Abstract
Controllable strong interactions between a nanocavity and a single emitter is important to manipulating optical emission in a nanophotonic system but challenging to achieve. Herein a three-dimensional DNA origami, named as DNA rack (DR) is proposed and demonstrated to deterministically and precisely assemble single emitters within ultra-small plasmonic nanocavities formed by closely coupled gold nanorods (AuNRs). Uniquely, the DR is in a saddle shape, with two tubular grooves that geometrically allow a snug fit and linearly align two AuNRs with a bending angle < 10°. It also includes a spacer at the saddle point to maintain the gap between AuNRs as small as 2–3 nm, forming a nanocavity estimated to be 20 nm3 and an experimentally measured Q factor of 7.3. A DNA docking strand is designed at the spacer to position a single fluorescent emitter at nanometer accuracy within the cavity. Using Cy5 as a model emitter, a ∼ 30-fold fluorescence enhancement and a significantly reduced emission lifetime (from 1.6 ns to 670 ps) were experimentally verified, confirming significant emitter-cavity interactions. This DR-templated assembly method is capable of fitting AuNRs of variable length-to-width aspect ratios to form anisotropic nanocavities and deterministically incorporate different single emitters, thus enabling flexible design of both cavity resonance and emission wavelengths to tailor light-matter interactions at nanometer scale.
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Tame, M. S.; McEnery, K. R.; Özdemir, Ş. K.; Lee, J.; Maier, S. A.; Kim, M. S. Quantum plasmonics. Nat. Phys. 2013, 9, 329–340.
Thompson, J. D.; Tiecke, T. G.; De Leon, N. P.; Feist, J.; Akimov, A. V.; Gullans, M.; Zibrov, A. S.; Vuletić, V.; Lukin, M. D. Coupling a single trapped atom to a nanoscale optical cavity. Science 2013, 340, 1202–1205.
Faraon, A.; Fushman, I.; Englund, D.; Stoltz, N.; Petroff, P.; Vučković, J. Coherent generation of non-classical light on a chip via photon-induced tunnelling and blockade. Nat. Phys. 2008, 4, 859–863.
Andreani, L. C.; Panzarini, G.; Gérard, J. M. Strong-coupling regime for quantum boxes in pillar microcavities: Theory. Phys. Rev. B 1999, 60, 13276–13279.
Minder, M.; Pittaluga, M.; Roberts, G. L.; Lucamarini, M.; Dynes, J. F.; Yuan, Z. L.; Shields, A. J. Experimental quantum key distribution beyond the repeaterless secret key capacity. Nat. Photon. 2019, 13, 334–338.
Hennessy, K.; Badolato, A.; Winger, M.; Gerace, D.; Atatüre, M.; Gulde, S.; Fält, S.; Hu, E. L.; Imamoğlu, A. Quantum nature of a strongly coupled single-quantum-dot-cavity system. Nature 2007, 445, 896–899.
Schlather, A. E.; Large, N.; Urban, A. S.; Nordlander, P.; Halas, N. J. Near-field mediated plexcitonic coupling and giant Rabi splitting in individual metallic dimers. Nano Lett. 2013, 13, 3281–3286.
Reithmaier, J. P.; Sęk, G.; Löffler, A.; Hofmann, C.; Kuhn, S.; Reitzenstein, S.; Keldysh, L. V.; Kulakovskii, V. D.; Reinecke, T. L.; Forchel, A. Strong coupling in a single quantum dot-semiconductor microcavity system. Nature 2004, 432, 197–200.
Srinivasan, K.; Painter, O. Linear and nonlinear optical spectroscopy of a strongly coupled microdisk-quantum dot system. Nature 2007, 450, 862–865.
Thon, S. M.; Rakher, M. T.; Kim, H.; Gudat, J.; Irvine, W. T. M; Petroff, P. M.; Bouwmeester, D. Strong coupling through optical positioning of a quantum dot in a photonic crystal cavity. Appl. Phys. Lett. 2009, 94, 111115.
Gopinath, A.; Miyazono, E.; Faraon, A.; Rothemund, P. W. K. Engineering and mapping nanocavity emission via precision placement of DNA origami. Nature 2016, 535, 401–405.
Akimov, A. V.; Mukherjee, A.; Yu, C. L.; Chang, D. E.; Zibrov, A. S.; Hemmer, P. R.; Park, H.; Lukin, M. D. Generation of single optical plasmons in metallic nanowires coupled to quantum dots. Nature 2007, 450, 402–406.
Chikkaraddy, R.; De Nijs, B.; Benz, F.; Barrow, S. J.; Scherman, O. A.; Rosta, E.; Demetriadou, A.; Fox, P.; Hess, O.; Baumberg, J. J. Single-molecule strong coupling at room temperature in plasmonic nanocavities. Nature 2016, 535, 127–130.
Hoang, T. B.; Akselrod, G. M.; Argyropoulos, C.; Huang, J. N.; Smith, D. R.; Mikkelsen, M. H. Ultrafast spontaneous emission source using plasmonic nanoantennas. Nat. Commun. 2015, 6, 7788.
Van Der Sar, T.; Hagemeier, J.; Pfaff, W.; Heeres, E. C.; Thon, S. M.; Kim, H.; Petroff, P. M.; Oosterkamp, T. H.; Bouwmeester, D.; Hanson, R. Deterministic nanoassembly of a coupled quantum emitter-photonic crystal cavity system. Appl. Phys. Lett., 2011, 98, 193103.
Riedrich-Moller, J.; Arend, C.; Pauly, C.; Mücklich, F.; Fischer, M.; Gsell, S.; Schreck, M.; Becher, C. Deterministic coupling of a single silicon-vacancy color center to a photonic crystal cavity in diamond. Nano Lett. 2014, 14, 5281–5287.
Rothemund, P. W. K. Folding DNA to create nanoscale shapes and patterns. Nature 2006, 440, 297–302.
Han, D. R.; Pal, S.; Nangreave, J.; Deng, Z.; Liu, Y.; Yan, H. DNA origami with complex curvatures in three-dimensional space. Science 2011, 332, 342–346.
Samanta, A.; Zhou, Y. D.; Zou, S. L.; Yan, H.; Liu Y. Fluorescence quenching of quantum dots by gold nanoparticles: a potential long range spectroscopic ruler. Nano Lett. 2014, 14, 5052–5057.
Pal, S.; Dutta, P.; Wang, H. N.; Deng, Z. T.; Zou, S. L.; Yan, H.; Liu, Y. Quantum efficiency modification of organic fluorophores using gold nanoparticles on DNA origami scaffolds. J. Phys. Chem. C 2013, 117, 12735–12744.
Xin, L.; Lu, M.; Both, S.; Pfeiffer, M.; Urban, M. J.; Zhou, C.; Yan, H.; Weiss, T.; Liu, N.; Lindfors, K. Watching a single fluorophore molecule walk into a plasmonic hotspot. ACS Photon. 2019, 6, 985–993.
Vietz, C.; Kaminska, I.; Paz, M. S.; Tinnefeld, P.; Acuna, G. P. Broadband fluorescence enhancement with self-assembled silver nanoparticle optical antennas. ACS Nano 2017, 11, 4969–4975.
Chikkaraddy, R.; Turek, V. A.; Kongsuwan, N.; Benz, F.; Carnegie, C.; Van De Goor, T.; De Nijs, B.; Demetriadou, A.; Hess, O.; Keyser, U. F. et al. Mapping nanoscale hotspots with single-molecule emitters assembled into plasmonic nanocavities using DNA origami. Nano Lett. 2018, 18, 405–411.
Roller, E. M.; Argyropoulos, C.; Hogele, A.; Liedl, T.; Pilo-Pais, M. Plasmon-exciton coupling using DNA templates. Nano Lett. 2016, 16, 5962–5966.
Lin, K. Q.; Yi, J.; Hu, S.; Liu, B. J.; Liu, J. Y.; Wang, X.; Ren, B. Size effect on SERS of gold nanorods demonstrated via single nanoparticle spectroscopy. J. Phys. Chem. C 2016, 120, 20806–20813.
Huang, C. P.; Yin, X. G.; Kong, L. B.; Zhu, Y. Y. Interactions of nanorod particles in the strong coupling regime. J. Phys. Chem. C 2010, 114, 21123–21131.
Jain, P. K.; Eustis, S.; El-Sayed, M. A. Plasmon coupling in nanorod assemblies: optical absorption, discrete dipole approximation simulation, and exciton-coupling model. J. Phys. Chem. B 2006, 110, 18243–18253.
Funston, A. M.; Novo, C.; Davis, T. J.; Mulvaney, P. Plasmon coupling of gold nanorods at short distances and in different geometries. Nano Lett. 2009, 9, 1651–1658.
Shao, L.; Woo, K. C.; Chen, H. J.; Jin, Z.; Wang, J. F.; Lin, H. Q. Angle-and energy-resolved plasmon coupling in gold nanorod dimers. ACS Nano 2010, 4, 3053–3062.
Link, S.; Mohamed, M. B.; El-Sayed, M. A. Simulation of the optical absorption spectra of gold nanorods as a function of their aspect ratio and the effect of the medium dielectric constant. J. Phys. Chem. B 1999, 103, 3073–3077.
Süel, G. Use of fluorescence microscopy to analyze genetic circuit dynamics. Methods Enzymol. 2011, 497, 275–293.
Liu, X. G.; Zhang, F.; Jing, X. X.; Pan, M. C.; Liu, P.; Li, W.; Zhu, B. W.; Li, J.; Chen, H.; Wang, L. H. et al. Complex silica composite nano-materials templated with DNA origami. Nature 2018, 559, 593–598.
Gole, A.; Murphy, C. J. Seed-mediated synthesis of gold nanorods: Role of the size and nature of the seed. Chem. Mater. 2004, 16, 3633–3640.
Mirkin, C. A.; Letsinger, R. L.; Mucic, R. C.; Storhoff, J. J. A DNA-based method for rationally assembling nanoparticles into macroscopic materials. Nature 1996, 382, 607–609.
Cocco, S.; Marko, J. F.; Monasson, R. Theoretical models for single-molecule DNA and RNA experiments: From elasticity to unzipping. C R Phys. 2002, 3, 569–584.
Roth, E.; Azaria, A. G.; Girshevitz, O.; Bitler, A.; Garini, Y. Measuring the conformation and persistence length of single-stranded DNA using a DNA origami structure. Nano Lett. 2018, 18, 6703–6709.
Chi, Q. J.; Wang, G. X.; Jiang, J. H. The persistence length and length per base of single-stranded DNA obtained from fluorescence correlation spectroscopy measurements using mean field theory. Phys. A Stat. Mech. Appl. 2013, 392, 1072–1079.
Hagerman, P. J. Flexibility of DNA. Annu. Rev. Biophys. Biophys. Chem. 1988, 17, 265–286.
Thacker, V. V.; Herrmann, L. O.; Sigle, D. O.; Zhang, T.; Liedl, T.; Baumberg, J. J.; Keyser, U. F. DNA origami based assembly of gold nanoparticle dimers for surface-enhanced Raman scattering. Nat. Commun. 2014, 5, 3448.
Simoncelli, S.; Roller, E. M.; Urban, P.; Schreiber, R.; Turberfield, A. J.; Liedl, T.; Lohmüller, T. Quantitative single-molecule surface-enhanced Raman scattering by optothermal tuning of DNA origami-assembled plasmonic nanoantennas. ACS Nano 2016, 10, 9809–9815.
Chang, W. S.; Ha, J. W.; Slaughter, L. S.; Link, S. Plasmonic nanorod absorbers as orientation sensors. Proc. Natl. Acad. Sci. USA 2010, 107, 2781–2786.
Moreels, I.; Lambert, K.; De Muynck, D.; Vanhaecke, F.; Poelman, D.; Martins, J. C.; Allan, G.; Hens, Z. Composition and size-dependent extinction coefficient of colloidal PbSe quantum dots. Chem. Mater. 2007, 19, 6101–6106.
Cai, Y. Y.; Liu, J. G.; Tauzin, L. J.; Huang, D.; Sung, E.; Zhang, H.; Joplin, A.; Chang, W. S.; Nordlander, P.; Link, S. Photoluminescence of gold nanorods: Purcell effect enhanced emission from hot carriers. ACS Nano 2018, 12, 976–985.
Fort, E.; Grésillon, S. Surface enhanced fluorescence. J. Phys. D: Appl. Phys. 2007, 41, 013001.
Giannini, V.; Fernández-Domínguez, A. I.; Heck, S. C.; Maier, S. A. Plasmonic nanoantennas: Fundamentals and their use in controlling the radiative properties of nanoemitters. Chem. Rev. 2011, 111, 3888–3912.
Purcell, E. M. Spontaneous emission probabilities at radio frequencies. In Confined Electrons and Photons. Burstein, E.; Weisbuch, C., Eds.; Springer: Boston, 1995; pp 839.
Kinkhabwala, A.; Yu, Z. F.; Fan, S. H.; Avlasevich, Y.; Müllen, K.; Moerner, W. E. Large single-molecule fluorescence enhancements produced by a bowtie nanoantenna. Nat. Photon. 2009, 3, 654–657.
Rose, A.; Hoang, T. B.; McGuire, F.; Mock, J. J.; Ciraci, C.; Smith, D. R.; Mikkelsen, M. H. Control of radiative processes using tunable plasmonic nanopatch antennas. Nano Lett. 2014, 14, 4797–4802.
Geddes, C. D.; Lakowicz, J. R. Editorial: Metal-enhanced fluorescence. J. Fluoresc. 2002, 12, 121–129.
Malicka, J.; Gryczynski, I.; Fang, J. Y.; Kusba, J.; Lakowicz, J. R. Photostability of Cy3 and Cy5-labeled DNA in the presence of metallic silver particles. J. Fluoresc. 2002, 12, 439–447.
Yoshie, T.; Scherer, A.; Hendrickson, J.; Khitrova, G.; Gibbs, H. M.; Rupper, G.; Ell, C.; Shchekin, O. B.; Deppe, D. G. Vacuum Rabi splitting with a single quantum dot in a photonic crystal nanocavity. Nature 2004, 432, 200–203.
Moreira, B. G.; You, Y.; Owczarzy, R. Cy3 and Cy5 dyes attached to oligonucleotide terminus stabilize DNA duplexes: Predictive thermodynamic model. Biophys. Chem. 2015, 198, 36–44.
Olmon, R. L.; Slovick, B.; Johnson, T. W.; Shelton, D.; Oh, S. H.; Boreman, G. D.; Raschke, M. B. Optical dielectric function of gold. Phys. Rev. B 2012, 86, 235147.
Carmichael, H. J.; Brecha, R. J.; Raizen, M. G.; Kimble, H. J.; Rice, P. R. Subnatural linewidth averaging for coupled atomic and cavity-mode oscillators. Phys. Rev. A 1989, 40, 5516–5519.
Acknowledgements
Y. L. thanks the support from an Army Research Office MURI award no. W911NF-12-1-0420. C. W. thanks the ASU startup funds and National Science Foundation under grant Nos. 1711412, 1838443, and 1847324 for partially supporting this research. Y. Y. thanks the ASU startup funds and National Science Foundation under grant Nos. 1809997 for partially supporting this research.
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Deterministic assembly of single emitters in sub-5 nanometer optical cavity formed by gold nanorod dimers on three-dimensional DNA origami
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Zhao, Z., Chen, X., Zuo, J. et al. Deterministic assembly of single emitters in sub-5 nanometer optical cavity formed by gold nanorod dimers on three-dimensional DNA origami. Nano Res. 15, 1327–1337 (2022). https://doi.org/10.1007/s12274-021-3661-z
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DOI: https://doi.org/10.1007/s12274-021-3661-z