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Engineering and mapping nanocavity emission via precision placement of DNA origami

Gopinath, Ashwin and Miyazono, Evan and Faraon, Andrei and Rothemund, Paul W. K. (2016) Engineering and mapping nanocavity emission via precision placement of DNA origami. Nature, 535 (7612). pp. 401-405. ISSN 0028-0836. doi:10.1038/nature18287.

[img] Archive (ZIP) (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. ) - Supplemental Material
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[img] Image (JPEG) (Extended Data Figure 1: DNA origami design showing position of Cy5 fluorophores) - Supplemental Material
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[img] Image (JPEG) (Extended Data Figure 2: Process flow for fabricating PCCs) - Supplemental Material
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[img] Image (JPEG) (Extended Data Figure 3: SEM imaging of isolated PCCs used for taking fluorescence spectra as a function of x-position) - Supplemental Material
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[img] Image (JPEG) (Extended Data Figure 4: AFM of isolated PCCs and control cavity) - Supplemental Material
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[img] Image (JPEG) (Extended Data Figure 5: Optical set-up for reflectance and fluorescence spectroscopy) - Supplemental Material
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[img] Image (JPEG) (Extended Data Figure 6: Comparison of unaveraged and averaged epifluorescence images of PCC array used for 2D mode map) - Supplemental Material
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[img] Image (JPEG) (Extended Data Figure 7: Raw fluorescence data demonstrating digital control of cavity emission) - Supplemental Material
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[img] Image (JPEG) (Extended Data Figure 8: Histograms of numerical data demonstrating digital control of cavity emission) - Supplemental Material
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[img] Image (JPEG) (Extended Data Figure 9: Schema for recreation of Vincent van Gogh’s painting The Starry Night (1889)) - Supplemental Material
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Many hybrid devices integrate functional molecular or nanoparticle components with microstructures, as exemplified by the nanophotonic devices that couple emitters to optical resonators for potential use in single-molecule detection, precision magnetometry, low threshold lasing and quantum information processing. 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-assembly of DNA origami 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 origami, suggest that our method is well suited for the rapid prototyping of a broad array of hybrid nanophotonic devices.

Item Type:Article
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URLURL TypeDescription Data ReadCube access
Miyazono, Evan0000-0003-2176-0335
Faraon, Andrei0000-0002-8141-391X
Rothemund, Paul W. K.0000-0002-1653-3202
Additional Information:© 2016 Nature Publishing Group. Received 27 October 2015. Accepted 19 April 2016. Published online 11 July 2016. 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. Author Contributions: 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. The authors declare no competing financial interests. Code availability: The code used to design and simulate the PCCs as well as code to generate Autocad files for electron beam lithography defining PCCs and binding sites is available as the zip-encoded Supplementary Data file.
Group:Kavli Nanoscience Institute
Funding AgencyGrant Number
Army Research Office (ARO)W911NF-11-1-0117
Office of Naval Research (ONR)N000141410702
Air Force Office of Scientific Research (AFOSR)FA9550-15-1-0252
Issue or Number:7612
Record Number:CaltechAUTHORS:20160711-114700984
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Official Citation:Engineering and mapping nanocavity emission via precision placement of DNA origami Ashwin Gopinath, Evan Miyazono, Andrei Faraon & Paul W. K. Rothemund Nature 535, 401–405 (21 July 2016) doi:10.1038/nature18287
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:68959
Deposited On:11 Jul 2016 20:56
Last Modified:11 Nov 2021 04:07

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