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Nanometrology and super-resolution imaging with DNA

  • DNA Nanotechnology: A Foundation for Programmable Nanoscale Materials
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Abstract

Structural DNA nanotechnology is revolutionizing the ways researchers construct arbitrary shapes and patterns in two and three dimensions on the nanoscale. Through Watson–Crick base pairing, DNA can be programmed to form nanostructures with high predictability, addressability, and yield. The ease with which structures can be designed and created has generated great interest for using DNA for a variety of metrology applications, such as in scanning probe microscopy and super-resolution imaging. An additional advantage of the programmable nature of DNA is that mechanisms for nanoscale metrology of the structures can be integrated within the DNA objects by design. This programmable structure–property relationship provides a powerful tool for developing nanoscale materials and smart rulers.

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References

  1. C. Wessner, Public/Private Partnerships for Innovation: Experiences and Perspectives from the U.S. (National Academy of Sciences, 2001), www.oecd.org/sti/inno/2730122.pdf.

  2. G. Satell, Harvard Business Review (2016), https://hbr.org/2016/06/technologyprogresses-when-business-government-and-academia-work-together.

  3. NSTC Commitee on Technology, Subcommitee of Nanoscale Science, Engineering, and Technology, Sustainable Nanomanufacturing—Creating the Industries of the Future (NSET, 2010), www.nano.gov//node/611.

  4. V. Zhrinov, Semiconductor Synthetic Biology (Semiconductor Research Corporation, 2017), www.src.org/program/grc/semisynbio.

  5. N.C. Seeman, Annu. Rev. Biochem. 79, 65 (2010).

    Article  CAS  Google Scholar 

  6. R.K. Leach, J. Claverley, C. Giusca, C.W. Jones, L. Nimishakavi, W.J. Sun, M. Tedaldi, A. Yacoot, Meas. Sci. Technol. 23, 074002 (2012).

    Article  Google Scholar 

  7. A. Rajendran, M. Endo, Y. Katsuda, K. Hidaka, H. Sugiyama, ACS Nano 5, 665 (2011).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  9. W. Liu, H. Zhong, R. Wang, N.C. Seeman, Angew. Chem. Int. Ed. Engl. 50, 264 (2011).

    Article  CAS  Google Scholar 

  10. S. Woo, P.W.K. Rothemund, Nat. Chem. 3, 620 (2011).

    Article  CAS  Google Scholar 

  11. A. Aghebat Rafat, T. Pirzer, M.B. Scheible, A. Kostina, F.C. Simmel, Angew. Chem. Int. Ed. Engl. 53, 7665 (2014).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  13. S. Woo, P.W.K. Rothemund, Nat. Commun. 5, 4889 (2014).

    Article  CAS  Google Scholar 

  14. Y. Suzuki, M. Endo, H. Sugiyama, Nat. Commun. 6, 8052 (2015).

    Article  CAS  Google Scholar 

  15. 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 

  16. J. Hahn, S.F. Wickham, W.M. Shih, S.D. Perrault, ACS Nano 8, 8765 (2014).

    Article  CAS  Google Scholar 

  17. H. Kim, S.P. Surwade, A. Powell, C. O’Donnell, H.T. Liu, Chem. Mater. 26, 5265 (2014).

    Article  CAS  Google Scholar 

  18. H. Auvinen, H.B. Zhang, Nonappa, A. Kopilow, E.H. Niemelä, S. Nummelin, A. Correia, H.A. Santos, V. Linko, M.A. Kostiainen, Adv. Healthc. Mater. 6, 1700692 (2017).

    Article  CAS  Google Scholar 

  19. N. Ponnuswamy, M.M.C. Bastings, B. Nathwani, J.H. Ryu, L.Y.T. Chou, M. Vinther, W.A. Li, F.M. Anastassacos, D.J. Mooney, W.M. Shih, Nat. Commun. 8, 15654 (2017).

    Article  CAS  Google Scholar 

  20. V. Korpelainen, V. Linko, J. Seppä, A. Lassila, M.A. Kostiainen, Meas. Sci. Technol. 28, 034001 (2017).

    Article  CAS  Google Scholar 

  21. X.C. Bai, T.G. Martin, S.H.W. Schemers, H. Dietz, Proc. Natl. Acad. Sci. U.S.A. 109, 20012 (2012).

    Article  Google Scholar 

  22. V. Linko, B. Shen, K. Tapio, J.J. Toppari, M.A. Kostiainen, S. Tuukkanen, Sci. Rep. 5, 15634 (2015).

    Article  CAS  Google Scholar 

  23. J. Seppä, V. Korpelainen, S. Bergstrand, H. Karlsson, L. Lillepea, A. Lassila, Meas. Sci. Technol. 25, 044013 (2014).

    Article  CAS  Google Scholar 

  24. S.W. Hell, S.J. Sahl, M. Bates, X.W. Zhuang, R. Heintzmann, M.J. Booth, J. Bewersdorf, G. Shtengel, H. Hess, P. Tinnefeld, A. Honigmann, S. Jakobs, I. Testa, L. Cognet, B. Lounis, H. Ewers, S.J. Davis, C. Eggeling, D. Klenerman, K.I. Willig, G. Vicidomini, M. Castello, A. Diaspro, T. Cordes, J. Phys. D Appl. Phys. 48, 443001 (2015).

    Article  CAS  Google Scholar 

  25. R. Jungmann, M. Scheible, F.C. Simmel, Wiley Interdiscip. Rev. Nanomed. Nanobiotechnol. 4, 66 (2012).

    Article  CAS  Google Scholar 

  26. M.J. Rust, M. Bates, X. Zhuang, Nat. Methods 3, 793 (2006).

    Article  CAS  Google Scholar 

  27. E. Betzig, G.H. Patterson, R. Sougrat, O.W. Lindwasser, S. Olenych, J.S. Bonifacino, M.W. Davidson, J. Lippincott-Schwartz, H.F. Hess, Science 313, 1642 (2006).

    Article  Google Scholar 

  28. A. Sharonov, R.M. Hochstrasser, Proc. Natl. Acad. Sci. U.S.A. 103, 18911 (2006).

    Article  CAS  Google Scholar 

  29. R. Jungmann, C. Steinhauer, M. Scheible, A. Kuzyk, P. Tinnefeld, F.C. Simmel, Nano Lett. 10, 4756 (2010).

    Article  CAS  Google Scholar 

  30. J. Schnitzbauer, M.T. Strauss, T. Schlichthaerle, F. Schueder, R. Jungmann, Nat. Protoc. 12, 1198 (2017).

    Article  CAS  Google Scholar 

  31. R. Jungmann, M.S. Avendano, J.B. Woehrstein, M. Dai, W.M. Shih, P. Yin, Nat. Methods 11, 313 (2014).

    Article  CAS  Google Scholar 

  32. M. Dai, R. Jungmann, P. Yin, Nat. Nanotechnol. 11, 798 (2016).

    Article  CAS  Google Scholar 

  33. C. Lin, R. Jungmann, A.M. Leifer, C. Li, D. Levner, G.M. Church, W.M. Shih, P. Yin, Nat. Chem. 4, 832 (2012).

    Article  CAS  Google Scholar 

  34. C. Steinhauer, R. Jungmann, T.L. Sobey, F.C. Simmel, P. Tinnefeld, Angew. Chem. Int. Ed. Engl. 48, 8870 (2009).

    Article  CAS  Google Scholar 

  35. http://www.gattaquant.com.

  36. J.J. Schmied, C. Forthmann, E. Pibiri, B. Lalkens, P. Nickels, T. Liedl, P. Tinnefeld, Nano Lett. 13, 781 (2013).

    Article  CAS  Google Scholar 

  37. J.J. Schmied, A. Gietl, P. Holzmeister, C. Forthmann, C. Steinhauer, T. Dammeyer, P. Tinnefeld, Nat. Methods 9, 1133 (2012).

    Article  CAS  Google Scholar 

  38. J.B. Woehrstein, M.T. Strauss, L.L. Ong, B. Wei, D.Y. Zhang, R. Jungmann, P. Yin, Sci. Adv. 3, e1602128 (2017).

    Article  CAS  Google Scholar 

  39. R. Jungmann, M.S. Avendano, M. Dai, J.B. Woehrstein, S.S. Agasti, Z. Feiger, A. Rodal, P. Yin, Nat. Methods 13, 439 (2016).

    Article  CAS  Google Scholar 

  40. H. Ta, J. Keller, M. Haltmeier, S.K. Saka, J. Schmied, F. Opazo, P. Tinnefeld, A. Munk, S.W. Hell, Nat. Commun. 6, 7977 (2015).

    Article  CAS  Google Scholar 

  41. S.C. Sidenstein, E. D’Este, M.J. Bohm, J.G. Danzl, V.N. Belov, S.W. Hell, Sci. Rep. 6, 26725 (2016).

    Article  CAS  Google Scholar 

  42. F. Balzarotti, Y. Eilers, K.C. Gwosch, A.H. Gynna, V. Westphal, F.D. Stefani, J. Elf, S.W. Hell, Science 355, 606 (2017).

    Article  CAS  Google Scholar 

  43. F. Gottfert, T. Pleiner, J. Heine, V. Westphal, D. Gorlich, S.J. Sahl, S.W. Hell, Proc. Natl. Acad. Sci. U.S.A. 114, 2125 (2017).

    Article  CAS  Google Scholar 

  44. P.D. Odermatt, A. Shivanandan, H. Deschout, R. Jankele, A.P. Nievergelt, L. Feletti, M.W. Davidson, A. Radenovic, G.E. Fantner, Nano Lett. 15, 4896 (2015).

    Article  CAS  Google Scholar 

  45. A. Monserrate, S. Casado, C. Flors, ChemPhysChem. 15, 647 (2014).

    Article  CAS  Google Scholar 

  46. P. Bondia, R. Jurado, S. Casado, J.M. Dominguez-Vera, N. Galvez, C. Flors, Small 13, 1603784 (2017).

    Article  CAS  Google Scholar 

  47. M. Nagase, H. Namatsu, K. Kurihara, K. Iwadate, K. Murase, Jpn. J. Appl. Phys. Pt. 1 34, 3382 (1995).

    Article  Google Scholar 

  48. M. Strauss, A. Genc, G. Dutrow, D.N. Horspool, L.A. Dworkin, Proc. 23rd Annu. SEMI Adv. Semicond. Manuf. Conf.–ASMC 2012 (Saratoga Springs, NY, 2012), p. 88.

  49. C.G. Frase, E. Buhr, K. Dirscherl, Meas. Sci. Technol. 18, 510 (2007).

    Article  CAS  Google Scholar 

  50. D.K. Bowen, B.K. Tanner, X-Ray Metrology in Semiconductor Manufacturing (Taylor & Francis, Boca Raton, FL, 2006).

  51. C.M. Green, K. Schutt, N. Morris, R.M. Zadegan, W.L. Hughes, W. Kuang, E. Graugnard, Nanoscale 9, 10205 (2017).

    Article  Google Scholar 

  52. R.J. Kershner, L.D. Bozano, C.M. Micheel, A.M. Hung, A.R. Fornof, J.N. Cha, C.T. Rettner, M. Bersani, J. Frommer, P.W.K. Rothemund, G.M. Wallraff, Nat. Nanotechnol. 4, 557 (2009).

    Article  CAS  Google Scholar 

  53. A. Gopinath, P.W.K. Rothemund, ACS Nano 8, 12030 (2014).

    Article  CAS  Google Scholar 

  54. D.N. Kim, F. Kilchherr, H. Dietz, M. Bathe, Nucleic Acids Res. 40, 2862 (2012).

    Article  CAS  Google Scholar 

  55. 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 

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

    Article  CAS  Google Scholar 

  57. R. Veneziano, S. Ratanalert, K. Zhang, F. Zhang, H. Yan, W. Chiu, M. Bathe, Science 352, 1534 (2016).

    Article  CAS  Google Scholar 

  58. V. Linko, M.A. Kostiainen, Nat. Biotechnol. 34, 826 (2016).

    Article  CAS  Google Scholar 

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Acknowledgements

E.G. and W.L.H. acknowledge the National Science Foundation Scalable NanoManufacturing Program (CMMI-1344915) and the Micron Foundation. W.L.H also acknowledges the National Institute of General Medical Sciences of the National Institutes of Health (K25GM093233). M.A.K. acknowledges the Academy of Finland (Project Number 308578). V.L. acknowledges the Academy of Finland (Project Number 286845) and the Jane and Aatos Erkko Foundation. R.J. acknowledges support by the Deutsche Forschungsgemeinschaft (DFG) through the Emmy Noether Program (DFG JU 2957/1–1), the Collaborative Research Center 1032 (Nanoagents for the spatiotemporal control of molecular and cellular reactions), the European Research Council (ERC) through an ERC Starting Grant (MolMap, Grant Agreement Number 680241), the Max Planck Society, the Max Planck Foundation, and the Center for Nanoscience.

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Correspondence to Elton Graugnard.

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Graugnard, E., Hughes, W.L., Jungmann, R. et al. Nanometrology and super-resolution imaging with DNA. MRS Bulletin 42, 951–958 (2017). https://doi.org/10.1557/mrs.2017.274

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