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Design, Simulation, and Experimental Demonstration of Self-assembled DNA Nanostructures and Motors

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Unconventional Programming Paradigms (UPP 2004)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 3566))

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Abstract

Self-assembly is the spontaneous self-ordering of substructures into superstructures, driven by the selective affinity of the substructures. Complementarity of DNA bases renders DNA an ideal material for programmable self-assembly of nanostructures. DNA self-assembly is the most advanced and versatile system that has been experimentally demonstrated for programmable construction of patterned systems on the molecular scale. The methodology of DNA self-assembly begins with the synthesis of single strand DNA molecules that self-assemble into macromolecular building blocks called DNA tiles. These tiles have single strand “sticky ends” that complement the sticky ends of other DNA tiles, facilitating further assembly into larger structures known as DNA tiling lattices. In principle, DNA tiling assemblies can form any computable two or three-dimensional pattern, however complex, with the appropriate choice of the tiles’ component DNA. Two-dimensional DNA tiling lattices composed of hundreds of thousands of tiles have been demonstrated experimentally. These assemblies can be used as programmable scaffolding to position molecular electronics and robotics components with precision and specificity, facilitating fabrication of complex nanoscale devices. We overview the evolution of DNA self-assembly techniques from pure theory, through simulation and design, and then to experimental practice. In particular, we begin with an overview of theoretical models and algorithms for DNA lattice self-assembly. Then we describe our software for the simulation and design of DNA tiling assemblies and DNA nano-mechanical devices. As an example, we discuss models, algorithms, and computer simulations for the key problem of error control in DNA lattice self-assembly. We then briefly discuss our laboratory demonstrations of DNA lattices and motors, including those using the designs aided by our software. These experimental demonstrations of DNA self-assemblies include the assembly of patterned objects at the molecular scale, the execution of molecular computations, and the autonomous DNA walking and computing devices.

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References

  1. Adleman, L.: Molecular computation of solutions to combinatorial problems. Science 266, 1021–1024 (1994)

    Article  Google Scholar 

  2. Adleman, L.: Towards a mathematical theory of self-assembly. Technical Report 00-722, University of Southern California (2000)

    Google Scholar 

  3. Adleman, L., Cheng, Q., Goel, A., Huang, M.D., Kempe, D., de Espans, P.M., Rothemund, P.W.K.: Combinatorial optimization problems in self-assembly. In: Proceedings of the thirty-fourth annual ACM symposium on Theory of computing, pp. 23–32. ACM Press, New York (2002)

    Chapter  Google Scholar 

  4. Adleman, L., Cheng, Q., Goel, A., Huang, M.D., Wasserman, H.: Linear self-assemblies: Equilibria, entropy, and convergence rate. In: Sixth International Conference on Difference Equations and Applications (2001)

    Google Scholar 

  5. Alberti, P., Mergny, J.L.: DNA duplex-quadruplex exchange as the basis for a nanomolecular machine. In: Proc. Natl. Acad. Sci. USA, vol. 100, pp. 1569–1573 (2003)

    Google Scholar 

  6. Benenson, Y., Paz-Elizur, T., Adar, R., Keinan, E., Livneh, Z., Shapiro, E.: Programmable and autonomous computing machine made of biomolecules. Nature 414, 430–434 (2001)

    Article  Google Scholar 

  7. Berger, R.: The undecidability of the domino problem. Memoirs of the American Mathematical Society 66 (1966)

    Google Scholar 

  8. Chen, Y., Wang, M., Mao, C.: An autonomous DNA nanomotor powered by a DNA enzyme. Angew. Chem. Int. Ed. 43, 3554–3557 (2004)

    Article  Google Scholar 

  9. Feng, L., Park, S.H., Reif, J.H., Yan, H.: A two-state DNA lattice switched by DNA nanoactuator. Angew. Chem. Int. Ed. 42, 4342–4346 (2003)

    Article  Google Scholar 

  10. Grunbaum, B., Shepard, G.C.: Tilings and Patterns, ch.11. H Freeman and Company, New York (1986)

    Google Scholar 

  11. Jonoska, N., Karl, S.: Ligation experiments in computing with dna. In: Proceedings of 1997 IEEE International Conference on Evolutionary Computation (ICEC 1997), pp. 261–265 (1997)

    Google Scholar 

  12. Jonoska, N., Karl, S.A., Saito, M.: Graph structures in dna computing. Computing with Bio-Molecules, theory and experiments, 93–110 (1998)

    Google Scholar 

  13. LaBean, T.H.: Introduction to self-assembling DNA nanostructures for computation and nanofabrication. In: Wang, J.T.L., Wu, C.H., Wang, P.P. (eds.) Computational Biology and Genome Informatics. World Scientific Publishing, Singapore (2003) ISBN 981-238-257-7

    Google Scholar 

  14. LaBean, T.H., Winfree, E., Reif, J.H.: Experimental progress in computation with DNA molecules. In: Proc. DNA Based Computers V (1999)

    Google Scholar 

  15. 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)

    Article  Google Scholar 

  16. Lagoudakis, M.G., LaBean, T.H.: 2-D DNA self-assembly for satisfiability. In: DNA Based Computers V. DIMACS, vol. 54, pp. 141–154. American Mathematical Society, Providence (2000)

    Google Scholar 

  17. Lewis, H.R., Papadimitriou, C.H.: Elements of the Theory of Computation. Prentice Hall, Englewood Cliffs (1981)

    MATH  Google Scholar 

  18. Li, H., Park, S.H., Reif, J.H., LaBean, T.H., Yan, H.: DNA templated self-assembly of protein and nanoparticle linear arrays. Journal of American Chemistry Society 126(2), 418–419 (2004)

    Article  Google Scholar 

  19. Li, J., Tan, W.: A single DNA molecule nanomotor. Nano Lett 2, 315–318 (2002)

    Article  Google Scholar 

  20. Liu, D., Park, S.H., Reif, J.H., LaBean, T.H.: DNA nanotubes self-assembled from triple-crossover tiles as templates for conductive nanowires. In: Proceedings of the National Academy of Science, vol. 101, pp. 717–722 (2004)

    Google Scholar 

  21. Liu, Q., Wang, L., Frutos, A.G., Condon, A.E., Corn, R.M., Smith, L.M.: DNA computing on surfaces. Nature 403, 175–179 (2000)

    Article  Google Scholar 

  22. Mao, C., LaBean, T.H., Reif, J.H., Seeman, N.C.: Logical computation using algorithmic self-assembly of DNA triple-crossover molecules. Nature 407, 493–496 (2000)

    Article  Google Scholar 

  23. Mao, C., Sun, W., Seeman, N.C.: Designed two-dimensional DNA holliday junction arrays visualized by atomic force microscopy. J. Am. Chem. Soc. 121, 5437–5443 (1999)

    Article  Google Scholar 

  24. Mao, C., Sun, W., Shen, Z., Seeman, N.C.: A DNA nanomechanical device based on the B-Z transition. Nature 397, 144–146 (1999)

    Article  Google Scholar 

  25. 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 (2004) (Submitted for publication)

    Google Scholar 

  26. Reif, J.H.: Paradigms for biomolecular computation. In: Calude, C.S., Casti, J., Dinneen, M.J. (eds.) First International Conference on Unconventional Models of Computation, Auckland, New Zealand, pp. 72–93. Springer, Heidelberg (1998)

    Google Scholar 

  27. Reif, J.H.: Local parallel biomolecular computation. In: Rubin, H., Wood, D.H. (eds.) DNA-Based Computers 3. DIMACS, vol. 48, pp. 217–254. American Mathematical Society, Providence (1999)

    Google Scholar 

  28. Reif, J.H.: The design of autonomous DNA nanomechanical devices: Walking and rolling DNA. In: Hagiya, M., Ohuchi, A. (eds.) DNA 2002. LNCS, vol. 2568, pp. 22–37. Springer, Heidelberg (2003); Published in Natural Computing. DNA 2002 2, 439–461 (2003)

    MathSciNet  Google Scholar 

  29. Reif, J.H., Sahu, S., Yin, P.: Compact error-resilient computational DNA tiling assemblies. In: Tenth International Meeting on DNA Based Computers, DNA10 (2004)

    Google Scholar 

  30. Reif, J.H.: The emergence of the discipline of biomolecular computation. Biomolecular Computing, New Generation Computing 20(3), 217–236 (2002)

    Article  MATH  MathSciNet  Google Scholar 

  31. Reif, J.H.: Molecular assembly and computation: From theory to experimental demonstrations. In: Widmayer, P., Triguero, F., Morales, R., Hennessy, M., Eidenbenz, S., Conejo, R. (eds.) ICALP 2002, vol. 2380, pp. 1–21. Springer, Heidelberg (2002)

    Chapter  Google Scholar 

  32. Reif, J.H., LaBean, T.H., Seeman, N.C.: Challenges and applications for self-assembled dna nanostructures. In: Condon, A., Rozenberg, G. (eds.) DNA 2000. LNCS, vol. 2054, pp. 173–198. Springer, Heidelberg (2001)

    Chapter  Google Scholar 

  33. Robinson, R.M.: Undecidability and non periodicity of tilings of the plane. Inventiones Math 12, 177–209 (1971)

    Article  Google Scholar 

  34. Rothemund, P.W.K., Winfree, E.: The program-size complexity of self-assembled squares (extended abstract). In: Proceedings of the thirty-second annual ACM symposium on Theory of computing, pp. 459–468. ACM Press, New York (2000)

    Chapter  Google Scholar 

  35. Seeman, N.C.: De novo design of sequences for nucleic acid structural engineering. J. Biomol. Struct. Dyn. 8, 573–581 (1990)

    Google Scholar 

  36. Seeman, N.C.: Nucleic acid nanostructures and topology. Angew. Chem. Int. Ed. 37, 3220–3238 (1998)

    Article  Google Scholar 

  37. Seeman, N.C.: DNA in a material world. Nature 421, 427–431 (2003)

    Article  MathSciNet  Google Scholar 

  38. Seeman, N.C., Zhang, Y., Chen, J.: DNA nanoconstructions. J. Vac. Sci. Technol. 12(4), 1895–1903 (1994)

    Article  Google Scholar 

  39. Sha, R., Liu, F., Bruist, M.F., Seeman, N.C.: Parallel helical domains in DNA branched junctions containing 5’, 5’ and 3’, 3’ linkages. Biochemistry 38, 2832–2841 (1999)

    Article  Google Scholar 

  40. Sherman, W.B., Seeman, N.C.: A precisely controlled DNA biped walking device. Nano Lett 4, 1203–1207 (2004)

    Article  Google Scholar 

  41. Shin, J.S., Pierce, N.A.: A synthetic DNA walker for molecular transport. J. Am. Chem. Soc. 126, 10834–10835

    Google Scholar 

  42. Simmel, F.C., Yurke, B.: Using DNA to construct and power a nanoactuator. Phys. Rev. E 63, 041913 (2001)

    Article  Google Scholar 

  43. Simmel, F.C., Yurke, B.: A DNA-based molecular device switchable between three distinct mechanical states. Appl. Phys. Lett. 80, 883–885 (2002)

    Article  Google Scholar 

  44. Turberfield, A.J., Mitchell, J.C., Yurke Jr., B., Mills, A.P., Blakey, M.I., Simmel, F.C.: DNA fuel for free-running nanomachines. Phys. Rev. Lett. 90, 118102 (2003)

    Article  Google Scholar 

  45. Wang, H.: Proving theorems by pattern recognition ii. Bell Systems Technical Journal 40, 1–41 (1961)

    Google Scholar 

  46. Winfree, E.: Complexity of restricted and unrestricted models of molecular computation. In: Lipton, R.J., Baum, E.B. (eds.) DNA Based Computers. DIMACS, vol. 27, pp. 187–198. American Mathematical Society, Providence (1995)

    Google Scholar 

  47. Winfree, E.: On the computational power of DNA annealing and ligation. In: Lipton, R.J., Baum, E.B. (eds.) DNA Based Computers 1. DIMACS, vol. 27, pp. 199–221. American Mathematical Society, Providence (1996)

    Google Scholar 

  48. Winfree, E.: Algorithmic Self-Assembly of DNA. PhD thesis, California Institute of Technology (1998)

    Google Scholar 

  49. Winfree, E.: Simulation of computing by self-assembly. Technical Report 1998.22, Caltech (1998)

    Google Scholar 

  50. Winfree, E., Bekbolatov, R.: Proofreading tile sets: logical error correction for algorithmic self-assembly. In: DNA Based Computers 9. LNCS, vol. 2943, pp. 126–144 (2004)

    Google Scholar 

  51. Winfree, E., Eng, T., Rozenberg, G.: String tile models for DNA computing by self-assembly. In: DNA Based Computers 6, pp. 63–88 (2000)

    Google Scholar 

  52. 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)

    Article  Google Scholar 

  53. Winfree, E., Yang, X., Seeman, N.C.: Universal computation via self-assembly of DNA: Some theory and experiments. In: Landweber, L.F., Baum, E.B. (eds.) DNA Based Computers II. DIMACS, vol. 44, pp. 191–213. American Mathematical Society, Providence (1996)

    Google Scholar 

  54. Yan, H., Feng, L., LaBean, T.H., Reif, J.H.: Parallel molecular computation of pair-wise xor using DNA string tile. J. Am. Chem. Soc. 125(47) (2003)

    Google Scholar 

  55. 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)

    Article  Google Scholar 

  56. 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)

    Article  Google Scholar 

  57. Yan, H., Zhang, X., Shen, Z., Seeman, N.C.: A robust DNA mechanical device controlled by hybridization topology. Nature 415, 62–65 (2002)

    Article  Google Scholar 

  58. Yin, P., Guo, B., Belmore, C., Palmeri, W., Winfree, E., LaBean, T.H., Reif, J.H.: TileSoft: Sequence optimization software for designing DNA secondary structures. Technical Report CS-2004-09, Duke University, Computer Science Department (2004)

    Google Scholar 

  59. Yin, P., Sahu, S., Turberfield, A.J., Reif, J.H.: Design of autonomous DNA cellular automata (2004) (in preparation)

    Google Scholar 

  60. Yin, P., Turberfield, A.J., Reif, J.H.: Designs of autonomous unidirectional walking DNA devices. DNA Based Computers 10 (2004)

    Google Scholar 

  61. Yin, P., Turberfield, A.J., Sahu, S., Reif, J.H.: Design of an autonomous DNA nanomechanical device capable of universal computation and universal translational motion. DNA Based Computers 10 (2004)

    Google Scholar 

  62. Yin, P., Yan, H., Daniell, X.G., Turberfield, A.J., Reif, J.H.: A unidirectional DNA walker moving autonomously along a linear track. Angew. Chem. Int. Ed. 43, 4906–4911 (2004)

    Article  Google Scholar 

  63. Yurke, B., Turberfield Jr., A.J., Mills, A.P., Simmel, F.C., Neumann, J.L.: A DNA-fuelled molecular machine made of DNA. Nature 406, 605–608 (2000)

    Article  Google Scholar 

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Authors and Affiliations

  1. Department of Computer Science, Duke University, Box 90129, Durham, NC, 27708-0129, USA

    John H. Reif, Thomas H. LaBean, Sudheer Sahu, Hao Yan & Peng Yin

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  1. John H. Reif
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  2. Thomas H. LaBean
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  3. Sudheer Sahu
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  4. Hao Yan
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  5. Peng Yin
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Editor information

Editors and Affiliations

  1. Université de Rennes I and INRIA/IRISA, Campus de Beaulieu, 35042, Rennes Cedex, France

    Jean-Pierre Banâtre

  2. INRIA Rhône-Alpes - POP ART project, 655 avenue de l’Europe, 38330, Montbonnot, France

    Pascal Fradet

  3. LaMI UMR 8042 CNRS – Université d’Evry, Genopole, 523 place des Terrasses de l’Agora, 91000, Evry, France

    Jean-Louis Giavitto  & Olivier Michel  & 

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Reif, J.H., LaBean, T.H., Sahu, S., Yan, H., Yin, P. (2005). Design, Simulation, and Experimental Demonstration of Self-assembled DNA Nanostructures and Motors. In: Banâtre, JP., Fradet, P., Giavitto, JL., Michel, O. (eds) Unconventional Programming Paradigms. UPP 2004. Lecture Notes in Computer Science, vol 3566. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11527800_14

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  • DOI: https://doi.org/10.1007/11527800_14

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-27884-9

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