Abstract
While algorithmic DNA self-assembly is, in theory, capable of forming complex patterns, its experimental demonstration has been limited by significant assembly errors. In this paper we describe a novel protection/deprotection strategy to strictly enforce the direction of tiling assembly growth to ensure the robustness of the assembly process. Tiles are initially inactive, meaning that each tile’s output pads are protected and cannot bind with other tiles. After other tiles bind to the tile’s input pads, the tile transitions to an active state and its output pads are exposed, allowing further growth. We prove that an activatable tile set is an instance of a compact, error-resilient and self-healing tile-set. We also describe a DNA design for activatable tiles and a deprotection mechanism using DNA polymerase enzymes and strand displacement. We conclude with a discussion on some applications of activatable tiles beyond computational tiling.
Access provided by Autonomous University of Puebla. Download to read the full chapter text
Chapter PDF
Similar content being viewed by others
References
Winfree, E.: Algorithmic Self-Assembly of DNA Caltech (1998)
Dirks, R.M., Pierce, N.A.: PNAS 101(43), 15275–15278 (2004)
Wang, H.: Bell System Tech Journal 40(1), 1–41 (1961)
Barish, R.D., Rothemund, P.W.K., Winfree, E.: Nano Letters 5(12), 2586–2592
Rothemund, P.W.K., Papadakis, N., Winfree, E.: PLoS Biology 2 (12), 424 (2004)
Reif, J.H., Sahu, S., Yin, P.: DNA10. In: Ferretti, C., Mauri, G., Zandron, C. (eds.) DNA Computing. LNCS, vol. 3384, pp. 293–307. Springer, Heidelberg (2005)
Chen, H.L., Goel, A.: DNA 10. In: Ferretti, C., Mauri, G., Zandron, C. (eds.) DNA Computing. LNCS, vol. 3384, pp. 62–75. Springer, Heidelberg (2005)
Winfree, E., Bekbolatov, R.: DNA 9. In: Chen, J., Reif, J.H. (eds.) DNA Computing. LNCS, vol. 2943, pp. 126–144. Springer, Heidelberg (2004)
Yan, H., Park, S.H., Finkelstein, G., Reif, J.H., LaBean, T.H.: Science 301(5641), 1882–1884 (2003)
LaBean, T.H., Yan, H., Kopatsch, J., Liu, F., Winfree, E., Reif, J.H., Seeman, N.C.: J. Am. Chem. Soc. 122, 1848–1860 (2000)
Winfree, E., Liu, F., Wenzler, L.A., Seeman, N.C.: Nature 394 (1998)
Thompson, B.J., Camien, M.N., Warner, R.C.: PNAS 73(7), 2299–2303 (July 1976)
http://www.cs.duke.edu/~reif/paper/urmi/activatable/activatable.pdf
Soloveichik, D., Winfree, E.: SICOMP 36(6), 1544–1569 (2007)
Winfree, E.: Simulations of Computing by Self-Assembly Caltech CS Report, 22 (1998)
Sahu, S., Reif, J.H.: DNA 12. In: Mao, C., Yokomori, T. (eds.) DNA Computing. LNCS, vol. 4287, pp. 223–238. Springer, Heidelberg (2006)
Saturno, J., Blanco, L., Salas, M., Esterban, J.A: J. Bio. Chem. 270(52), 31235–31243 (1995)
Thompson, B.J., Escarmis, C., Parker, B., Slater, W.C., Doniger, J., Tessman, I., Warner, R.C.: J. Mol. Biol. 91, 409–419 (1975)
Adleman, L., Cheng, Q., Goel, A., Huang, M.D.: Proceedings of STOC. pp. 740–748 (2001)
Schulman, R., Winfree, E.: DNA 10. In: Ferretti, C., Mauri, G., Zandron, C. (eds.) DNA Computing. LNCS, vol. 3384, pp. 319–328. Springer, Heidelberg (2005)
Grothues, D., Cantor, C.R., Smith, C.L.: Nuc. Acid. Res. 21(5), 1321–1322 (1993)
Rosenbaum, D.M., Liu, D.R.: J. Am. Chem. Soc. 125, 13924–13925 (2003)
Fujibayashi, K., Murata, S.: DNA 10. In: Ferretti, C., Mauri, G., Zandron, C. (eds.) DNA Computing. LNCS, vol. 3384, pp. 113–127. Springer, Heidelberg (2005)
Fujibayashi, K., Zhang, D., Winfree, E., Murata, S.: In submission
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2008 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Majumder, U., LaBean, T.H., Reif, J.H. (2008). Activatable Tiles: Compact, Robust Programmable Assembly and Other Applications. In: Garzon, M.H., Yan, H. (eds) DNA Computing. DNA 2007. Lecture Notes in Computer Science, vol 4848. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-77962-9_2
Download citation
DOI: https://doi.org/10.1007/978-3-540-77962-9_2
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-77961-2
Online ISBN: 978-3-540-77962-9
eBook Packages: Computer ScienceComputer Science (R0)