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Engineering and mapping nanocavity emission via precision placement of DNA origami


Many hybrid devices integrate functional molecular or nanoparticle components with microstructures, as exemplified by the nanophotonic devices that couple emitters to optical resonators1 for potential use in single-molecule detection2,3, precision magnetometry4, low threshold lasing5,6 and quantum information processing7,8,9,10,11,12. These systems also illustrate a common difficulty for hybrid devices: although many proof-of-principle devices exist, practical applications face the challenge of how to incorporate large numbers of chemically diverse functional components into microfabricated resonators at precise locations. Here we show that the directed self-assembly13,14 of DNA origami15 onto lithographically patterned binding sites allows reliable and controllable coupling of molecular emitters to photonic crystal cavities (PCCs). The precision of this method is sufficient to enable us to visualize the local density of states within PCCs by simple wide-field microscopy and to resolve the antinodes of the cavity mode at a resolution of about one-tenth of a wavelength. By simply changing the number of binding sites, we program the delivery of up to seven DNA origami onto distinct antinodes within a single cavity and thereby digitally vary the intensity of the cavity emission. To demonstrate the scalability of our technique, we fabricate 65,536 independently programmed PCCs on a single chip. These features, in combination with the widely used modularity of DNA origami16,17,18,19,20, suggest that our method is well suited for the rapid prototyping of a broad array of hybrid nanophotonic devices.

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Figure 1: DNA origami, binding sites for placement, and photonic crystal cavities.
Figure 2: PL spectra as a function of emitter position.
Figure 3: Visualization of the LDOS via wide-field microscopy.
Figure 4: Digital control of cavity emission.

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We acknowledge funding from the Army Research Office (award W911NF-11-1-0117), the Office of Naval Research (award N000141410702), the Air Force Office of Scientific Research (Young Investigator award FA9550-15-1-0252), and the US National Science Foundation (Expeditions in Computing numbers 0832824 and 1317694, Molecular Programming Project; We thank J. Fakonas for discussions and B. Fultz for use of his spectrometer. Device fabrication was done at Caltech’s Kavli Nanoscience Institute.

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Authors and Affiliations



A.G. and P.W.K.R. conceived the project. A.G. performed origami synthesis, nanofabrication, AFM, SEM and fluorescence microscopy. A.G. and E.M. built the set-up for microphotoluminescence spectroscopy. All authors contributed to data interpretation and manuscript preparation.

Corresponding authors

Correspondence to Ashwin Gopinath or Paul W. K. Rothemund.

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The authors declare no competing financial interests.

Extended data figures and tables

Extended Data Figure 1 DNA origami design showing position of Cy5 fluorophores.

a, We used a triangular DNA origami shape, ~130 nm on each edge, as an adaptor to position fluorophores within a photonic crystal cavity (PCC). The origami is composed of a 7,249-nucleotide (nt) single-stranded scaffold (the commercially available single-stranded genome of the M13mp18 bacteriophage) and approximately 200 commercially synthesized ‘staple strands’ which are typically 32 nucleotides in length. Mixed together and annealed from 90 to 20 °C over the course of about 6 h, the strands self-assemble to form equilateral triangles in high yield. Three trapezoidal domains make up this ‘sameside sharp triangle’ design. Red filled circles indicate 15 positions at which staples were extended on their 5′ end with 18-nt poly-T linkers for the synthesis of origami bearing n = 15 Cy5. Blue rings indicate the subset of positions used for origami bearing n = 3 Cy5. To these linkers, 21-nt poly-A ‘subcomponent’ strands modified with a 5′ Cy5 were hybridized. Because the Cy5 modification is on their 5′ ends, subcomponent strands put Cy5 within a few nucleotides of the origami surface, less than 1 nm from where linkers extend from the origami surface (rather than at the 6-nm-away distal end of the linker/Cy5 strand hybrid). b, Schema showing both components of the fine structure of a DNA origami (gaps between helices, and crossover positions, where helices are tangent) with linker/Cy5-label positions noted as in a. The white outer ring has a 62.4-nm diameter and the white inner ring has a 31.2-nm diameter. As in a, red dots indicate the subset of positions used for origami bearing n = 15 Cy5 and blue rings around red dots indicate positions used for origami bearing n = 3 Cy5. Rainbow colours on the origami trace the path of the scaffold as it progresses through the origami structure, from red to purple. c, Buffer AFM image showing fine structure of origami without linkers/Cy5 strands for comparison with b. d, Buffer AFM image showing origami with n = 3 linkers and Cy5 strands. In this AFM image the Cy5-labelled duplexes appear to fall on the inside of the inner triangular hole, perhaps due to adhesion to the mica substrate used in these high-resolution experiments. High-resolution imaging of origami dried onto SiN is difficult, and so the exact conformation of Cy5-labelled duplexes on resonators was not determined. However, because the carboxylated sites bind DNA strongly, it seems likely that Cy5-labelled duplexes would behave similarly and fall within the 54-nm triangular hole of the origami, between 30 and 60 nm from the centre of the origami.

Extended Data Figure 2 Process flow for fabricating PCCs.

a, Fabrication of isolated PCCs for widely spaced arrays (Fig. 2). b, Fabrication of PCCs in close-packed arrays (Figs 3, 4). Note that back-side alignment markers are omitted from b for clarity. After either fabrication process substrates are incubated in origami solution, rinsed of excess origami, subjected to an ethanol dilution series, and air-dried.

Extended Data Figure 3 SEM imaging of isolated PCCs used for taking fluorescence spectra as a function of x-position.

An 8 × 21 array was used. a, Positions 01 to 21 each indicate a row of eight copies of isolated PCCs having origami positioned at the same x-offset, as exemplified in Extended Data Fig. 4. Red squares indicate broken PCC membranes which were not used. b, Intact membrane. c, Typical broken membrane. d, Zoom-in of PCC. e, Cross-section of PCC membrane. Scale bars: a, 300 μm; b, 2 μm; d, 1 μm; e, 500 nm.

Extended Data Figure 4 AFM of isolated PCCs and control cavity.

a, Schema and representative AFM for each of 21 offsets at which spectra (Fig. 2b) were measured. b, Dry AFM of a control PCC filled with origami (n = 15 Cy5/origami). Scale bar, 250 nm. c, PL reference spectra (red) for Cy5-origami on open SiN, and for Cy5-origami filling a cavity, as in b.

Extended Data Figure 5 Optical set-up for reflectance and fluorescence spectroscopy.

The 650-nm long-pass filter (650 LP) was used only for fluorescence spectroscopy. Details in Methods.

Extended Data Figure 6 Comparison of unaveraged and averaged epifluorescence images of PCC array used for 2D mode map.

a, A single epifluorescence image of a single array. b, An average of five images taken of five different PCC arrays, as in Fig. 3c. Scale bars, 23 μm.

Extended Data Figure 7 Raw fluorescence data demonstrating digital control of cavity emission.

The central panel diagrams eight different arrangements of origami (white triangles) within PCCs, with the number of origami ranging from zero to seven. The left panel shows an epifluorescence image of eight PCC arrays, each containing 512 copies of a PCC with the origami arrangement diagrammed in the adjacent row of the central panel; each origami has n = 3 Cy5. The right panel shows an analogous epifluorescence image of eight PCC arrays for which each origami has n = 15 Cy5. Histograms summarizing these epifluorescence data are given in Extended Data Fig. 8. See Fig. 4b for plots showing the linearity of intensity as the number of origami are increased. Scale bars, 50 μm.

Extended Data Figure 8 Histograms of numerical data demonstrating digital control of cavity emission.

Eight different arrangements of origami were loaded into PCCs, with the number of origami ranging from zero to seven (see centre panel, Extended Fig. 7). 512 identical PCCs of each of the nonzero arrangements were imaged by epifluorescence microscopy (Extended Data Fig. 7, left and right panels) and their intensity was quantified. These data, for n = 3 Cy5 origami (a) and n = 15 Cy5 origami (b) are represented by coloured histograms labelled ‘one’ through ‘seven’. The number of PCCs with a given fluorescence intensity is plotted on the y-axis. c, Summary of means and standard deviations (for intensity measured as counts) from Gaussian fits in a, b. The peaks of these histograms are plotted in Fig. 4b.

Extended Data Figure 9 Schema for recreation of Vincent van Gogh’s painting The Starry Night (1889).

See Fig. 4c for recreation. a, Original image from Wikimedia Commons ( Because our current emitters and cavities provide only one color, with only eight levels of intensity, the original image was converted to greyscale (b) and then further converted to have three-bit colour depth (c). Because of the difficulty of handling extremely large suspended SiN membranes (which easily break) we limited our recreation to a low-resolution 256 × 256 = 65,536 pixel version, which was then further broken down into sixteen 64 × 64 pixel arrays (d). With one PCC per pixel, these arrays were small enough that we could fabricate and handle the resulting SiN membranes without too much breakage, image them separately, and then reassemble the sixteen images into a 4 × 4 array for the final recreation (Fig. 4c).

Extended Data Table 1 Troubleshooting guide for origami placement

Supplementary information

Supplementary Data

This file contains Supplementary Data including (1) a DNA origami caDNAno design file and corresponding Microsoft Excel sequence list, (2) PCC design files as Matlab and Autocad scripts, and (3) FDTD simulations as Lumerical scripts. These files have been combined as a single .zip file. (ZIP 287 kb)

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Gopinath, A., Miyazono, E., Faraon, A. et al. Engineering and mapping nanocavity emission via precision placement of DNA origami. Nature 535, 401–405 (2016).

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