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Practical aspects of structural and dynamic DNA nanotechnology

Published online by Cambridge University Press:  08 December 2017

Pengfei Wang
Affiliation:
Wallace H. Coulter Department of Biomedical Engineering, Emory University, and Georgia Institute of Technology, USA; pengfei.wang@emory.edu
Gourab Chatterjee
Affiliation:
Department of Electrical Engineering, University of Washington, USA; gourab@uw.edu
Hao Yan
Affiliation:
School of Molecular Sciences, Biodesign Institute, Arizona State University, USA; hao.yan@asu.edu
Thomas H. LaBean
Affiliation:
North Carolina State University, USA; thlabean@ncsu.edu
Andrew J. Turberfield
Affiliation:
Department of Physics, University of Oxford, UK; andrew.turberfield@physics.ox.ac.uk
Carlos E. Castro
Affiliation:
Department of Mechanical and Aerospace Engineering, The Ohio State University, USA; castro.39@osu.edu
Georg Seelig
Affiliation:
Paul G. Allen School of Computer Science & Engineering, and Department of Electrical Engineering, University of Washington, USA; gseelig@uw.edu
Yonggang Ke
Affiliation:
Wallace H. Coulter Department of Biomedical Engineering, Emory University, and Georgia Institute of Technology, USA; yonggang.ke@emory.edu
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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.

Type
Research Article
Copyright
Copyright © Materials Research Society 2017 

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References

Roh, Y.H., Ruiz, R.C., Peng, S., Lee, J.B., Luo, D., Chem. Soc. Rev. 40, 5730 (2011).
Strunz, T., Oroszlan, K., Schafer, R., Guntherodt, H.J., Proc. Natl. Acad. Sci. U.S.A. 96, 11277 (1999).
Wang, M.D., Yin, H., Landick, R., Gelles, J., Block, S.M., Biophys. J. 72, 1335 (1997).
Pedersen, R.O., Marchi, A.N., Majikes, J., Nash, J.A., Estrich, N.A., Courson, D.S., Hall, C.K., Craig, S.L., LaBean, T.H., in Handbook of Nanomaterials Properties, Bhushan, B., Luo, D., Schricker, S.R., Sigmund, W., Eds. (Springer, Berlin, 2014), p. 1125.
Seeman, N.C., Kallenbach, N.R., Biophys. J. 44, 201 (1983).
Fu, T.J., Seeman, N.C., Biochemistry 32, 3211 (1993).
He, Y., Chen, Y., Liu, H., Ribbe, A.E., Mao, C., J. Am. Chem. Soc. 127, 12202 (2005).
Wang, P., Wu, S., Tian, C., Yu, G., Jiang, W., Wang, G., Mao, C., J. Am. Chem. Soc. 138, 13579 (2016).
Zheng, J., Birktoft, J.J., Chen, Y., Wang, T., Sha, R., Constantinou, P.E., Ginell, S.L., Mao, C., Seeman, N.C., Nature 461, 74 (2009).
Zhang, F., Liu, Y., Yan, H., J. Am. Chem. Soc. 135, 7458 (2013).
Ke, Y.G., Ong, L.L., Shih, W.M., Yin, P., Science 338, 1177 (2012).
Wei, B., Dai, M.J., Yin, P., Nature 485, 623 (2012).
Ke, Y., Ong, L.L., Sun, W., Song, J., Dong, M., Shih, W.M., Yin, P., Nat. Chem. 6, 994 (2014).
Rothemund, P.W.K., Nature 440, 297 (2006).
Douglas, S.M., Dietz, H., Liedl, T., Hogberg, B., Graf, F., Shih, W.M., Nature 459, 414 (2009).
Ke, Y.G., Douglas, S.M., Liu, M.H., Sharma, J., Cheng, A.C., Leung, A., Liu, Y., Shih, W.M., Yan, H., J. Am. Chem. Soc. 131, 15903 (2009).
Ke, Y.G., Voigt, N.V., Gothelf, K.V., Shih, W.M., J. Am. Chem. Soc. 134, 1770 (2012).
Veneziano, R., Ratanalert, S., Zhang, K., Zhang, F., Yan, H., Chiu, W., Bathe, M., Science 352, 6293 (2016).
Benson, E., Mohammed, A., Gardell, J., Masich, S., Czeizler, E., Orponen, P., Hogberg, B., Nature 523, 441 (2015).
Marchi, A.N., Saaem, I., Vogen, B.N., Brown, S., LaBean, T.H., Nano Lett. 14, 5740 (2014).
Wang, P., Gaitanaros, S., Lee, S., Bathe, M., Shih, W.M., Ke, Y., J. Am. Chem. Soc. 138, 7733 (2016).
Gerling, T., Wagenbauer, K.F., Neuner, A.M., Dietz, H., Science 347, 1446 (2015).
Williams, S., Lund, K., Lin, C., Wonka, P., Lindsay, S., Yan, H., “Tiamat: A Three-Dimensional Editing Tool for Complex DNA Structures,” 14th Int. Mtg. DNA Comput., Yan, H., Goel, A., Simmel, F.C., Sosík, P., Eds. (Prague, Czech Republic, June 2–9, 2008), pp. 90101.
Zhu, J., Wei, B., Yuan, Y., Mi, Y., Nucleic Acids Res. 37, 2164 (2009).
Andersen, E.S., Dong, M., Nielsen, M.M., Jahn, K., Lind-Thomsen, A., Mamdouh, W., Gothelf, K.V., Besenbacher, F., Kjems, J., ACS Nano 2, 1213 (2008).
Douglas, S.M., Marblestone, A.H., Teerapittayanon, S., Vazquez, A., Church, G.M., Shih, W.M., Nucleic Acids Res. 37, 5001 (2009).
Castro, C.E., Kilchherr, F., Kim, D.-N., Shiao, E.L., Wauer, T., Wortmann, P., Bathe, M., Dietz, H., Nat. Methods 8, 221 (2011).
Bath, J., Turberfield, A.J., Nat. Nanotechnol. 2, 275 (2007).
Surana, S., Bhat, J.M., Koushika, S.P., Krishnan, Y., Nat. Commun. 2, 340 (2011).
Mao, C.D., Sun, W.Q., Shen, Z.Y., Seeman, N.C., Nature 397, 144 (1999).
Ellington, A.D., Szostak, J.W., Nature 346, 818 (1990).
Asanuma, H., Ito, T., Yoshida, T., Liang, X.G., Komiyama, M., Angew. Chem. Int. Ed. Engl. 38, 2393 (1999).
Yin, P., Yan, H., Daniell, X.G., Turberfield, A.J., Reif, J.H., Angew. Chem. Int. Ed. Engl. 43, 4906 (2004).
Stojanovic, M.N., Stefanovic, D., Nat. Biotechnol. 21, 1069 (2003).
Benenson, Y., Gil, B., Ben-Dor, U., Adar, R., Shapiro, E., Nature 429, 423 (2004).
Liedl, T., Simmel, F.C., Nano Lett. 5, 1894 (2005).
Yurke, B., Turberfield, A.J., Mills, A.P., Simmel, F.C., Neumann, J.L., Nature 406, 605 (2000).
Srinivas, N., Ouldridge, T.E., Sulc, P., Schaeffer, J.M., Yurke, B., Louis, A.A., Doye, J.P., Winfree, E., Nucleic Acids Res. 41, 10641 (2013).
Qian, L., Winfree, E., Science 332, 1196 (2011).
Turberfield, A.J., Mitchell, J.C., Yurke, B., Mills, A.P., Blakey, M.I., Simmel, F.C., Phys. Rev. Lett. 90, 118102 (2003).
Bath, J., Green, S.J., Turberfield, A.J., Angew. Chem. Int. Ed. Engl. 44, 4358 (2005).
Tian, Y., He, Y., Chen, Y., Yin, P., Mao, C.D., Angew. Chem. Int. Ed. Engl. 44, 4355 (2005).
You, M.X., Chen, Y., Zhang, X.B., Liu, H.P., Wang, R.W., Wang, K.L., Williams, K.R., Tan, W.H., Angew. Chem. Int. Ed. Engl. 51, 2457 (2012).
He, Y., Liu, D.R., Nat. Nanotechnol. 5, 778 (2010).
Douglas, S.M., Bachelet, I., Church, G.M., Science 335, 831 (2012).
Asanuma, H., Liang, X., Nishioka, H., Matsunaga, D., Liu, M., Komiyama, M., Nat. Protoc. 2, 203 (2007).
Bustamante, C., Smith, S.B., Liphardt, J., Smith, D., Curr. Opin. Struct. Biol. 10, 279 (2000).
Kim, Y.J., Kim, D.N., PloS One 11, e0153228 (2016).
Castro, C.E., Su, H.J., Marras, A.E., Zhou, L., Johnson, J., Nanoscale 7, 5913 (2015).
Zhou, L., Marras, A.E., Su, H.J., Castro, C.E., ACS Nano 8, 27 (2013).
Zhou, L., Marras, A.E., Castro, C.E., Su, H.-J., J. Mech. Robot. 8, 051013 (2016).
Marras, A.E., Zhou, L., Su, H.J., Castro, C.E., Proc. Natl. Acad. Sci. U.S.A. 112, 713 (2015).
Zhou, L., Marras, A.E., Su, H.J., Castro, C.E., Nano Lett. 15, 1815 (2015).
Hudoba, M.W., Luo, Y., Zacharias, A., Poirier, M.G., Castro, C.E., ACS Nano 11, 6566 (2017).
Song, J., Li, Z., Wang, P., Meyer, T., Mao, C., Ke, Y., Science 357 (2017).
Pan, J., Li, F., Cha, T.G., Chen, H., Choi, J.H., Curr. Opin. Biotechnol. 34, 56 (2015).
Omabegho, T., Sha, R., Seeman, N.C., Science 324, 67 (2009).
Cha, T.G., Pan, J., Chen, H., Salgado, J., Li, X., Mao, C., Choi, J.H., Nat. Nanotechnol. 9, 39 (2014).
Wickham, S.F., Bath, J., Katsuda, Y., Endo, M., Hidaka, K., Sugiyama, H., Turberfield, A.J., Nat. Nanotechnol. 7, 169 (2012).
Ketterer, P., Willner, E.M., Dietz, H., Sci. Adv. 2, e1501209 (2016).
Liedl, T., Hogberg, B., Tytell, J., Ingber, D.E., Shih, W.M., Nat. Nanotechnol. 5, 520 (2010).
Bauer, J., Meza, L.R., Schaedler, T.A., Schwaiger, R., Zheng, X., Valdevit, L., Adv. Mater. 29, 1701850 (2017).
Tikhomirov, G., Petersen, P., Qian, L., Nat. Nanotechnol. 12, 251 (2017).
Adleman, L.M., Science 266, 1021 (1994).
Chen, S.X., Seelig, G., J. Am. Chem. Soc. 138, 5076 (2016).
Bhalla, V., Bajpai, R.P., Bharadwaj, L.M., EMBO Rep. 4, 442 (2003).
Chen, Y.J., Dalchau, N., Srinivas, N., Phillips, A., Cardelli, L., Soloveichik, D., Seelig, G., Nat. Nanotechnol. 8, 755 (2013).
Qian, L., Winfree, E., Bruck, J., Nature 475, 368 (2011).
Zhang, D.Y., Seelig, G., Nat. Chem. 3, 103 (2011).
Chatterjee, G., Dalchau, N., Muscat, R.A., Phillips, A., Seelig, G., Nat. Nanotechnol. 12, 920 (2017).
Dalchau, N., Chandran, H., Gopalkrishnan, N., Phillips, A., Reif, J., ACS Synth. Biol. 4, 898 (2015).
Epstein, I.R., Xu, B., Nat. Nanotechnol. 11, 312 (2016).
Chirieleison, S.M., Allen, P.B., Simpson, Z.B., Ellington, A.D., Chen, X., Nat. Chem. 5, 1000 (2013).
Zadorin, A.S., Rondelez, Y., Galas, J.-C., Estevez-Torres, A., Phys. Rev. Lett. 114, 068301 (2015).

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