Abstract
During the past decade, DNA origami has become a popular method to build custom two- (2D) and three-dimensional (3D) DNA nanostructures. These programmable structures could further serve as templates for accurate nanoscale patterning, and therefore they could find uses in various biotechnological applications. However, to transfer the spatial information of DNA origami to metal nanostructures has been limited to either direct nanoparticle-based patterning or chemical growth of metallic seed particles that are attached to the DNA objects. Here, we present an alternative way by combining DNA origami with conventional lithography techniques. With this DNA-assisted lithography (DALI) method, we can create plasmonic, entirely metallic nanostructures in a highly accurate and parallel manner on different substrates. We demonstrate our technique by patterning a transparent substrate with discrete bowtie-shaped nanoparticles, i.e., “nanoantennas” or “optical antennas,” with a feature size of approximately 10 nm. Owing to the versatility of DNA origami, this method can be effortlessly generalized to other shapes and sizes.
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References
Jones MR, Seeman NC, Mirkin CA (2015) Programmable materials and the nature of the DNA bond. Science 347:1260901. https://doi.org/10.1126/science.1260901
Nummelin S, Kommeri J, Kostiainen MA, Linko V (2018) Evolution of structural DNA nanotechnology. Adv Mater 30:1703721. https://doi.org/10.1002/adma.201703721
Rothemund PWK (2006) Folding DNA to create nanoscale shapes and patterns. Nature 440:297–302. https://doi.org/10.1038/nature04586
Douglas SM, Dietz H, Liedl T, Högberg B, Graf F, Shih WM (2009) Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459:414–418. https://doi.org/10.1038/nature08016
Linko V, Kostiainen MA (2016) Automated design of DNA origami. Nat Biotechnol 34:826–827. https://doi.org/10.1038/nbt.3647
Langecker M, Arnaut V, Martin TG, List J, Renner S, Mayer M, Dietz H, Simmel FC (2012) Synthetic lipid membrane channels formed by designed DNA nanostructures. Science 338:932–936. https://doi.org/10.1126/science.1225624
Linko V, Nummelin S, Aarnos L, Tapio K, Toppari JJ, Kostiainen MA (2016) DNA-based enzyme reactors and systems. Nanomaterials 6:139. https://doi.org/10.3390/nano6080139
Kuzyk A, Schreiber R, Fan Z, Pardatscher G, Roller E-M, Högele A, Simmel FC, Govorov AO, Liedl T (2012) DNA-based self-assembly of chiral plasmonic nanostructures with tailored optical response. Nature 483:311–314. https://doi.org/10.1038/nature10889
Linko V, Ora A, Kostiainen MA (2015) DNA nanostructures as smart drug-delivery vehicles and molecular devices. Trends Biotechnol 33:586–594. https://doi.org/10.1016/j.tibtech.2015.08.001
Maune HT, Han S, Barish RD, Bockrath M, Goddard WA III, Rothemund PWK, Winfree E (2010) Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates. Nat Nanotechnol 5:61–66. https://doi.org/10.1038/nnano.2009.311
Shen B, Linko V, Dietz H, Toppari JJ (2015) Dielectrophoretic trapping of multilayer DNA origami nanostructures and DNA origami-induced local destruction of silicon dioxide. Electrophoresis 36:255–262. https://doi.org/10.1002/elps.201400323
Tapio K, Leppiniemi J, Shen B, Hytönen VP, Fritzsche W, Toppari JJ (2016) Toward single electron nanoelectronics using self-assembled DNA structure. Nano Lett 16:6780–6786. https://doi.org/10.1021/acs.nanolett.6b02378
Gopinath A, Miyazono E, Faraon A, Rothemund PWK (2016) Engineering and mapping nanocavity emission via precision placement of DNA origami. Nature 535:401–405. https://doi.org/10.1038/nature18287
Ding B, Deng Z, Yan H, Cabrini S, Zuckermann RN, Bokor J (2010) Gold nanoparticle self-similar chain structure organized by DNA origami. J Am Chem Soc 132:3248–3249. https://doi.org/10.1021/ja9101198
Tan SJ, Campolongo MJ, Luo D, Cheng W (2011) Building plasmonic nanostructures with DNA. Nat Nanotechnol 6:268–276. https://doi.org/10.1038/nnano.2011.49
Helmi S, Ziegler C, Kauert DJ, Seidel R (2014) Shape-controlled synthesis of gold nanostructures using DNA origami molds. Nano Lett 14:6693–6698. https://doi.org/10.1021/nl503441v
Sun W, Boulais E, Hakobyan Y, Wang WL, Guan A, Bathe M, Yin P (2014) Casting inorganic structures with DNA molds. Science 346:1258361. https://doi.org/10.1126/science.1258361
Pilo-Pais M, Goldberg S, Samano E, LaBean TH, Finkelstein G (2011) Connecting the nanodots: programmable nanofabrication of fused metal shapes on DNA templates. Nano Lett 11:3489–3492. https://doi.org/10.1021/nl202066c
Schreiber R, Kempter S, Holler S, Schüller V, Schiffels D, Simmel SS, Nickels PC, Liedl T (2011) DNA origami-templated growth of arbitrarily shaped metal nanoparticles. Small 7:1795–1799. https://doi.org/10.1002/smll.201100465
Shen B, Tapio K, Linko V, Kostiainen MA, Toppari JJ (2016) Metallic nanostructures based on DNA nanoshapes. Nanomaterials 6:146. https://doi.org/10.3390/nano6080146
Surwade SP, Zhou F, Wei B, Sun W, Powell A, O’Donnell C, Yin P, Liu H (2013) Nanoscale growth and patterning of inorganic oxides using DNA nanostructure templates. J Am Chem Soc 135:6778–6781. https://doi.org/10.1021/ja401785h
Shen B, Linko V, Tapio K, Kostiainen MA, Toppari JJ (2015) Custom-shaped metal nanostructures based on DNA origami silhouettes. Nanoscale 7:11267–11272. https://doi.org/10.1039/c5nr02300a
Shen B, Linko V, Tapio K, Pikker S, Lemma T, Gopinath A, Gothelf KV, Kostiainen MA, Toppari JJ (2018) Plasmonic nanostructures through DNA-assisted lithography. Sci Adv 4:eaap8978. https://doi.org/10.1126/sciadv.aap8978
Ke Y, Douglas SM, Liu M, Sharma J, Cheng A, Leung A, Liu Y, Shih WM, Yan H (2009) Multilayer DNA origami packed on a square lattice. J Am Chem Soc 131:15903–15908. https://doi.org/10.1021/ja906381y
Castro CE, Kilchherr F, Kim D-N, Shiao EL, Wauer T, Wortmann P, Bathe M, Dietz H (2011) A primer to scaffolded DNA origami. Nat Methods 8:221–229. https://doi.org/10.1038/nmeth.1570
Dietz H, Douglas SM, Shih WM (2009) Folding DNA into twisted and curved nanoscale shapes. Science 325:725–730. https://doi.org/10.1126/science.1174251
Marty F, Rousseau L, Saadany B, Mercier B, Français O, Mita Y, Bourouina T (2005) Advanced etching of silicon based on deep reactive ion etching for silicon high aspect ratio microstructures and three-dimensional micro- and nanostructures. Microelectron J 36:673–677. https://doi.org/10.1016/j.mejo.2005.04.039
Linko V, Shen B, Tapio K, Toppari JJ, Kostiainen MA, Tuukkanen S (2015) One-step large-scale deposition of salt-free DNA origami nanostructures. Sci Rep 5:15634. https://doi.org/10.1038/srep15634
Acknowledgments
Financial support from the Academy of Finland (projects 286845, 130900, 218182, 263526, 289947, 135193), Jane and Aatos Erkko Foundation, Sigrid Jusélius Foundation, Vilho, Yrjö and Kalle Väisälä Foundation and Finnish Cultural Foundation is gratefully acknowledged. This work was carried out under the Academy of Finland Centers of Excellence Programme (2014–2019).
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Shen, B., Linko, V., Toppari, J.J. (2018). DNA-Assisted Molecular Lithography. In: Zuccheri, G. (eds) DNA Nanotechnology. Methods in Molecular Biology, vol 1811. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8582-1_20
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DOI: https://doi.org/10.1007/978-1-4939-8582-1_20
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