Skip to main content
SpringerLink
Log in
Book cover

Encyclopedia of Nanotechnology pp 1–22Cite as

DNA Origami as Programmable Nanofabrication Tools

  • 620 Accesses

Synonyms

Structural DNA nanotechnology

Definition

DNA origami is a self-assembly technique, where a long single-stranded DNA (scaffold), usually from the genome of a bacteriophage, is folded into a designed path with the help of a set of synthetic oligonucleotides (staples). This bottom-up nanofabrication approach is capable of generating large numbers of identical DNA structures with designed geometry. The structures can be further functionalized or decorated to produce versatile nanostructures.

Introduction

Apart from being the genetic material for various forms of life, DNA has also emerged as a promising engineering material for nanotechnology. Based on its excellent ability to recognize its complementary sequence, the binding of DNA can be programmed by sequence design. This idea gave birth to the field of structural DNA nanotechnology. Carefully designed oligonucleotides have been demonstrated to assemble into polyhedrons [1], 2D lattice [2], and 3D crystals that facilitate...

Keywords

  • Electroless Plating
  • Hard Mask
  • Aptamer Sequence
  • Nanometer Accuracy
  • Folding Path

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

This is a preview of subscription content, access via your institution.

References

  1. He, Y., Ye, T., Su, M., Zhang, C., Ribbe, A.E., Jiang, W., Mao, C.: Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra. Nature 452(7184), 198–201 (2008)

    CrossRef  Google Scholar 

  2. Yan, H., Park, S.H., Finkelstein, G., Reif, J.H., LaBean, T.H.: DNA-templated self-assembly of protein arrays and highly conductive nanowires. Science 301(5641), 1882–1884 (2003)

    CrossRef  Google Scholar 

  3. Zheng, J., Birktoft, J.J., Chen, Y., Wang, T., Sha, R., Constantinou, P.E., Ginell, S.L., Mao, C., Seeman, N.C.: From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal. Nature 461(7260), 74–77 (2009)

    CrossRef  Google Scholar 

  4. Rothemund, P.W.: Folding DNA to create nanoscale shapes and patterns. Nature 440(7082), 297–302 (2006)

    CrossRef  Google Scholar 

  5. Jungmann, R., Liedl, T., Sobey, T.L., Shih, W., Simmel, F.C.: Isothermal assembly of DNA origami structures using denaturing agents. J. Am. Chem. Soc. 130(31), 10062–10063 (2008)

    CrossRef  Google Scholar 

  6. Zhao, Z., Liu, Y., Yan, H.: Organizing DNA origami tiles into larger structures using preformed scaffold frames. Nano Lett. 11(7), 2997–3002 (2011)

    CrossRef  Google Scholar 

  7. BR, H., Liedl, T., Shih, W.M.: Folding DNA origami from a double-stranded source of scaffold. J. Am. Chem. Soc. 131(26), 9154–9155 (2009)

    CrossRef  Google Scholar 

  8. Fu, Y., Zeng, D., Chao, J., Jin, Y., Zhang, Z., Liu, H., Li, D., Ma, H., Huang, Q., Gothelf, K.V.: Single-step rapid assembly of DNA origami nanostructures for addressable nanoscale bioreactors. J. Am. Chem. Soc. 135(2), 696–702 (2012)

    CrossRef  Google Scholar 

  9. Chen, H., Cha, T.-G., Pan, J., Choi, J.H.: Hierarchically assembled DNA origami tubules with reconfigurable chirality. Nanotechnology 24(43), 435601 (2013)

    CrossRef  Google Scholar 

  10. Andersen, E.S., Dong, M., Nielsen, M.M., Jahn, K., Lind-Thomsen, A., Mamdouh, W., Gothelf, K.V., Besenbacher, F., Kjems, J.: DNA origami design of dolphin-shaped structures with flexible tails. ACS Nano 2(6), 1213–1218 (2008)

    CrossRef  Google Scholar 

  11. Douglas, S.M., Dietz, H., Liedl, T., Högberg, B., Graf, F., Shih, W.M.: Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459(7245), 414–418 (2009)

    CrossRef  Google Scholar 

  12. Liedl, T., Högberg, B., Tytell, J., Ingber, D.E., Shih, W.M.: Self-assembly of three-dimensional prestressed tensegrity structures from DNA. Nat. Nanotechnol. 5(7), 520–524 (2010)

    CrossRef  Google Scholar 

  13. Han, D., Pal, S., Yang, Y., Jiang, S., Nangreave, J., Liu, Y., Yan, H.: DNA gridiron nanostructures based on four-arm junctions. Science 339(6126), 1412–1415 (2013)

    CrossRef  Google Scholar 

  14. Dietz, H., Douglas, S.M., Shih, W.M.: Folding DNA into twisted and curved nanoscale shapes. Science 325(5941), 725–730 (2009)

    CrossRef  Google Scholar 

  15. Hao, E., Schatz, G.C.: Electromagnetic fields around silver nanoparticles and dimers. J. Chem. Phys. 120(1), 357–366 (2004)

    CrossRef  Google Scholar 

  16. Shalaev, V.M.: Optical negative-index metamaterials. Nat. Photonics 1(1), 41–48 (2007)

    CrossRef  Google Scholar 

  17. Ding, B., Deng, Z., Yan, H., Cabrini, S., Zuckermann, R.N., Bokor, J.: Gold nanoparticle self-similar chain structure organized by DNA origami. J. Am. Chem. Soc. 132(10), 3248–3249 (2010)

    CrossRef  Google Scholar 

  18. Jin, Z., Sun, W., Ke, Y., Shih, C.-J., Paulus, G.L., Wang, Q.H., Mu, B., Yin, P., Strano, M.S.: Metallized DNA nanolithography for encoding and transferring spatial information for graphene patterning. Nat. Commun. 4, 1663 (2013)

    CrossRef  Google Scholar 

  19. Pilo-Pais, M., Watson, A., Demers, S., LaBean, T.H., Finkelstein, G.: Surface-enhanced Raman scattering plasmonic enhancement using DNA origami-based complex metallic nanostructures. Nano Lett. 14(4), 2099–2104 (2014)

    CrossRef  Google Scholar 

  20. Kühler, P., Roller, E.-M., Schreiber, R., Liedl, T., Lohmüller, T., Feldmann, J.: Plasmonic DNA-origami nanoantennas for surface enhanced Raman spectroscopy. Nano Lett. 14(5), 2914–2919 (2014)

    CrossRef  Google Scholar 

  21. Kuzyk, A., Schreiber, R., Fan, Z., Pardatscher, G., Roller, E.-M., Högele, A., Simmel, F.C., Govorov, A.O., Liedl, T.: DNA-based self-assembly of chiral plasmonic nanostructures with tailored optical response. Nature 483(7389), 311–314 (2012)

    CrossRef  Google Scholar 

  22. Medintz, I.L., Uyeda, H.T., Goldman, E.R., Mattoussi, H.: Quantum dot bioconjugates for imaging, labelling and sensing. Nat. Mater. 4(6), 435–446 (2005)

    CrossRef  Google Scholar 

  23. Ko, S.H., Du, K., Liddle, J.A.: Quantum-dot fluorescence lifetime engineering with DNA origami constructs. Angew. Chem. Int. Ed. 52(4), 1193–1197 (2013)

    CrossRef  Google Scholar 

  24. Choi, J.H., Chen, K.H., Strano, M.S.: Aptamer-capped nanocrystal quantum dots: a new method for label-free protein detection. J. Am. Chem. Soc. 128(49), 15584–15585 (2006)

    CrossRef  Google Scholar 

  25. Deng, Z., Samanta, A., Nangreave, J., Yan, H., Liu, Y.: Robust DNA-functionalized core/shell quantum dots with fluorescent emission spanning from UV–vis to near-IR and compatible with DNA-directed self-assembly. J. Am. Chem. Soc. 134(42), 17424–17427 (2012)

    CrossRef  Google Scholar 

  26. Ma, N., Sargent, E.H., Kelley, S.O.: One-step DNA-programmed growth of luminescent and biofunctionalized nanocrystals. Nat. Nanotechnol. 4(2), 121–125 (2008)

    CrossRef  Google Scholar 

  27. Steinhauer, C., Jungmann, R., Sobey, T.L., Simmel, F.C., Tinnefeld, P.: DNA origami as a nanoscopic ruler for super-resolution microscopy. Angew. Chem. Int. Ed. 48(47), 8870–8873 (2009)

    CrossRef  Google Scholar 

  28. Helmig, S., Rotaru, A., Arian, D., Kovbasyuk, L., Arnbjerg, J., Ogilby, P.R., Kjems, J., Mokhir, A., Besenbacher, F., Gothelf, K.V.: Single molecule atomic force microscopy studies of photosensitized singlet oxygen behavior on a DNA origami template. ACS Nano 4(12), 7475–7480 (2010)

    CrossRef  Google Scholar 

  29. Ellington, A.D., Szostak, J.W.: Selection in vitro of single-stranded DNA molecules that fold into specific ligand-binding structures. Nature 355(6363), 850–852 (1992)

    CrossRef  Google Scholar 

  30. Tintoré, M., Gállego, I., Manning, B., Eritja, R., Fàbrega, C.: DNA origami as a DNA repair nanosensor at the single-molecule level. Angew. Chem. Int. Ed. 52(30), 7747–7750 (2013)

    CrossRef  Google Scholar 

  31. Wang, Z.-G., Liu, Q., Ding, B.: Shape-controlled nanofabrication of conducting polymer on planar DNA templates. Chem. Mater. 26(11), 3364–3367 (2014)

    CrossRef  Google Scholar 

  32. Travascio, P., Li, Y., Sen, D.: DNA-enhanced peroxidase activity of a DNA aptamer-hemin complex. Chem. Biol. 5(9), 505–517 (1998)

    CrossRef  Google Scholar 

  33. Surwade, S.P., Zhou, F., Wei, B., Sun, W., Powell, A., O’Donnell, C., Yin, P., Liu, H.: Nanoscale growth and patterning of inorganic oxides using DNA nanostructure templates. J. Am. Chem. Soc. 135(18), 6778–6781 (2013)

    CrossRef  Google Scholar 

  34. Surwade, S.P., Zhao, S., Liu, H.: Molecular lithography through DNA-mediated etching and masking of SiO2. J. Am. Chem. Soc. 133(31), 11868–11871 (2011)

    CrossRef  Google Scholar 

  35. Pinheiro, A.V., Han, D., Shih, W.M., Yan, H.: Challenges and opportunities for structural DNA nanotechnology. Nat. Nanotechnol. 6(12), 763–772 (2011)

    CrossRef  Google Scholar 

  36. Liu, W., Zhong, H., Wang, R., Seeman, N.C.: Crystalline two-dimensional DNA-origami arrays. Angew. Chem. 123(1), 278–281 (2011)

    CrossRef  Google Scholar 

  37. Asanuma, H., Liang, X., Nishioka, H., Matsunaga, D., Liu, M., Komiyama, M.: Synthesis of azobenzene-tethered DNA for reversible photo-regulation of DNA functions: hybridization and transcription. Nat. Protoc. 2(1), 203–212 (2007)

    CrossRef  Google Scholar 

  38. Yang, Y., Endo, M., Hidaka, K., Sugiyama, H.: Photo-controllable DNA origami nanostructures assembling into predesigned multiorientational patterns. J. Am. Chem. Soc. 134(51), 20645–20653 (2012)

    CrossRef  Google Scholar 

  39. Zhang, D.Y., Winfree, E.: Control of DNA strand displacement kinetics using toehold exchange. J. Am. Chem. Soc. 131(47), 17303–17314 (2009)

    CrossRef  Google Scholar 

  40. Andersen, E.S., Dong, M., Nielsen, M.M., Jahn, K., Subramani, R., Mamdouh, W., Golas, M.M., Sander, B., Stark, H., Oliveira, C.L.: Self-assembly of a nanoscale DNA box with a controllable lid. Nature 459(7243), 73–76 (2009)

    CrossRef  Google Scholar 

  41. Douglas, S.M., Bachelet, I., Church, G.M.: A logic-gated nanorobot for targeted transport of molecular payloads. Science 335(6070), 831–834 (2012)

    CrossRef  Google Scholar 

  42. Kuzuya, A., Sakai, Y., Yamazaki, T., Xu, Y., Komiyama, M.: Nanomechanical DNA origami ‘single-molecule beacons’ directly imaged by atomic force microscopy. Nat. Commun. 2, 449 (2011)

    CrossRef  Google Scholar 

  43. Zhou, L., Marras, A.E., Su, H.-J., Castro, C.E.: DNA origami compliant nanostructures with tunable mechanical properties. ACS Nano 8(1), 27–34 (2013)

    CrossRef  Google Scholar 

  44. Chen, H., Weng, T.-W., Riccitelli, M., Cui, Y., Irudayaraj, J., Choi, J.H.: Understanding the mechanical properties of DNA origami tiles and controlling the kinetics of their folding and unfolding reconfiguration. J. Am. Chem. Soc. 136, 6995–7005 (2014)

    CrossRef  Google Scholar 

  45. Yang, H., Luo, G., Karnchanaphanurach, P., Louie, T.-M., Rech, I., Cova, S., Xun, L., Xie, X.S.: Protein conformational dynamics probed by single-molecule electron transfer. Science 302(5643), 262–266 (2003)

    CrossRef  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. School of Mechanical Engineering, Purdue University, 585 Purdue Mall, West Lafayette, IN, 47907, USA

    Haorong Chen, Feiran Li, Jing Pan, Jungwook Choi & Jong Hyun Choi

Authors
  1. Haorong Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Feiran Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jing Pan
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jungwook Choi
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jong Hyun Choi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jong Hyun Choi .

Editor information

Editors and Affiliations

  1. Biomimetics (NLB²), Ohio State University Nanoprobe Lab. for Bio- & Nanotechnology, Columbus, Ohio, USA

    Bharat Bhushan

Rights and permissions

Reprints and Permissions

Copyright information

© 2015 Springer Science+Business Media Dordrecht

About this entry

Cite this entry

Chen, H., Li, F., Pan, J., Choi, J., Choi, J.H. (2015). DNA Origami as Programmable Nanofabrication Tools. In: Bhushan, B. (eds) Encyclopedia of Nanotechnology. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-6178-0_100907-1

Download citation

  • DOI: https://doi.org/10.1007/978-94-007-6178-0_100907-1

  • Received:

  • Accepted:

  • Published:

  • Publisher Name: Springer, Dordrecht

  • Online ISBN: 978-94-007-6178-0

  • eBook Packages: Springer Reference Chemistry & Mat. ScienceReference Module Physical and Materials Science

search

Navigation