the correlation between assembly conditions and superlattice orientations on surfaces, lattice domain sizes, twining, and surface coverage. The demonstrated approach opens possibilities for bridging self-assembly with traditional top-down nanofabrication for creating engineered 3D nanoscale materials over macroscopic areas with nano- and micro-scale controls.

Fig. 1. Surface-directed patterning of 3D DNA-frame superlattice on oxide surfaces.

a Schematic illustrating the patterning of PEG template by EBL, followed by the deposition of a layer of octahedral DNA frames, and crystallization of 3D DNA crystals on patterned oxide surfaces with bifunctionalized and monofunctionalized surfaces. b Schematics and representation of surface-patterned DNA frame superlattice on bifunctionalized Si/SiO₂, Al₂O₃, TiO₂, and ZnO surfaces, respectively. The edge length of the microwells is 100 µm for Si/SiO₂ and 20 µm for Al₂O₃, TiO₂, and ZnO surfaces. The SiO₂ refers to the native oxide layer on the silicon wafer without additional coating. c Optical images showcasing the patterned DNA frame superlattices over a macroscopic area (10 mm²). Field stitches have been utilized to present a larger view. The inset features a photograph of the superlattice-patterned silicon wafer following silication, accompanied by a ruler marked with an overall length of 1 cm for scale reference.

Fig. 2. Growth of superlattices from DNA frame bifunctionalized and monofunctionalized Si/SiO₂ surfaces.

a Optical image of DNA frame superlattices on bifunctionalized Si/SiO₂ surface in non-patterned regions. The inset showcases an SEM image of the silicated superlattices. b Optical image of DNA origami frame superlattices on monofunctionalized Si/SiO₂ surface in non-patterned regions. The inset showcases an SEM image of the silicated superlattices. c Schematic and SEM images illustrating surface-patterned DNA origami frame superlattices on bifunctionalized Si/SiO₂ surface, along with a magnified view of a crystal highlighting the crystal structures. d Schematic and SEM images, including top and side views, of surface-patterned DNA frame superlattices on monofunctionalized Si/SiO₂ surface. e DNA frame superlattices grown along different crystallographic orientations from the substrates. Left to Right: Sequentially arranged schematics depicting the (100), (110), and (111) planes from which crystals were grown, schematics of the superlattices, SEM images of the shaped single crystals on the surface, corresponding experimental SAXS data, simulated SAXS data, and an overlay of the experimental SAXS and simulated SAXS data.

Fig. 3. Microwell size effect on superlattice surface orientation.

a–d SEM images illustrating DNA origami frame superlattices grown on patterned monofunctionalized Si/SiO₂ surface in microwell arrays of 100, 50, and 20 µm, alongside a reference image of a non-patterned area. Blue arrows denote crystals deviating from growing along the <111> direction due to edge effects, pink arrows indicate non-<111> crystals not located at the edges, and green arrows highlight crystals displaying non-<111> due to twinning. e Histogram showing the percentages of superlattice grown along the < 111> direction (as obtained for number crystals, N (for different microwell sizes, a), such as N (20 µm) = 148, N (50 µm) = 648, N (100 µm) = 875, N(nonpatterned) = 2520)) in microwell arrays with different sizes and non-patterned area on monofunctionalized Si/SiO₂ surfaces. f Probability of <111> orientation on the inverse of microwell size (1/a). Circles represent experimental data, and a line is a model fit to the data.

Fig. 4. Effect of surface hydrophilicity and microwell size on crystal growth.

a Schematic and optical images of DNA frame superlattice grown on piranha solution freshly treated silicon wafers or aged silicon wafers (exposed to air for days after piranha solution etching) with 100 µm and 20 µm microwell arrays (In both cases, DNA frame concentration was 150 nM). The top-left images are water contact angle measurements of the silicon wafers. The microwells were outlined with green dash lines. b Histogram of crystal sizes (N = 151–173) and the percentages of surface coverage of crystals over microwells (N = 39–99) on freshly etched vs aged silicon wafers. c Representation of crystals grown in a microwell array with 20 µm size and 100 µm spacing on freshly etched surfaces. d Representation of crystals grown in a microwell array with 10 µm microwell and 100 µm spacing on freshly etched surfaces.

Fig. 5. Re-growth of surface-patterned superlattice.

a Schematic and optical microscopy images of DNA frame superlattice patterned on 100 μm microwell arrays after 1st growth and 2nd growth (DNA frame concentration was 100 nM for 1st growth and 150 nM for the 2nd growth). b Histogram of crystal sizes (N = 156–177) and the percentages of surface coverage of crystals over microwells (N = 34–38) after 1st growth and 2nd growth.

Fig. 6. Surface patterned DNA frame superlattices in arbitrarily shaped patterns and with incorporated nano-cargos.

a SEM image of a DNA frame superlattice patterned as a smiley face on bifunctionalzied Si/SiO₂ surfaces. Optical microscopy images of DNA frame superlattice patterned as Brookhaven National Laboratory logo across millimeter scales. b Optical images of DNA frame superlattice incorporated with AuNPs (10 nm in diameter) patterned as a dog cartoon and in 100 µm, 10 µm microwell arrays. c Optical images of DNA frame superlattice encaged with Alexa 488 labeled streptavidin patterned as the logo of Columbia University Engineering School.