Hostname: page-component-cd9895bd7-p9bg8 Total loading time: 0 Render date: 2024-12-23T14:27:14.442Z Has data issue: false hasContentIssue false
  • English
  • Français

Self-organizing materials built with DNA

Published online by Cambridge University Press:  08 December 2017

Friedrich C. Simmel  and
Rebecca Schulman
Friedrich C. Simmel
Affiliation:
Technical University Munich, Germany; [email protected]
Rebecca Schulman
Affiliation:
Johns Hopkins University, USA; [email protected]
Get access

Abstract

Biological systems illustrate how complex and dynamic physical and chemical interactions between many different components can produce organized structures across length scales, ranging from angstroms to hundreds of meters, and precise temporal control over diverse material dynamics. While mechanisms for pattern formation such as reaction-diffusion processes, message passing, or rule-based assembly have been studied extensively using mathematical models, it can be difficult to create synthetic materials that implement these mechanisms. Here, we describe how DNA nanotechnology techniques make it possible to systematically build systems capable of complex self-organization or pattern formation across scales. DNA-programmed short-range interactions can be used to build aperiodic crystals and assemblies with long-range order, form patterns using reaction-diffusion and chemical message passing, and create self-organizing or stimulus-responsive amorphous materials, including gels or cell-sized compartments. Exploiting principles from self-organization using DNA-based interactions makes it possible to build materials with complex long-range order and intelligent spatiotemporal responses to a variety of stimuli using relatively simple bottom-up methods.

Type
Research Article
Information
MRS Bulletin , Volume 42 , Issue 12: DNA Nanotechnology: A foundation for Programmable Nanoscale Materials , December 2017 , pp. 913 - 919
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

Valladas, H., Clottes, J., Geneste, J.-M., Garcia, M.A., Arnold, M., Cachier, H., Tisnérat-Laborde, N., Nature 413, 479 (2001).CrossRefGoogle Scholar
Haeckel, E., Art Forms in Nature (Prestel, Munich, Germany, 2004).Google Scholar
Thompson, D.A.W., On Growth and Form (Cambridge University Press, Cambridge, UK, 2014).CrossRefGoogle Scholar
Schrödinger, E., What Is Life? The Physical Aspect of the Living Cell (Cambridge University Press, Cambridge, UK, 1944).Google Scholar
Cartwright, J.H.E., Mackay, A.L., Philos. Trans. R. Soc. Lond. A 370, 2807 (2012).Google Scholar
Turing, A.M., Philos. Trans. R. Soc. Lond. B 237, 37 (1952).Google Scholar
Von Neumann, J., Burks, A.W., Theory of Self-Reproducing Automata (University of Illinois Press, Urbana, IL, 1966).Google Scholar
Wolfram, S., Nature 311, 419 (1984).CrossRefGoogle Scholar
Cross, M.C., Hohenberg, P.C., Rev. Mod. Phys. 65, 851 (1993).CrossRefGoogle Scholar
Soloveichik, D., Seelig, G., Winfree, E., Proc. Natl. Acad. Sci. U.S.A. 107, 5393 (2010).CrossRefGoogle Scholar
Prince, E., Wilson, A.J.C., International Tables for Crystallography (Kluwer Academic Publishers, Dordrecht, 2004).Google Scholar
Baake, M., Grimm, U., Aperiodic Order, Volume 1: A Mathematical Invitation, Encyclopedia of Mathematics and Its Applications , Book 149 (Cambridge University Press, Cambridge, UK, 2013).Google Scholar
Levine, D., Steinhardt, P.J., Phys. Rev. Lett. 53, 2477 (1984).CrossRefGoogle Scholar
Tikhomirov, G., Petersen, P., Qian, L., Nat. Nanotechnol. 12, 251 (2017).CrossRefGoogle Scholar
Winfree, E., Algorithmic Self-Assembly of DNA (California Institute of Technology, Pasadena, CA, 1998).Google Scholar
Rothemund, P.W., Papadakis, N., Winfree, E., PLoS Biol. 2, e424 (2004).CrossRefGoogle Scholar
Barish, R.D., Schulman, R., Rothemund, P.W., Winfree, E., Proc. Natl. Acad. Sci. U.S.A. 106, 6054 (2009).CrossRefGoogle Scholar
Cook, M., Rothemund, P.W., Winfree, E., “Self-Assembled Circuit Patterns,” 9th Int. Workshop DNA-Based Comput., Chen, J.. Reif, J., Eds. (Springer, Berlin, 2004), p. 91.Google Scholar
Soloveichik, D., Winfree, E., SIAM J. Comput. 36, 1544 (2007).Google Scholar
Rothemund, P.W., Winfree, E., “The Program-Size Complexity of Self-Assembled Squares,” Proc. 32nd Annu. ACM Symp. Theory Comput. (ACM, New York, 2000), p. 459.Google Scholar
Cohen, M.F., Shade, J., Hiller, S., Deussen, O., ACM Trans. Graph. 22, 287 (2003).CrossRefGoogle Scholar
Schulman, R., Yurke, B., Winfree, E., Proc. Natl. Acad. Sci. U.S.A. 109, 6405 (2012).CrossRefGoogle Scholar
Winfree, E., “Self-Healing Tile Sets,” in Nanotechnology: Science and Computation, Natural Computing Series (Springer, Berlin, Germany, 2006), p. 55.CrossRefGoogle Scholar
Padilla, J.E., Sha, R., Kristiansen, M., Chen, J., Jonoska, N., Seeman, N.C., Angew. Chem. Int. Ed. 54, 5939 (2015).CrossRefGoogle Scholar
Lotka, A.J., J. Am. Chem. Soc. 42, 1595 (1920).Google Scholar
Winfree, A.T., J. Chem. Educ. 61, 661 (1984).CrossRefGoogle Scholar
Wang, P., Chatterjee, G., Tan, H., LaBean, T.H., Turberfield, A.J., Castro, C.E., Seelig, G., Ke, Y., MRS Bull. 42 (12), 889 (2017).CrossRefGoogle Scholar
Zhang, D.Y., Seelig, G., Nat. Chem. 3, 103 (2011).CrossRefGoogle Scholar
Kim, J., Khetarpal, I., Sen, S., Murray, R.M., Nucleic Acids Res. 42, 6078 (2014).CrossRefGoogle Scholar
Seelig, G., Soloveichik, D., Zhang, D.Y., Winfree, E., Science 314, 1585 (2006).CrossRefGoogle Scholar
Qian, L., Winfree, E., Science 332, 1196 (2011).Google Scholar
Qian, L., Winfree, E., Bruck, J., Nature 475, 368 (2011).CrossRefGoogle Scholar
Chen, Y.J., Dalchau, N., Srinivas, N., Phillips, A., Cardelli, L., Soloveichik, D., Seelig, G., Nat. Nanotechnol. 8, 755 (2013).CrossRefGoogle Scholar
Kim, J., Winfree, E., Mol. Syst. Biol. 7, 465 (2011).CrossRefGoogle Scholar
Montagne, K., Plasson, R., Sakai, Y., Fujii, T., Rondelez, Y., Mol. Syst. Biol. 7, 466 (2011).Google Scholar
Schwarz-Schilling, M., Kim, J., Cuba, C., Weitz, M., Franco, E., Simmel, F.C., Methods Mol. Biol. 1342, 185 (2016).CrossRefGoogle Scholar
Fuji, T., Rondelez, Y., ACS Nano 7, 27 (2013).CrossRefGoogle Scholar
Padirac, A., Fuji, T., Estévez-Torres, A., Rondelez, Y., J. Am. Chem. Soc. 135, 14586 (2013).CrossRefGoogle Scholar
Zadorin, A.S., Rondelez, Y., Gines, G., Dilhas, V., Urtel, G., Zambrano, A., Galas, J.-C., Estevez-Torres, A., Nat. Chem. 9, 990 (2017).Google Scholar
Gines, G., Zadorin, A.S., Galas, J.C., Fuji, T., Estevez-Torres, A., Rondelez, Y., Nat. Nanotechnol. 12, 351 (2017).CrossRefGoogle Scholar
Grossi, G., Jaekel, A., Andersen, E.S., Saccà, B., MRS Bull. 42 (12), 920 (2017).CrossRefGoogle Scholar
Zadorin, A.S., Rondelez, Y., Galas, J.C., Estevez-Torres, A., Phys. Rev. Lett. 114, 068301 (2015).CrossRefGoogle Scholar
Weitz, M., Kim, J., Kapsner, K., Winfree, E., Franco, E., Simmel, F.C., Nat. Chem. 6, 295 (2014).Google Scholar
Hasatani, K., Leocmach, M., Genot, A.J., Estevez-Torres, A., Fujii, T., Rondelez, Y., Chem. Commun. 49, 8090 (2013).CrossRefGoogle Scholar
Langecker, M., Arnaut, V., Martin, T.G., List, J., Renner, S., Mayer, M., Dietz, H., Simmel, F.C., Science 338, 932 (2012).CrossRefGoogle Scholar
Krishnan, S., Ziegler, D., Arnaut, V., Martin, T.G., Kapsner, K., Henneberg, K., Bausch, A.R., Dietz, H., Simmel, F.C., Nat. Commun. 7, 12787 (2016).CrossRefGoogle Scholar
Kurokawa, C., Fujiwara, K., Morita, M., Kawamata, I., Kawagishi, Y., Sakai, A., Murayama, Y., Nomura, Shin-ichiro M., Murata, S., Takinoue, M., “DNA Cytoskeleton for Stabilizing Artificial Cells,” Proc. Natl. Acad. Sci. U.S.A. 114, 7228 (2017).Google Scholar
Sato, Y., Hiratsuka, Y., Kawamata, I., Murata, S., Nomura, Shin-ichiro M., Sci. Rob. 2, eaal3735 (2017).Google Scholar
Um, S.H., Lee, J.B., Park, N., Kwon, S.Y., Umbach, C.C., Luo, D., Nat. Mater. 5, 797 (2006).Google Scholar
Douglas, S.M., Chou, J.J., Shih, W.M., Proc. Natl. Acad. Sci. U.S.A. 104, 6644 (2007).CrossRefGoogle Scholar
Siavashpouri, M., Wachauf, C.H., Zakhary, M.J., Praetorius, F., Dietz, H., Dogic, Z., Nat. Mater. 16, 849 (2017).CrossRefGoogle Scholar
Mohammed, A.M., Šulc, P., Zenk, J., Schulman, R., Nat. Nanotechnol. 12, 312 (2017).Google Scholar
Kahn, J.S., Hu, Y., Willner, I., Acc. Chem. Res. 50, 680 (2017).CrossRefGoogle Scholar
Liedl, T., Dietz, H., Yurke, B., Simmel, F., Small 3, 1688 (2007).CrossRefGoogle Scholar
Cangialosi, A., Yoon, C., Liu, J., Huang, Q., Guo, J., Nguyen, T.D., Gracias, D.H., Schulman, R., Science 357, 1126 (2017).Google Scholar
Gothelf, K., MRS Bull. 42 (12), 897 (2017).CrossRefGoogle Scholar