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Reliable Self-assembly by Self-triggered Activation of Enveloped DNA Tiles

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Theory and Practice of Natural Computing (TPNC 2013)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 8273))

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Abstract

Although the design of DNA tiles has been optimised for efficient and specific self-assembly, assembly errors occur so often that applications for molecular computation remain limited. We propose the use of an enveloped tile consisting of a DX- base tile that carries a protector tile to suppress erroneous tile assembly. The design of the enveloped tile promotes the dissociation of the protector tile from the base tile through a self-triggered activation process, which keeps the outputs of the base tile stay protected until both base tile inputs have bonded correctly to the assembly. The enveloped tile design, the self-triggered activation that removes the protector tile and preliminary modelling results are presented.

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References

  1. A., W.P., van der, H.T., Fernando, M.H., pakowitz Andrew S, Rob, P., Jonathan, W., Cees, D., Nelson, P.C.: : High flexibility of dna on short length scales probed by atomic force microscopy. Nature 2(1), 1748–3387 (2006)

    Google Scholar 

  2. Bhalla, N., Bentley, P., Vize, P., Jacob, C.: Staging the self-assembly process using morphological information. In: European Conf. on Artificial Life (ECAL), pp. 93–100 (2011)

    Google Scholar 

  3. Chen, H.L., Schulman, R., Goel, A., Winfree, E.: Reducing facet nucleation during algorithmic self-assembly. Nano Lett. 7(9), 2913–2919 (2007)

    Article  Google Scholar 

  4. Fujibayashi, K., Zhang, D.Y., Winfree, E., Murata, S.: Error suppression mechanisms for dna tile self-assembly and their simulation. Natural Computing 8(3), 589–612 (2009)

    Article  MathSciNet  MATH  Google Scholar 

  5. Chen, H.-L., Goel, A.: Error free self-assembly using error prone tiles. In: Ferretti, C., Mauri, G., Zandron, C. (eds.) DNA10. LNCS, vol. 3384, pp. 62–75. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  6. Majumder, U., LaBean, T.H., Reif, J.H.: Activatable tiles: Compact, robust programmable assembly and other applications. In: Garzon, M.H., Yan, H. (eds.) DNA 13. LNCS, vol. 4848, pp. 15–25. Springer, Heidelberg (2008)

    Chapter  Google Scholar 

  7. Panyutin, I., Hsieh, P.: The kinetics of spontaneous dna branch migration. PNAS 91, 2021–2025 (1994)

    Article  Google Scholar 

  8. Schulman, R., Winfree, E.: Programmable control of nucleation for algorithmic self-assembly. In: Ferretti, C., Mauri, G., Zandron, C. (eds.) DNA 10. LNCS, vol. 3384, pp. 319–328. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  9. Winfree, E.: On the computational power of dna annealing and ligation. In: DNA Based Computers. DIMACS, vol. 27. American Mathematical Society (1995)

    Google Scholar 

  10. Winfree, E., Bekbolatov, R.: Proofreading tile sets: Error correction for algorithmic self-assembly. In: Chen, J., Reif, J.H. (eds.) DNA 9. LNCS, vol. 2943, pp. 126–144. Springer, Heidelberg (2004)

    Chapter  Google Scholar 

  11. Winfree, E., Liu, F., Wenzler, L.A., Seeman, N.: Design and self-assembly of two-dimensional dna crystals. Nature 394(6693), 539–544 (1998)

    Article  Google Scholar 

  12. Woo, S., Rothemund, P.W.K.: Programmable molecular recognition based on the geometry of dna nanostructures. Nat. Chem. 3(8), 620–627 (2011)

    Article  Google Scholar 

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Gautam, V.K., Haddow, P.C., Kuiper, M. (2013). Reliable Self-assembly by Self-triggered Activation of Enveloped DNA Tiles. In: Dediu, AH., Martín-Vide, C., Truthe, B., Vega-Rodríguez, M.A. (eds) Theory and Practice of Natural Computing. TPNC 2013. Lecture Notes in Computer Science, vol 8273. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-45008-2_6

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  • DOI: https://doi.org/10.1007/978-3-642-45008-2_6

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-45007-5

  • Online ISBN: 978-3-642-45008-2

  • eBook Packages: Computer ScienceComputer Science (R0)

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