DNA-Assisted Molecular Lithography

  • Boxuan Shen
  • Veikko Linko
  • J. Jussi ToppariEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1811)


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.

Key words

Nucleic acids DNA nanotechnology DNA origami Self-assembly Thin films Metal nanostructures Nanoparticles Plasmonics 



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).


  1. 1.
    Jones MR, Seeman NC, Mirkin CA (2015) Programmable materials and the nature of the DNA bond. Science 347:1260901. CrossRefPubMedGoogle Scholar
  2. 2.
    Nummelin S, Kommeri J, Kostiainen MA, Linko V (2018) Evolution of structural DNA nanotechnology. Adv Mater 30:1703721. CrossRefGoogle Scholar
  3. 3.
    Rothemund PWK (2006) Folding DNA to create nanoscale shapes and patterns. Nature 440:297–302. CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    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. CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Linko V, Kostiainen MA (2016) Automated design of DNA origami. Nat Biotechnol 34:826–827. CrossRefPubMedGoogle Scholar
  6. 6.
    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. CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Linko V, Nummelin S, Aarnos L, Tapio K, Toppari JJ, Kostiainen MA (2016) DNA-based enzyme reactors and systems. Nanomaterials 6:139. CrossRefPubMedCentralGoogle Scholar
  8. 8.
    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. CrossRefPubMedGoogle Scholar
  9. 9.
    Linko V, Ora A, Kostiainen MA (2015) DNA nanostructures as smart drug-delivery vehicles and molecular devices. Trends Biotechnol 33:586–594. CrossRefPubMedGoogle Scholar
  10. 10.
    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. CrossRefGoogle Scholar
  11. 11.
    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. CrossRefPubMedGoogle Scholar
  12. 12.
    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. CrossRefPubMedGoogle Scholar
  13. 13.
    Gopinath A, Miyazono E, Faraon A, Rothemund PWK (2016) Engineering and mapping nanocavity emission via precision placement of DNA origami. Nature 535:401–405. CrossRefPubMedGoogle Scholar
  14. 14.
    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. CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Tan SJ, Campolongo MJ, Luo D, Cheng W (2011) Building plasmonic nanostructures with DNA. Nat Nanotechnol 6:268–276. CrossRefPubMedGoogle Scholar
  16. 16.
    Helmi S, Ziegler C, Kauert DJ, Seidel R (2014) Shape-controlled synthesis of gold nanostructures using DNA origami molds. Nano Lett 14:6693–6698. CrossRefPubMedGoogle Scholar
  17. 17.
    Sun W, Boulais E, Hakobyan Y, Wang WL, Guan A, Bathe M, Yin P (2014) Casting inorganic structures with DNA molds. Science 346:1258361. CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    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. CrossRefPubMedGoogle Scholar
  19. 19.
    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. CrossRefPubMedGoogle Scholar
  20. 20.
    Shen B, Tapio K, Linko V, Kostiainen MA, Toppari JJ (2016) Metallic nanostructures based on DNA nanoshapes. Nanomaterials 6:146. CrossRefPubMedCentralGoogle Scholar
  21. 21.
    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. CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Shen B, Linko V, Tapio K, Kostiainen MA, Toppari JJ (2015) Custom-shaped metal nanostructures based on DNA origami silhouettes. Nanoscale 7:11267–11272. CrossRefGoogle Scholar
  23. 23.
    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. Scholar
  24. 24.
    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. CrossRefPubMedPubMedCentralGoogle Scholar
  25. 25.
    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. CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Dietz H, Douglas SM, Shih WM (2009) Folding DNA into twisted and curved nanoscale shapes. Science 325:725–730. CrossRefPubMedPubMedCentralGoogle Scholar
  27. 27.
    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. CrossRefGoogle Scholar
  28. 28.
    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. CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Physics, Nanoscience CenterUniversity of JyväskyläJyväskyläFinland
  2. 2.Biohybrid Materials, Department of Bioproducts and BiosystemsAalto UniversityAaltoFinland

Personalised recommendations