Hostname: page-component-586b7cd67f-2brh9 Total loading time: 0 Render date: 2024-11-26T00:46:18.278Z Has data issue: false hasContentIssue false
  • English
  • Français

Practical aspects of structural and dynamic DNA nanotechnology

Published online by Cambridge University Press:  08 December 2017

Pengfei Wang ,
Gourab Chatterjee ,
Hao Yan ,
Thomas H. LaBean ,
Andrew J. Turberfield ,
Carlos E. Castro ,
Georg Seelig  and
Yonggang Ke
Pengfei Wang
Affiliation:
Wallace H. Coulter Department of Biomedical Engineering, Emory University, and Georgia Institute of Technology, USA; [email protected]
Gourab Chatterjee
Affiliation:
Department of Electrical Engineering, University of Washington, USA; [email protected]
Hao Yan
Affiliation:
School of Molecular Sciences, Biodesign Institute, Arizona State University, USA; [email protected]
Thomas H. LaBean
Affiliation:
North Carolina State University, USA; [email protected]
Andrew J. Turberfield
Affiliation:
Department of Physics, University of Oxford, UK; [email protected]
Carlos E. Castro
Affiliation:
Department of Mechanical and Aerospace Engineering, The Ohio State University, USA; [email protected]
Georg Seelig
Affiliation:
Paul G. Allen School of Computer Science & Engineering, and Department of Electrical Engineering, University of Washington, USA; [email protected]
Yonggang Ke
Affiliation:
Wallace H. Coulter Department of Biomedical Engineering, Emory University, and Georgia Institute of Technology, USA; [email protected]
Get access

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
Information
MRS Bulletin , Volume 42 , Issue 12: DNA Nanotechnology: A foundation for Programmable Nanoscale Materials , December 2017 , pp. 889 - 896
Copyright
Copyright © Materials Research Society 2017 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Roh, Y.H., Ruiz, R.C., Peng, S., Lee, J.B., Luo, D., Chem. Soc. Rev. 40, 5730 (2011).Google Scholar
Strunz, T., Oroszlan, K., Schafer, R., Guntherodt, H.J., Proc. Natl. Acad. Sci. U.S.A. 96, 11277 (1999).Google Scholar
Wang, M.D., Yin, H., Landick, R., Gelles, J., Block, S.M., Biophys. J. 72, 1335 (1997).Google Scholar
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.Google Scholar
Seeman, N.C., Kallenbach, N.R., Biophys. J. 44, 201 (1983).Google Scholar
Fu, T.J., Seeman, N.C., Biochemistry 32, 3211 (1993).CrossRefGoogle Scholar
He, Y., Chen, Y., Liu, H., Ribbe, A.E., Mao, C., J. Am. Chem. Soc. 127, 12202 (2005).Google Scholar
Wang, P., Wu, S., Tian, C., Yu, G., Jiang, W., Wang, G., Mao, C., J. Am. Chem. Soc. 138, 13579 (2016).CrossRefGoogle Scholar
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).CrossRefGoogle Scholar
Zhang, F., Liu, Y., Yan, H., J. Am. Chem. Soc. 135, 7458 (2013).Google Scholar
Ke, Y.G., Ong, L.L., Shih, W.M., Yin, P., Science 338, 1177 (2012).Google Scholar
Wei, B., Dai, M.J., Yin, P., Nature 485, 623 (2012).Google Scholar
Ke, Y., Ong, L.L., Sun, W., Song, J., Dong, M., Shih, W.M., Yin, P., Nat. Chem. 6, 994 (2014).Google Scholar
Rothemund, P.W.K., Nature 440, 297 (2006).Google Scholar
Douglas, S.M., Dietz, H., Liedl, T., Hogberg, B., Graf, F., Shih, W.M., Nature 459, 414 (2009).CrossRefGoogle Scholar
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).Google Scholar
Ke, Y.G., Voigt, N.V., Gothelf, K.V., Shih, W.M., J. Am. Chem. Soc. 134, 1770 (2012).Google Scholar
Veneziano, R., Ratanalert, S., Zhang, K., Zhang, F., Yan, H., Chiu, W., Bathe, M., Science 352, 6293 (2016).Google Scholar
Benson, E., Mohammed, A., Gardell, J., Masich, S., Czeizler, E., Orponen, P., Hogberg, B., Nature 523, 441 (2015).Google Scholar
Marchi, A.N., Saaem, I., Vogen, B.N., Brown, S., LaBean, T.H., Nano Lett. 14, 5740 (2014).Google Scholar
Wang, P., Gaitanaros, S., Lee, S., Bathe, M., Shih, W.M., Ke, Y., J. Am. Chem. Soc. 138, 7733 (2016).Google Scholar
Gerling, T., Wagenbauer, K.F., Neuner, A.M., Dietz, H., Science 347, 1446 (2015).Google Scholar
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. 90–101.Google Scholar
Zhu, J., Wei, B., Yuan, Y., Mi, Y., Nucleic Acids Res. 37, 2164 (2009).Google Scholar
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).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
Castro, C.E., Kilchherr, F., Kim, D.-N., Shiao, E.L., Wauer, T., Wortmann, P., Bathe, M., Dietz, H., Nat. Methods 8, 221 (2011).Google Scholar
Bath, J., Turberfield, A.J., Nat. Nanotechnol. 2, 275 (2007).CrossRefGoogle Scholar
Surana, S., Bhat, J.M., Koushika, S.P., Krishnan, Y., Nat. Commun. 2, 340 (2011).CrossRefGoogle Scholar
Mao, C.D., Sun, W.Q., Shen, Z.Y., Seeman, N.C., Nature 397, 144 (1999).Google Scholar
Ellington, A.D., Szostak, J.W., Nature 346, 818 (1990).CrossRefGoogle Scholar
Asanuma, H., Ito, T., Yoshida, T., Liang, X.G., Komiyama, M., Angew. Chem. Int. Ed. Engl. 38, 2393 (1999).Google Scholar
Yin, P., Yan, H., Daniell, X.G., Turberfield, A.J., Reif, J.H., Angew. Chem. Int. Ed. Engl. 43, 4906 (2004).CrossRefGoogle Scholar
Stojanovic, M.N., Stefanovic, D., Nat. Biotechnol. 21, 1069 (2003).Google Scholar
Benenson, Y., Gil, B., Ben-Dor, U., Adar, R., Shapiro, E., Nature 429, 423 (2004).Google Scholar
Liedl, T., Simmel, F.C., Nano Lett. 5, 1894 (2005).Google Scholar
Yurke, B., Turberfield, A.J., Mills, A.P., Simmel, F.C., Neumann, J.L., Nature 406, 605 (2000).Google Scholar
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).Google Scholar
Qian, L., Winfree, E., Science 332, 1196 (2011).Google Scholar
Turberfield, A.J., Mitchell, J.C., Yurke, B., Mills, A.P., Blakey, M.I., Simmel, F.C., Phys. Rev. Lett. 90, 118102 (2003).Google Scholar
Bath, J., Green, S.J., Turberfield, A.J., Angew. Chem. Int. Ed. Engl. 44, 4358 (2005).CrossRefGoogle Scholar
Tian, Y., He, Y., Chen, Y., Yin, P., Mao, C.D., Angew. Chem. Int. Ed. Engl. 44, 4355 (2005).CrossRefGoogle Scholar
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).Google Scholar
He, Y., Liu, D.R., Nat. Nanotechnol. 5, 778 (2010).CrossRefGoogle Scholar
Douglas, S.M., Bachelet, I., Church, G.M., Science 335, 831 (2012).Google Scholar
Asanuma, H., Liang, X., Nishioka, H., Matsunaga, D., Liu, M., Komiyama, M., Nat. Protoc. 2, 203 (2007).CrossRefGoogle Scholar
Bustamante, C., Smith, S.B., Liphardt, J., Smith, D., Curr. Opin. Struct. Biol. 10, 279 (2000).Google Scholar
Kim, Y.J., Kim, D.N., PloS One 11, e0153228 (2016).Google Scholar
Castro, C.E., Su, H.J., Marras, A.E., Zhou, L., Johnson, J., Nanoscale 7, 5913 (2015).CrossRefGoogle Scholar
Zhou, L., Marras, A.E., Su, H.J., Castro, C.E., ACS Nano 8, 27 (2013).Google Scholar
Zhou, L., Marras, A.E., Castro, C.E., Su, H.-J., J. Mech. Robot. 8, 051013 (2016).Google Scholar
Marras, A.E., Zhou, L., Su, H.J., Castro, C.E., Proc. Natl. Acad. Sci. U.S.A. 112, 713 (2015).CrossRefGoogle Scholar
Zhou, L., Marras, A.E., Su, H.J., Castro, C.E., Nano Lett. 15, 1815 (2015).Google Scholar
Hudoba, M.W., Luo, Y., Zacharias, A., Poirier, M.G., Castro, C.E., ACS Nano 11, 6566 (2017).CrossRefGoogle Scholar
Song, J., Li, Z., Wang, P., Meyer, T., Mao, C., Ke, Y., Science 357 (2017).Google Scholar
Pan, J., Li, F., Cha, T.G., Chen, H., Choi, J.H., Curr. Opin. Biotechnol. 34, 56 (2015).CrossRefGoogle Scholar
Omabegho, T., Sha, R., Seeman, N.C., Science 324, 67 (2009).CrossRefGoogle Scholar
Cha, T.G., Pan, J., Chen, H., Salgado, J., Li, X., Mao, C., Choi, J.H., Nat. Nanotechnol. 9, 39 (2014).Google Scholar
Wickham, S.F., Bath, J., Katsuda, Y., Endo, M., Hidaka, K., Sugiyama, H., Turberfield, A.J., Nat. Nanotechnol. 7, 169 (2012).Google Scholar
Ketterer, P., Willner, E.M., Dietz, H., Sci. Adv. 2, e1501209 (2016).CrossRefGoogle Scholar
Liedl, T., Hogberg, B., Tytell, J., Ingber, D.E., Shih, W.M., Nat. Nanotechnol. 5, 520 (2010).Google Scholar
Bauer, J., Meza, L.R., Schaedler, T.A., Schwaiger, R., Zheng, X., Valdevit, L., Adv. Mater. 29, 1701850 (2017).Google Scholar
Tikhomirov, G., Petersen, P., Qian, L., Nat. Nanotechnol. 12, 251 (2017).Google Scholar
Adleman, L.M., Science 266, 1021 (1994).CrossRefGoogle Scholar
Chen, S.X., Seelig, G., J. Am. Chem. Soc. 138, 5076 (2016).CrossRefGoogle Scholar
Bhalla, V., Bajpai, R.P., Bharadwaj, L.M., EMBO Rep. 4, 442 (2003).CrossRefGoogle Scholar
Chen, Y.J., Dalchau, N., Srinivas, N., Phillips, A., Cardelli, L., Soloveichik, D., Seelig, G., Nat. Nanotechnol. 8, 755 (2013).Google Scholar
Qian, L., Winfree, E., Bruck, J., Nature 475, 368 (2011).CrossRefGoogle Scholar
Zhang, D.Y., Seelig, G., Nat. Chem. 3, 103 (2011).Google Scholar
Chatterjee, G., Dalchau, N., Muscat, R.A., Phillips, A., Seelig, G., Nat. Nanotechnol. 12, 920 (2017).Google Scholar
Dalchau, N., Chandran, H., Gopalkrishnan, N., Phillips, A., Reif, J., ACS Synth. Biol. 4, 898 (2015).Google Scholar
Epstein, I.R., Xu, B., Nat. Nanotechnol. 11, 312 (2016).Google Scholar
Chirieleison, S.M., Allen, P.B., Simpson, Z.B., Ellington, A.D., Chen, X., Nat. Chem. 5, 1000 (2013).CrossRefGoogle Scholar
Zadorin, A.S., Rondelez, Y., Galas, J.-C., Estevez-Torres, A., Phys. Rev. Lett. 114, 068301 (2015).Google Scholar