Abstract
Self-repair is essential to all living systems, providing the ability to remain functional in spite of gradual damage. In the context of self-assembly of self-repairing synthetic biomolecular systems, recently Winfree developed a method for transforming a set of DNA tiles into its self-healing counterpart at the cost of increasing the lattice area by a factor of 25. The overall focus of this paper, however, is to develop compact designs for self-repairing tiling assemblies with reasonable constraints on crystal growth. Specifically, we use a special class of DNA tiling designs called reversible tiling which when carefully designed can provide inherent self-repairing capabilities to patterned DNA lattices. We further note that we can transform any irreversible computational DNA tile set to its reversible counterpart and hence improve the self-repairability of the computational lattice. But doing the transform with an optimal number of tiles, is still an open question.
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Liu, D., Wang, M.S., Deng, Z.X., Walulu, R., Mao, C.D.: J. Am. Chem. Soc. 126, 2324–2325 (2004)
LaBean, T.H., Yan, H., Kopatsch, J., Liu, F., Winfree, E., Reif, J.H., Seeman, N.C.: The construction, analysis, ligation and self-assembly of DNA triple crossover complexes. J. Am. Chem. Soc. 122, 1848–1860 (2000)
Mao, C., Sun, W., Seeman, N.C.: J. Am. Chem. Soc. 121, 5437–5443 (1999)
Winfree, E., Liu, F., Wenzler, L.A., Seeman, N.C.: Design and self-assembly of two-dimensional DNA crystals. Nature 394(6693), 539–544 (1998)
Yan, H., LaBean, T.H., Feng, L., Reif, J.H.: Directed nucleation assembly of DNA tile complexes for barcode patterned DNA lattices. Proc. Natl. Acad. Sci. USA 100(14), 8103–8108 (2003)
Yan, H., Park, S.H., Finkelstein, G., Reif, J.H., LaBean, T.H.: DNA-templated self-assembly of protein arrays and highly conductive nanowires. Science 301(5641), 1882–1884 (2003)
Winfree, E., Bekbolatov, R.: Proofreading tile sets: Error correction for algorithmic self-assembly. In: Chen, J., Reif, J.H. (eds.) DAN 2003. LNCS, vol. 2943, pp. 126–144. Springer, Heidelberg (2004)
Winfree, E.: Self Healing Tile Sets. Nanotechnology: Science and Computation, 3–21 (2006)
Reif, J.H., Sahu, S., Yin, P.: Compact error-resilient computational DNA tiling assemblies. In: Tenth International Meeting on DNA Based Computers (DNA10) (2004)
Chen, H.L., Goel, A.: Error Free Self-Assembly using error-prone tiles. DNA Computing 10 (2004)
Schulman, R., Winfree, E.: Controlling nucleation rate in algorithmic self-assembly. DNA Computing 10 (2004)
Hertzberg, R.: Deformation and Fracture Mechanics of Engineering Materials. John Wiley and Sons, NY (1996)
Winfree, E.: Simulations of Computing by Self-Assembly, Caltech CS Tech Report 1998.22
Winfree, E.: On the Computational Power of DNA Annealing and Ligation. DNA Based Computers, 199–221 (1996)
Cook, M., Rothemund, P.W.K., Winfree, E.: Self-Assembled circuit patterns. In: DNA Computers 9. LNCS, vol. 294, pp. 91–107. Springer, Heidelberg (2004)
Toffoli, T.: Reversible Computing, Automata, Languages and Programming, pp. 632–644. Springer, Heidelberg
Barish, R.D., Rothemund, P.W.K., Winfre, E.: Two Computational Primitives for Algorithmic Self-Assembly: Copying and Counting. Nano Letters 5(12), 2586–2592
Rothemund, P.W.K., Papadakis, N., Winfree, E.: Algorithmic Self-Assembly of DNA Sierpinski Triangles. PLoS Biology 2(12), e424 (2004)
Rothemund, P.W.K.: Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006)
Park, S.H., Pistol, C., Ahn, S.J., Reif, J.H., Lebeck, A.R., Dwyer, C., LaBean, T.H.: Finite-size, Fully-Addressable DNA Tile Lattices Formed by Hierarchical Assembly Procedures. Angewandte Chemie 45, 735–739 (2006)
Morita, K.: Reversible simulation of one-dimensional irreversible cellular automata. Theoret. Comput. Sci. 148, 157–163 (1995)
Hönberg, B., Olin, H.: Programmable Self-Assembly-Unique Structures and Bond Uniqueness. J. Comput. Theor. Nanosci. 3, 1–7 (2006)
Provot, X.: Deformation Constraints in a Mass Spring Model to Describe Rigid Cloth Behavior. In: Proc. Graphics Interface, vol. 95, pp. 147–154 (1995)
White, S.R., Sottos, N.R., Geubelle, P.H., Moore, J.S., Kessler, M.R., Sriram, S.R., Brown, E.N., Viswanathan, S.: Autonomic healing of polymer composites. Nature 409, 794–797 (2001)
Pistol, C., Lebeck, A.R., Dwyer, C.: Design Automation for DNA Self-Assembled Nanostructures. In: Proceedings of the 43rd Design Automation Conference (DAC) (July 2006)
Park, S.-H., Yin, P., Liu, Y., Reif, J.H., LaBean, T.H., Yan, H.: Programmable DNA Self-assemblies for Nanoscale Organization of Ligands and Proteins. Nano Letters 5, 729–733 (2005)
Sahu, S., Reif, J.: Capabilities and Limits of Compact Error Resilience Methods for Algorithmic Self-Assembly in Two and Three Dimensions. In: Twelfth International Meeting on DNA Based Computers (DNA12), Seoul, Korea, June 5-9 (2006)
Seeman, N.C.: J. Biomol. Struct. Dyn. 8, 573 (1990)
Winfree, E., Liu, F., Wenzler, L.A., Seeman, N.C.: Nature, 394 (1998)
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Majumder, U., Sahu, S., LaBean, T.H., Reif, J.H. (2006). Design and Simulation of Self-repairing DNA Lattices. In: Mao, C., Yokomori, T. (eds) DNA Computing. DNA 2006. Lecture Notes in Computer Science, vol 4287. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11925903_15
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DOI: https://doi.org/10.1007/11925903_15
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-49024-1
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