Skip to main content
SpringerLink
Log in

Practical aspects of structural and dynamic DNA nanotechnology

  • DNA Nanotechnology: A Foundation for Programmable Nanoscale Materials
  • Published:
MRS Bulletin Aims and scope Submit manuscript

Abstract

DNA nanostructures are a set of materials with well-defined physical, chemical, and biological properties that can be used on their own or incorporated with other materials for many applications. Herein, the practical aspects of utilizing DNA nanostructures (structural or dynamic) as materials are comprehensively covered. This article first summarizes properties of DNA molecules and practical considerations and then discusses the fundamental design principles of structural DNA nanostructures. Finally, various aspects of dynamic DNA nanostructure-based actuation and computation are included.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Figure 1
Figure 2
Figure 3
Figure 4

Similar content being viewed by others

References

  1. Y.H. Roh, R.C. Ruiz, S. Peng, J.B. Lee, D. Luo, Chem. Soc. Rev. 40, 5730 (2011).

    Article  CAS  Google Scholar 

  2. T. Strunz, K. Oroszlan, R. Schafer, H.J. Guntherodt, Proc. Natl. Acad. Sci. U.S.A. 96, 11277 (1999).

    Article  Google Scholar 

  3. M.D. Wang, H. Yin, R. Landick, J. Gelles, S.M. Block, Biophys. J. 72, 1335 (1997).

    Article  Google Scholar 

  4. R.O. Pedersen, A.N. Marchi, J. Majikes, J.A. Nash, N.A. Estrich, D.S. Courson, C.K. Hall, S.L. Craig, T.H. LaBean, in Handbook of Nanomaterials Properties, B. Bhushan, D. Luo, S.R. Schricker, W. Sigmund, Eds. (Springer, Berlin, 2014), p. 1125.

  5. N.C. Seeman, N.R. Kallenbach, Biophys. J. 44, 201 (1983).

    Article  Google Scholar 

  6. T.J. Fu, N.C. Seeman, Biochemistry 32, 3211 (1993).

    Article  Google Scholar 

  7. Y. He, Y. Chen, H. Liu, A.E. Ribbe, C. Mao, J. Am. Chem. Soc. 127, 12202 (2005).

    Article  CAS  Google Scholar 

  8. P. Wang, S. Wu, C. Tian, G. Yu, W. Jiang, G. Wang, C. Mao, J. Am. Chem. Soc. 138, 13579 (2016).

    Article  CAS  Google Scholar 

  9. J. Zheng, J.J. Birktoft, Y. Chen, T. Wang, R. Sha, P.E. Constantinou, S.L. Ginell, C. Mao, N.C. Seeman, Nature 461, 74 (2009).

    Article  CAS  Google Scholar 

  10. F. Zhang, Y. Liu, H. Yan, J. Am. Chem. Soc. 135, 7458 (2013).

    Article  CAS  Google Scholar 

  11. Y.G. Ke, L.L. Ong, W.M. Shih, P. Yin, Science 338, 1177 (2012).

    Article  CAS  Google Scholar 

  12. B. Wei, M.J. Dai, P. Yin, Nature 485, 623 (2012).

    Article  CAS  Google Scholar 

  13. Y. Ke, L.L. Ong, W. Sun, J. Song, M. Dong, W.M. Shih, P. Yin, Nat. Chem. 6, 994 (2014).

    Article  CAS  Google Scholar 

  14. P.W.K. Rothemund, Nature 440, 297 (2006).

    Article  CAS  Google Scholar 

  15. S.M. Douglas, H. Dietz, T. Liedl, B. Hogberg, F. Graf, W.M. Shih, Nature 459, 414 (2009).

    Article  CAS  Google Scholar 

  16. Y.G. Ke, S.M. Douglas, M.H. Liu, J. Sharma, A.C. Cheng, A. Leung, Y. Liu, W.M. Shih, H. Yan, J. Am. Chem. Soc. 131, 15903 (2009).

    Article  CAS  Google Scholar 

  17. Y.G. Ke, N.V. Voigt, K.V. Gothelf, W.M. Shih, J. Am. Chem. Soc. 134, 1770 (2012).

    Article  CAS  Google Scholar 

  18. R. Veneziano, S. Ratanalert, K. Zhang, F. Zhang, H. Yan, W. Chiu, M. Bathe, Science 352, 6293 (2016).

    Article  Google Scholar 

  19. E. Benson, A. Mohammed, J. Gardell, S. Masich, E. Czeizler, P. Orponen, B. Hogberg, Nature 523, 441 (2015).

    Article  CAS  Google Scholar 

  20. A.N. Marchi, I. Saaem, B.N. Vogen, S. Brown, T.H. LaBean, Nano Lett. 14, 5740 (2014).

    Article  CAS  Google Scholar 

  21. P. Wang, S. Gaitanaros, S. Lee, M. Bathe, W.M. Shih, Y. Ke, J. Am. Chem. Soc. 138, 7733 (2016).

    Article  CAS  Google Scholar 

  22. T. Gerling, K.F. Wagenbauer, A.M. Neuner, H. Dietz, Science 347, 1446 (2015).

    Article  CAS  Google Scholar 

  23. S. Williams, K. Lund, C. Lin, P. Wonka, S. Lindsay, H. Yan, “Tiamat: A Three-Dimensional Editing Tool for Complex DNA Structures,” 14th Int. Mtg. DNA Comput., H. Yan, A. Goel, F.C. Simmel, P. Sosík, Eds. (Prague, Czech Republic, June 2–9, 2008), pp. 90–101.

  24. J. Zhu, B. Wei, Y. Yuan, Y. Mi, Nucleic Acids Res. 37, 2164 (2009).

    Article  CAS  Google Scholar 

  25. E.S. Andersen, M. Dong, M.M. Nielsen, K. Jahn, A. Lind-Thomsen, W. Mamdouh, K.V. Gothelf, F. Besenbacher, J. Kjems, ACS Nano 2, 1213 (2008).

    Article  CAS  Google Scholar 

  26. S.M. Douglas, A.H. Marblestone, S. Teerapittayanon, A. Vazquez, G.M. Church, W.M. Shih, Nucleic Acids Res. 37, 5001 (2009).

    Article  CAS  Google Scholar 

  27. C.E. Castro, F. Kilchherr, D.-N. Kim, E.L. Shiao, T. Wauer, P. Wortmann, M. Bathe, H. Dietz, Nat. Methods 8, 221 (2011).

    Article  CAS  Google Scholar 

  28. J. Bath, A.J. Turberfield, Nat. Nanotechnol. 2, 275 (2007).

    Article  CAS  Google Scholar 

  29. S. Surana, J.M. Bhat, S.P. Koushika, Y. Krishnan, Nat. Commun. 2, 340 (2011).

    Article  CAS  Google Scholar 

  30. C.D. Mao, W.Q. Sun, Z.Y. Shen, N.C. Seeman, Nature 397, 144 (1999).

    Article  CAS  Google Scholar 

  31. A.D. Ellington, J.W. Szostak, Nature 346, 818 (1990).

    Article  Google Scholar 

  32. H. Asanuma, T. Ito, T. Yoshida, X.G. Liang, M. Komiyama, Angew. Chem. Int. Ed. Engl. 38, 2393 (1999).

    Article  Google Scholar 

  33. P. Yin, H. Yan, X.G. Daniell, A.J. Turberfield, J.H. Reif, Angew. Chem. Int. Ed. Engl. 43, 4906 (2004).

    Article  CAS  Google Scholar 

  34. M.N. Stojanovic, D. Stefanovic, Nat. Biotechnol. 21, 1069 (2003).

    Article  CAS  Google Scholar 

  35. Y. Benenson, B. Gil, U. Ben-Dor, R. Adar, E. Shapiro, Nature 429, 423 (2004).

    Article  CAS  Google Scholar 

  36. T. Liedl, F.C. Simmel, Nano Lett. 5, 1894 (2005).

    Article  CAS  Google Scholar 

  37. B. Yurke, A.J. Turberfield, A.P. Mills, F.C. Simmel, J.L. Neumann, Nature 406, 605 (2000).

    Article  CAS  Google Scholar 

  38. N. Srinivas, T.E. Ouldridge, P. Sulc, J.M. Schaeffer, B. Yurke, A.A. Louis, J.P. Doye, E. Winfree, Nucleic Acids Res. 41, 10641 (2013).

    Article  CAS  Google Scholar 

  39. L. Qian, E. Winfree, Science 332, 1196 (2011).

    Article  CAS  Google Scholar 

  40. A.J. Turberfield, J.C. Mitchell, B. Yurke, A.P. Mills, M.I. Blakey, F.C. Simmel, Phys. Rev. Lett. 90, 118102 (2003).

    Article  CAS  Google Scholar 

  41. J. Bath, S.J. Green, A.J. Turberfield, Angew. Chem. Int. Ed. Engl. 44, 4358 (2005).

    Article  CAS  Google Scholar 

  42. Y. Tian, Y. He, Y. Chen, P. Yin, C.D. Mao, Angew. Chem. Int. Ed. Engl. 44, 4355 (2005).

    Article  CAS  Google Scholar 

  43. M.X. You, Y. Chen, X.B. Zhang, H.P. Liu, R.W. Wang, K.L. Wang, K.R. Williams, W.H. Tan, Angew. Chem. Int. Ed. Engl. 51, 2457 (2012).

    Article  CAS  Google Scholar 

  44. Y. He, D.R. Liu, Nat. Nanotechnol. 5, 778 (2010).

    Article  CAS  Google Scholar 

  45. S.M. Douglas, I. Bachelet, G.M. Church, Science 335, 831 (2012).

    Article  CAS  Google Scholar 

  46. H. Asanuma, X. Liang, H. Nishioka, D. Matsunaga, M. Liu, M. Komiyama, Nat. Protoc. 2, 203 (2007).

    Article  CAS  Google Scholar 

  47. C. Bustamante, S.B. Smith, J. Liphardt, D. Smith, Curr. Opin. Struct. Biol. 10, 279 (2000).

    Article  Google Scholar 

  48. Y.J. Kim, D.N. Kim, PloS One 11, e0153228 (2016).

    Article  CAS  Google Scholar 

  49. C.E. Castro, H.J. Su, A.E. Marras, L. Zhou, J. Johnson, Nanoscale 7, 5913 (2015).

    Article  Google Scholar 

  50. L. Zhou, A.E. Marras, H.J. Su, C.E. Castro, ACS Nano 8, 27 (2013).

    Article  CAS  Google Scholar 

  51. L. Zhou, A.E. Marras, C.E. Castro, H.-J. Su, J. Mech. Robot. 8, 051013 (2016).

    Article  Google Scholar 

  52. A.E. Marras, L. Zhou, H.J. Su, C.E. Castro, Proc. Natl. Acad. Sci. U.S.A. 112, 713 (2015).

    Article  CAS  Google Scholar 

  53. L. Zhou, A.E. Marras, H.J. Su, C.E. Castro, Nano Lett. 15, 1815 (2015).

    Article  CAS  Google Scholar 

  54. M.W. Hudoba, Y. Luo, A. Zacharias, M.G. Poirier, C.E. Castro, ACS Nano 11, 6566 (2017).

    Article  CAS  Google Scholar 

  55. J. Song, Z. Li, P. Wang, T. Meyer, C. Mao, Y. Ke, Science 357 (2017).

  56. J. Pan, F. Li, T.G. Cha, H. Chen, J.H. Choi, Curr. Opin. Biotechnol. 34, 56 (2015).

    Article  CAS  Google Scholar 

  57. T. Omabegho, R. Sha, N.C. Seeman, Science 324, 67 (2009).

    Article  CAS  Google Scholar 

  58. T.G. Cha, J. Pan, H. Chen, J. Salgado, X. Li, C. Mao, J.H. Choi, Nat. Nanotechnol. 9, 39 (2014).

    Article  CAS  Google Scholar 

  59. S.F. Wickham, J. Bath, Y. Katsuda, M. Endo, K. Hidaka, H. Sugiyama, A.J. Turberfield, Nat. Nanotechnol. 7, 169 (2012).

    Article  CAS  Google Scholar 

  60. P. Ketterer, E.M. Willner, H. Dietz, Sci. Adv. 2, e1501209 (2016).

    Article  CAS  Google Scholar 

  61. T. Liedl, B. Hogberg, J. Tytell, D.E. Ingber, W.M. Shih, Nat. Nanotechnol. 5, 520 (2010).

    Article  CAS  Google Scholar 

  62. J. Bauer, L.R. Meza, T.A. Schaedler, R. Schwaiger, X. Zheng, L. Valdevit, Adv. Mater. 29, 1701850 (2017).

    Article  CAS  Google Scholar 

  63. G. Tikhomirov, P. Petersen, L. Qian, Nat. Nanotechnol. 12, 251 (2017).

    Article  CAS  Google Scholar 

  64. L.M. Adleman, Science 266, 1021 (1994).

    Article  Google Scholar 

  65. S.X. Chen, G. Seelig, J. Am. Chem. Soc. 138, 5076 (2016).

    Article  CAS  Google Scholar 

  66. V. Bhalla, R.P. Bajpai, L.M. Bharadwaj, EMBO Rep. 4, 442 (2003).

    Article  CAS  Google Scholar 

  67. Y.J. Chen, N. Dalchau, N. Srinivas, A. Phillips, L. Cardelli, D. Soloveichik, G. Seelig, Nat. Nanotechnol. 8, 755 (2013).

    Article  CAS  Google Scholar 

  68. L. Qian, E. Winfree, J. Bruck, Nature 475, 368 (2011).

    Article  CAS  Google Scholar 

  69. D.Y. Zhang, G. Seelig, Nat. Chem. 3, 103 (2011).

    Article  CAS  Google Scholar 

  70. G. Chatterjee, N. Dalchau, R.A. Muscat, A. Phillips, G. Seelig, Nat. Nanotechnol. 12, 920 (2017).

    Article  CAS  Google Scholar 

  71. N. Dalchau, H. Chandran, N. Gopalkrishnan, A. Phillips, J. Reif, ACS Synth. Biol. 4, 898 (2015).

    Article  CAS  Google Scholar 

  72. I.R. Epstein, B. Xu, Nat. Nanotechnol. 11, 312 (2016).

    Article  CAS  Google Scholar 

  73. S.M. Chirieleison, P.B. Allen, Z.B. Simpson, A.D. Ellington, X. Chen, Nat. Chem. 5, 1000 (2013).

    Article  CAS  Google Scholar 

  74. A.S. Zadorin, Y. Rondelez, J.-C. Galas, A. Estevez-Torres, Phys. Rev. Lett. 114, 068301 (2015).

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Wallace H. Coulter Department of Biomedical Engineering, Emory University, and Georgia Institute of Technology, USA

    Pengfei Wang & Yonggang Ke

  2. Department of Electrical Engineering, University of Washington, USA

    Gourab Chatterjee

  3. School of Molecular Sciences, Biodesign Institute, Arizona State University, USA

    Hao Yan

  4. North Carolina State University, USA

    Thomas H. LaBean

  5. Department of Physics, University of Oxford, UK

    Andrew J. Turberfield

  6. Department of Mechanical and Aerospace Engineering, The Ohio State University, USA

    Carlos E. Castro

  7. Paul G. Allen School of Computer Science & Engineering, and Department of Electrical Engineering, University of Washington, USA

    Georg Seelig

Authors
  1. Pengfei Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Gourab Chatterjee
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Hao Yan
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Thomas H. LaBean
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Andrew J. Turberfield
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Carlos E. Castro
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Georg Seelig
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Yonggang Ke
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Pengfei Wang.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wang, P., Chatterjee, G., Yan, H. et al. Practical aspects of structural and dynamic DNA nanotechnology. MRS Bulletin 42, 889–896 (2017). https://doi.org/10.1557/mrs.2017.272

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1557/mrs.2017.272

Search

Navigation