One-step large-scale deposition of salt-free DNA origami nanostructures

Abstract

DNA origami nanostructures have tremendous potential to serve as versatile platforms in self-assembly -based nanofabrication and in highly parallel nanoscale patterning. However, uniform deposition and reliable anchoring of DNA nanostructures often requires specific conditions, such as pre-treatment of the chosen substrate or a fine-tuned salt concentration for the deposition buffer. In addition, currently available deposition techniques are suitable merely for small scales. In this article, we exploit a spray-coating technique in order to resolve the aforementioned issues in the deposition of different 2D and 3D DNA origami nanostructures. We show that purified DNA origamis can be controllably deposited on silicon and glass substrates by the proposed method. The results are verified using either atomic force microscopy or fluorescence microscopy depending on the shape of the DNA origami. DNA origamis are successfully deposited onto untreated substrates with surface coverage of about 4 objects/mm(2). Further, the DNA nanostructures maintain their shape even if the salt residues are removed from the DNA origami fabrication buffer after the folding procedure. We believe that the presented one-step spray-coating method will find use in various fields of material sciences, especially in the development of DNA biochips and in the fabrication of metamaterials and plasmonic devices through DNA metallisation.

Figure 1. DNA origami nanostructures for patterning.

(a) Seeman tile (ST), (b) double-triangle (DT), (c) hexagonal tube (HT) and (d) 60-helix bundle (HB). (b–d) are CanDo-simulated deformed solution shapes, resolved using caDNAno design files as inputs. (e) Agarose gel electrophoresis of the well-folded DNA structures described in (a–d). S = scaffold strand (M13mp18), which is used as a reference sample. (f) A schematic view of patterning a substrate (white colour) through an optionally used mechanical mask (green colour, openings 1–2 mm in diameter). DNA origami nanostructures (blue 60-helix bundles) are sprayed onto the substrate using an airbrush device. Figure (f) is not in scale.

Figure 2. Agarose gel electrophoresis for all four types of DNA origami structures.

Fold = DNA structures after folding in the folding buffer (FOB) (for ST and DT FOB is 1× TAE + 12.5 mM Mg²⁺ and for HT and HB 1× TAE + 20 mM Mg²⁺). Filt = DNA structures filtered with pure water. Filt+FOB = Filtered DNA structures stored in water for 1 day, after which the buffer conditions have been adjusted to the same as for folding. S is a scaffold strand (M13mp18), which is used as a reference sample.

Figure 3. Purified and salt-free 2D DNA origami nanostructures deposited onto the untreated silicon substrates using a spray-coating technique.

AFM images of (a) Seeman tile (ST) and (b) double-triangle (DT) coated substrates. The scale bars are 1 μm. (c,d) Zoomed-in images of single objects. The scale bars are 100 nm. (e,f) Histograms of the nearest-neighbour distances for deposited ST and DT origami shapes. The deposition was carried out using optimised parameters for homogeneous coating.

Figure 4. Patterning substrates with fluorescently labelled DNA origamis.

(a) A photograph of a mechanical polydimethylsiloxane (PDMS) mask (with round 1.8 mm diameter openings) on top of the glass substrate. (b) A schematic view of the patterning setup. Spray-coating of labelled DNA origamis is carried out through the PDMS mask. (c) Fluorescence micrographs of patterns created using sequential spray-coating of Cy5-labelled and purified 60-helix bundles (HB) onto a glass substrate. HBs were deposited first through a mask with large holes (1.8 mm in diameter, blue dashed circle) and after that through a mask having slightly smaller holes (1 mm in diameter, yellow dashed circle). The scale bars are 1 mm. (d) Fluorescence micrographs of the glass substrates after coating with Cy5-labelled and purified HBs (left) and hexagonal tubes (right). Micrographs in (d) were taken after the mask removal at the edges of the formed round patterns (diameter 1.8 mm) as indicated by the black square and the dashed lines. The scale bars are 50 μm.