Programming DNA origami patterning with non-canonical DNA-based metallization reactions

Abstract

The inherent specificity of DNA sequence hybridization has been extensively exploited to develop bioengineering applications. Nevertheless, the structural potential of DNA has been far less explored for creating non-canonical DNA-based reactions. Here we develop a DNA origami-enabled highly localized metallization reaction for intrinsic metallization patterning with 10-nm resolution. Both theoretical and experimental studies reveal that low-valence metal ions (Cu²⁺ and Ag⁺) strongly coordinate with DNA bases in protruding clustered DNA (pcDNA) prescribed on two-dimensional DNA origami, which results in effective attraction within flexible pcDNA strands for site-specific pcDNA condensation. We find that the metallization reactions occur selectively on prescribed sites while not on origami substrates. This strategy is generically applicable for free-style metal painting of alphabet letters, digits and geometric shapes on all-DNA substrates with near-unity efficiency. We have further fabricated single- and double-layer nanoscale printed circuit board (nano-PCB) mimics, shedding light on bio-inspired fabrication for nanoelectronic and nanophotonic applications.

Fig. 1

Selective on-origami DNA condensation and metallization. a Illustration of condensation and subsequent site-specific metal plating processes for fabricating a digit 8 pattern on a single-origami breadboard with a size of 100 × 70 nm². b AFM images of metalized digit 8 patterns constructed with different Cu²⁺ concentrations. Scale bar: 50 nm. c Tomographic measurements of cross-sectional areas. Tomography images (showing red masks on original AFM images) of origami substrates (cross-sections at 1 nm height) and metallized areas (cross-sections at 3 nm height) from typical samples. Scale bar: 100 nm. d Normalized occupancy ratios of the areas on origami at different heights of cross-sections obtained from tomography analysis (left) of the patterns showing in (b). The size of the origami substrate (measured from the cross-sectional area at 1 nm—half the original origami height) is represented with 100%. Metallized area proportions with different Cu²⁺ concentrations obtained from the normalized occupancy data at 3 nm height (1 nm above from the origami substrate) (right). e Geometry-minimized structure of Cu-G and Cu-C complexes obtained from quantum mechanical calculations.

Fig. 2

Number and length effects of pcDNA on DCIMP. a AFM 3D reconstruction (top) and side view (bottom) of a metalized rectangular origami having eight discrete sites with varied numbers of 15-base pcDNA strands. b Distribution of increased height values and statistic analysis of height increase on sites with varied number of strands. The error bars are the standard deviation for N = 108, 108 and 128 samples with different number of strands. c Distribution of increased height values and statistic analysis of height increase on sites with varied length of pcDNA strands. The error bars are the standard deviation for N = 103, 128, 147 and 225 samples with different length of pcDNA strands.

Fig. 3

Characterization of DCIMP. a A small-sized digit 8 pattern enabling the measurement of line width and density. Scale bar: 25 nm. b Force-distance (FD) curve-based AFM (FD-based AFM) characterization of nanomechanical properties of metalized patterns. The error bars are the standard deviation for N = 25 and 25 samples with the origami and the metalized patterns, respectively. c Cu plating on a whole triangular origami with STEM and elemental mapping characterization. Scale bar: 50 nm. d Ag plating on a whole triangular origami with STEM and elemental mapping characterization. Scale bar: 50 nm.

Fig. 4

Fabricating nano-PCB mimics with DCIMP. a A seven-segment digit 8 design is employed to fabricate nano-PCB mimics on a rectangular origami. To show the generality, we fabricated digits from 0 to 9 and several typical alphabets, as shown in corresponding AFM images. b Schematic illustration of the fabrication process of Cu-Ag bi-metallic nanocircuits. c AFM characterization of the Cu-Ag bi-metallic sample prepared at different stages. The size of the integrated panel is 100 × 280 nm². Scale bars: 50 nm.