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
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.
G. Satell, Harvard Business Review (2016), https://hbr.org/2016/06/technologyprogresses-when-business-government-and-academia-work-together.
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.
V. Zhrinov, Semiconductor Synthetic Biology (Semiconductor Research Corporation, 2017), www.src.org/program/grc/semisynbio.
N.C. Seeman, Annu. Rev. Biochem. 79, 65 (2010).
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).
A. Rajendran, M. Endo, Y. Katsuda, K. Hidaka, H. Sugiyama, ACS Nano 5, 665 (2011).
G. Tikhomirov, P. Petersen, L. Qian, Nat. Nanotechnol. 12, 251 (2017).
W. Liu, H. Zhong, R. Wang, N.C. Seeman, Angew. Chem. Int. Ed. Engl. 50, 264 (2011).
S. Woo, P.W.K. Rothemund, Nat. Chem. 3, 620 (2011).
A. Aghebat Rafat, T. Pirzer, M.B. Scheible, A. Kostina, F.C. Simmel, Angew. Chem. Int. Ed. Engl. 53, 7665 (2014).
T. Gerling, K.F. Wagenbauer, A.M. Neuner, H. Dietz, Science 347, 1446 (2015).
S. Woo, P.W.K. Rothemund, Nat. Commun. 5, 4889 (2014).
Y. Suzuki, M. Endo, H. Sugiyama, Nat. Commun. 6, 8052 (2015).
C.E. Castro, F. Kilchherr, D.N. Kim, E.L. Shiao, T. Wauer, P. Wortmann, M. Bathe, H. Dietz, Nat. Methods 8, 221 (2011).
J. Hahn, S.F. Wickham, W.M. Shih, S.D. Perrault, ACS Nano 8, 8765 (2014).
H. Kim, S.P. Surwade, A. Powell, C. O’Donnell, H.T. Liu, Chem. Mater. 26, 5265 (2014).
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).
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).
V. Korpelainen, V. Linko, J. Seppä, A. Lassila, M.A. Kostiainen, Meas. Sci. Technol. 28, 034001 (2017).
X.C. Bai, T.G. Martin, S.H.W. Schemers, H. Dietz, Proc. Natl. Acad. Sci. U.S.A. 109, 20012 (2012).
V. Linko, B. Shen, K. Tapio, J.J. Toppari, M.A. Kostiainen, S. Tuukkanen, Sci. Rep. 5, 15634 (2015).
J. Seppä, V. Korpelainen, S. Bergstrand, H. Karlsson, L. Lillepea, A. Lassila, Meas. Sci. Technol. 25, 044013 (2014).
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).
R. Jungmann, M. Scheible, F.C. Simmel, Wiley Interdiscip. Rev. Nanomed. Nanobiotechnol. 4, 66 (2012).
M.J. Rust, M. Bates, X. Zhuang, Nat. Methods 3, 793 (2006).
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).
A. Sharonov, R.M. Hochstrasser, Proc. Natl. Acad. Sci. U.S.A. 103, 18911 (2006).
R. Jungmann, C. Steinhauer, M. Scheible, A. Kuzyk, P. Tinnefeld, F.C. Simmel, Nano Lett. 10, 4756 (2010).
J. Schnitzbauer, M.T. Strauss, T. Schlichthaerle, F. Schueder, R. Jungmann, Nat. Protoc. 12, 1198 (2017).
R. Jungmann, M.S. Avendano, J.B. Woehrstein, M. Dai, W.M. Shih, P. Yin, Nat. Methods 11, 313 (2014).
M. Dai, R. Jungmann, P. Yin, Nat. Nanotechnol. 11, 798 (2016).
C. Lin, R. Jungmann, A.M. Leifer, C. Li, D. Levner, G.M. Church, W.M. Shih, P. Yin, Nat. Chem. 4, 832 (2012).
C. Steinhauer, R. Jungmann, T.L. Sobey, F.C. Simmel, P. Tinnefeld, Angew. Chem. Int. Ed. Engl. 48, 8870 (2009).
J.J. Schmied, C. Forthmann, E. Pibiri, B. Lalkens, P. Nickels, T. Liedl, P. Tinnefeld, Nano Lett. 13, 781 (2013).
J.J. Schmied, A. Gietl, P. Holzmeister, C. Forthmann, C. Steinhauer, T. Dammeyer, P. Tinnefeld, Nat. Methods 9, 1133 (2012).
J.B. Woehrstein, M.T. Strauss, L.L. Ong, B. Wei, D.Y. Zhang, R. Jungmann, P. Yin, Sci. Adv. 3, e1602128 (2017).
R. Jungmann, M.S. Avendano, M. Dai, J.B. Woehrstein, S.S. Agasti, Z. Feiger, A. Rodal, P. Yin, Nat. Methods 13, 439 (2016).
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).
S.C. Sidenstein, E. D’Este, M.J. Bohm, J.G. Danzl, V.N. Belov, S.W. Hell, Sci. Rep. 6, 26725 (2016).
F. Balzarotti, Y. Eilers, K.C. Gwosch, A.H. Gynna, V. Westphal, F.D. Stefani, J. Elf, S.W. Hell, Science 355, 606 (2017).
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).
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).
A. Monserrate, S. Casado, C. Flors, ChemPhysChem. 15, 647 (2014).
P. Bondia, R. Jurado, S. Casado, J.M. Dominguez-Vera, N. Galvez, C. Flors, Small 13, 1603784 (2017).
M. Nagase, H. Namatsu, K. Kurihara, K. Iwadate, K. Murase, Jpn. J. Appl. Phys. Pt. 1 34, 3382 (1995).
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.
C.G. Frase, E. Buhr, K. Dirscherl, Meas. Sci. Technol. 18, 510 (2007).
D.K. Bowen, B.K. Tanner, X-Ray Metrology in Semiconductor Manufacturing (Taylor & Francis, Boca Raton, FL, 2006).
C.M. Green, K. Schutt, N. Morris, R.M. Zadegan, W.L. Hughes, W. Kuang, E. Graugnard, Nanoscale 9, 10205 (2017).
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).
A. Gopinath, P.W.K. Rothemund, ACS Nano 8, 12030 (2014).
D.N. Kim, F. Kilchherr, H. Dietz, M. Bathe, Nucleic Acids Res. 40, 2862 (2012).
S.M. Douglas, A.H. Marblestone, S. Teerapittayanon, A. Vazquez, G.M. Church, W.M. Shih, Nucleic Acids Res. 37, 5001 (2009).
E. Benson, A. Mohammed, J. Gardell, S. Masich, E. Czeizler, P. Orponen, B. Högberg, Nature 523, 441 (2015).
R. Veneziano, S. Ratanalert, K. Zhang, F. Zhang, H. Yan, W. Chiu, M. Bathe, Science 352, 1534 (2016).
V. Linko, M.A. Kostiainen, Nat. Biotechnol. 34, 826 (2016).
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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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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DOI: https://doi.org/10.1557/mrs.2017.274