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Nanometrology and super-resolution imaging with DNA

Published online by Cambridge University Press:  08 December 2017

Elton Graugnard ,
William L. Hughes ,
Ralf Jungmann ,
Mauri A. Kostiainen  and
Veikko Linko
Elton Graugnard
Affiliation:
Micron School of Materials Science & Engineering, Boise State University, USA; eltongraugnard@boisestate.edu
William L. Hughes
Affiliation:
Micron School of Materials Science & Engineering, Boise State University, USA; willhughes@boisestate.edu
Ralf Jungmann
Affiliation:
Ludwig Maximilian University Munich, Max Planck Institute of Biochemistry, Germany; jungmann@biochem.mpg.de
Mauri A. Kostiainen
Affiliation:
School of Chemical Engineering, Aalto University, Finland; mauri.kostiainen@aalto.fi
Veikko Linko
Affiliation:
School of Chemical Engineering, Aalto University, Finland; veikko.linko@aalto.fi
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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.

Type
Research Article
Information
MRS Bulletin , Volume 42 , Issue 12: DNA Nanotechnology: A foundation for Programmable Nanoscale Materials , December 2017 , pp. 951 - 959
Copyright
Copyright © Materials Research Society 2017 

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References

Wessner, C., Public/Private Partnerships for Innovation: Experiences and Perspectives from the U.S. (National Academy of Sciences, 2001), www.oecd.org/sti/inno/2730122.pdf.Google Scholar
Satell, G., Harvard Business Review (2016), https://hbr.org/2016/06/technology-progresses-when-business-government-and-academia-work-together.Google Scholar
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.Google Scholar
Zhrinov, V., Semiconductor Synthetic Biology (Semiconductor Research Corporation, 2017), www.src.org/program/grc/semisynbio.Google Scholar
Seeman, N.C., Annu. Rev. Biochem. 79, 65 (2010).Google Scholar
Leach, R.K., Claverley, J., Giusca, C., Jones, C.W., Nimishakavi, L., Sun, W.J., Tedaldi, M., Yacoot, A., Meas. Sci. Technol. 23, 074002 (2012).Google Scholar
Rajendran, A., Endo, M., Katsuda, Y., Hidaka, K., Sugiyama, H., ACS Nano 5, 665 (2011).CrossRefGoogle Scholar
Tikhomirov, G., Petersen, P., Qian, L., Nat. Nanotechnol. 12, 251 (2017).CrossRefGoogle Scholar
Liu, W., Zhong, H., Wang, R., Seeman, N.C., Angew. Chem. Int. Ed. Engl. 50, 264 (2011).CrossRefGoogle Scholar
Woo, S., Rothemund, P.W.K., Nat. Chem. 3, 620 (2011).Google Scholar
Aghebat Rafat, A., Pirzer, T., Scheible, M.B., Kostina, A., Simmel, F.C., Angew. Chem. Int. Ed. Engl. 53, 7665 (2014).Google Scholar
Gerling, T., Wagenbauer, K.F., Neuner, A.M., Dietz, H., Science 347, 1446 (2015).Google Scholar
Woo, S., Rothemund, P.W.K., Nat. Commun. 5, 4889 (2014).Google Scholar
Suzuki, Y., Endo, M., Sugiyama, H., Nat. Commun. 6, 8052 (2015).Google Scholar
Castro, C.E., Kilchherr, F., Kim, D.N., Shiao, E.L., Wauer, T., Wortmann, P., Bathe, M., Dietz, H., Nat. Methods 8, 221 (2011).CrossRefGoogle Scholar
Hahn, J., Wickham, S.F., Shih, W.M., Perrault, S.D., ACS Nano 8, 8765 (2014).Google Scholar
Kim, H., Surwade, S.P., Powell, A., O’Donnell, C., Liu, H.T., Chem. Mater. 26, 5265 (2014).Google Scholar
Auvinen, H., Zhang, H.B., Nonappa, , Kopilow, A., Niemelä, E.H., Nummelin, S., Correia, A., Santos, H.A., Linko, V., Kostiainen, M.A., Adv. Healthc. Mater. 6, 1700692 (2017).Google Scholar
Ponnuswamy, N., Bastings, M.M.C., Nathwani, B., Ryu, J.H., Chou, L.Y.T., Vinther, M., Li, W.A., Anastassacos, F.M., Mooney, D.J., Shih, W.M., Nat. Commun. 8, 15654 (2017).Google Scholar
Korpelainen, V., Linko, V., Seppä, J., Lassila, A., Kostiainen, M.A., Meas. Sci. Technol. 28, 034001 (2017).Google Scholar
Bai, X.C., Martin, T.G., Schemers, S.H.W., Dietz, H., Proc. Natl. Acad. Sci. U.S.A. 109, 20012 (2012).Google Scholar
Linko, V., Shen, B., Tapio, K., Toppari, J.J., Kostiainen, M.A., Tuukkanen, S., Sci. Rep. 5, 15634 (2015).Google Scholar
Seppä, J., Korpelainen, V., Bergstrand, S., Karlsson, H., Lillepea, L., Lassila, A., Meas. Sci. Technol. 25, 044013 (2014).Google Scholar
Hell, S.W., Sahl, S.J., Bates, M., Zhuang, X.W., Heintzmann, R., Booth, M.J., Bewersdorf, J., Shtengel, G., Hess, H., Tinnefeld, P., Honigmann, A., Jakobs, S., Testa, I., Cognet, L., Lounis, B., Ewers, H., Davis, S.J., Eggeling, C., Klenerman, D., Willig, K.I., Vicidomini, G., Castello, M., Diaspro, A., Cordes, T., J. Phys. D Appl. Phys. 48, 443001 (2015).Google Scholar
Jungmann, R., Scheible, M., Simmel, F.C., Wiley Interdiscip. Rev. Nanomed. Nanobiotechnol. 4, 66 (2012).Google Scholar
Rust, M.J., Bates, M., Zhuang, X., Nat. Methods 3, 793 (2006).Google Scholar
Betzig, E., Patterson, G.H., Sougrat, R., Lindwasser, O.W., Olenych, S., Bonifacino, J.S., Davidson, M.W., Lippincott-Schwartz, J., Hess, H.F., Science 313, 1642 (2006).Google Scholar
Sharonov, A., Hochstrasser, R.M., Proc. Natl. Acad. Sci. U.S.A. 103, 18911 (2006).Google Scholar
Jungmann, R., Steinhauer, C., Scheible, M., Kuzyk, A., Tinnefeld, P., Simmel, F.C., Nano Lett. 10, 4756 (2010).Google Scholar
Schnitzbauer, J., Strauss, M.T., Schlichthaerle, T., Schueder, F., Jungmann, R., Nat. Protoc. 12, 1198 (2017).CrossRefGoogle Scholar
Jungmann, R., Avendano, M.S., Woehrstein, J.B., Dai, M., Shih, W.M., Yin, P., Nat. Methods 11, 313 (2014).CrossRefGoogle Scholar
Dai, M., Jungmann, R., Yin, P., Nat. Nanotechnol. 11, 798 (2016).Google Scholar
Lin, C., Jungmann, R., Leifer, A.M., Li, C., Levner, D., Church, G.M., Shih, W.M., Yin, P., Nat. Chem. 4, 832 (2012).CrossRefGoogle Scholar
Steinhauer, C., Jungmann, R., Sobey, T.L., Simmel, F.C., Tinnefeld, P., Angew. Chem. Int. Ed. Engl. 48, 8870 (2009).CrossRefGoogle Scholar
http://www.gattaquant.com.Google Scholar
Schmied, J.J., Forthmann, C., Pibiri, E., Lalkens, B., Nickels, P., Liedl, T., Tinnefeld, P., Nano Lett. 13, 781 (2013).Google Scholar
Schmied, J.J., Gietl, A., Holzmeister, P., Forthmann, C., Steinhauer, C., Dammeyer, T., Tinnefeld, P., Nat. Methods 9, 1133 (2012).Google Scholar
Woehrstein, J.B., Strauss, M.T., Ong, L.L., Wei, B., Zhang, D.Y., Jungmann, R., Yin, P., Sci. Adv. 3, e1602128 (2017).CrossRefGoogle Scholar
Jungmann, R., Avendano, M.S., Dai, M., Woehrstein, J.B., Agasti, S.S., Feiger, Z., Rodal, A., Yin, P., Nat. Methods 13, 439 (2016).Google Scholar
Ta, H., Keller, J., Haltmeier, M., Saka, S.K., Schmied, J., Opazo, F., Tinnefeld, P., Munk, A., Hell, S.W., Nat. Commun. 6, 7977 (2015).Google Scholar
Sidenstein, S.C., D’Este, E., Bohm, M.J., Danzl, J.G., Belov, V.N., Hell, S.W., Sci. Rep. 6, 26725 (2016).CrossRefGoogle Scholar
Balzarotti, F., Eilers, Y., Gwosch, K.C., Gynna, A.H., Westphal, V., Stefani, F.D., Elf, J., Hell, S.W., Science 355, 606 (2017).Google Scholar
Gottfert, F., Pleiner, T., Heine, J., Westphal, V., Gorlich, D., Sahl, S.J., Hell, S.W., Proc. Natl. Acad. Sci. U.S.A. 114, 2125 (2017).Google Scholar
Odermatt, P.D., Shivanandan, A., Deschout, H., Jankele, R., Nievergelt, A.P., Feletti, L., Davidson, M.W., Radenovic, A., Fantner, G.E., Nano Lett. 15, 4896 (2015).CrossRefGoogle Scholar
Monserrate, A., Casado, S., Flors, C., ChemPhysChem. 15, 647 (2014).Google Scholar
Bondia, P., Jurado, R., Casado, S., Dominguez-Vera, J.M., Galvez, N., Flors, C., Small 13, 1603784 (2017).Google Scholar
Nagase, M., Namatsu, H., Kurihara, K., Iwadate, K., Murase, K., Jpn. J. Appl. Phys. Pt. 1 34, 3382 (1995).CrossRefGoogle Scholar
Strauss, M., Genc, A., Dutrow, G., Horspool, D.N., Dworkin, L.A., Proc. 23rd Annu. SEMI Adv. Semicond. Manuf. Conf.–ASMC 2012 (Saratoga Springs, NY, 2012), p. 88.Google Scholar
Frase, C.G., Buhr, E., Dirscherl, K., Meas. Sci. Technol. 18, 510 (2007).Google Scholar
Bowen, D.K., Tanner, B.K., X-Ray Metrology in Semiconductor Manufacturing (Taylor & Francis, Boca Raton, FL, 2006).Google Scholar
Green, C.M., Schutt, K., Morris, N., Zadegan, R.M., Hughes, W.L., Kuang, W., Graugnard, E., Nanoscale 9, 10205 (2017).CrossRefGoogle Scholar
Kershner, R.J., Bozano, L.D., Micheel, C.M., Hung, A.M., Fornof, A.R., Cha, J.N., Rettner, C.T., Bersani, M., Frommer, J., Rothemund, P.W.K., Wallraff, G.M., Nat. Nanotechnol. 4, 557 (2009).Google Scholar
Gopinath, A., Rothemund, P.W.K., ACS Nano 8, 12030 (2014).Google Scholar
Kim, D.N., Kilchherr, F., Dietz, H., Bathe, M., Nucleic Acids Res. 40, 2862 (2012).Google Scholar
Douglas, S.M., Marblestone, A.H., Teerapittayanon, S., Vazquez, A., Church, G.M., Shih, W.M., Nucleic Acids Res. 37, 5001 (2009).Google Scholar
Benson, E., Mohammed, A., Gardell, J., Masich, S., Czeizler, E., Orponen, P., Högberg, B., Nature 523, 441 (2015).Google Scholar
Veneziano, R., Ratanalert, S., Zhang, K., Zhang, F., Yan, H., Chiu, W., Bathe, M., Science 352, 1534 (2016).Google Scholar
Linko, V., Kostiainen, M.A., Nat. Biotechnol. 34, 826 (2016).CrossRefGoogle Scholar