Genetic Programming and Evolvable Machines

, Volume 4, Issue 2, pp 111–122 | Cite as

Using DNA to Power Nanostructures

  • Bernard Yurke
  • Allen P. MillsJr.


DNA hybridization has been used to power a number of DNA-based nanostructures constructed out of DNA. Here some considerations that go into DNA-based motor design are briefly reviewed. The emphasis will be on the operation of toeholds, single-stranded sections of DNA that facilitate the process of strand removal during certain points in the operation of a DNA-based motor. Reaction kinetics measurements for toehold mediated strand exchange are reported. These measurements have served as a guide for choosing toehold lengths.

molecular motors DNA nanostructures toeholds strand exchange reaction kinetics 


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  1. 1.
    V. Balzani, A. Credi, F. M. Raymo, and J. F. Stoddart, “Artifical molecular machines,” Angew. Chem. Int. Ed., vol. 39,no. 19, pp. 3349-3391, 2000.CrossRefGoogle Scholar
  2. 2.
    R.J. Britten and D.E. Kohne, “Repeated Sequences in DNA,” Science, vol. 161,no. 3841, pp. 529-540, 1968.Google Scholar
  3. 3.
    J. H. Chen and N. C. Seeman, “Synthesis from DNA of a molecule with the connectivity of a cube,” Nature, vol. 350,no. 6319, pp. 631-633, 1991.CrossRefGoogle Scholar
  4. 4.
    X. N. Chen, B. Zehnbauer, A. Gnirke, and P.-Y. Kwok, “Fluorescence energy transfer detection as a homogeneous DNA diagnostic method,” Proc. Natl. Acad. Sci. USA, vol. 94,no. 20, pp. 10756-10761, 1991.CrossRefGoogle Scholar
  5. 5.
    A. K. Eggleston and S. C. Kowalczykowski, “An overview of homologous pairing and DNA strand exchange proteins,” Biochemie, vol. 73,no. 2–3, pp. 163-176, 1991.CrossRefGoogle Scholar
  6. 6.
    M. Eigen and P. Schuster, The Hypercycle, A Principle of Natural Self-Organization, Springer: Berlin, 1979.Google Scholar
  7. 7.
    E. H. Ekland, J. W. Szostak, and D. P. Bartel, “Structurally complex and highly-active RNA ligases derived from random RNA sequences,” Science, vol. 269,no. 5222, pp. 364-370, 1995.Google Scholar
  8. 8.
    B. Essevaz-Roulet, U. Bockelmann, and F. Heslot, “Mechanical separation of the complementary strands of DNA,” Proc. Natl. Acad. Sci., USA, vol. 94,no. 22, pp. 11935-11940, 1997.CrossRefGoogle Scholar
  9. 9.
    C. Green and C. Tibbetts, “Reassociation rate limited displacement of DNA strands by branch migration,” Nucl. Acids Res., vol. 9,no. 8, pp. 1905-1918, 1981.Google Scholar
  10. 10.
    M. J. Heller and L. E. Morrison, in Rapid Detection and Identification of Infectious Agents, D. T. Kingsbury and S. Falkow (eds.), Academic Press, New York, 1985, pp. 245-256.Google Scholar
  11. 11.
    K. D. James and A. D. Ellington, “The search for missing links between self-replicating nucleic-acids and the RNA world,” Origins of Life and Evolution of the Biosphere, vol. 25,no. 6, pp. 515-530, 1995.CrossRefGoogle Scholar
  12. 12.
    W. K. Johnston, P. J. Unrau, M. S. Lawrence, M. E. Glasner, and D. P. Bartel, “RNA-catalyzed RNA polymerization: Accurate and general RNA-templated primer extension,” Science, vol. 292,no. 5520, pp. 1319-1325, 2001.CrossRefGoogle Scholar
  13. 13.
    N. Koumura, R. W. J. Zijlstra, R. A. van Delden, N. Harada, and B. L. Feringa, “Light-driven monodirectional molecular rotor,” Nature, vol. 401,no. 6749, pp. 152-155, 1999.CrossRefGoogle Scholar
  14. 14.
    T. Li and K.C. Nicolaou, “Chemical self-replication of palindromic duplex DNA,” Nature, vol. 369,no. 6477, pp. 218-221, 1994.CrossRefGoogle Scholar
  15. 15.
    J. J. Li and W. Tan, “A single DNA molecule nanomotor,” Nano Lett., vol. 2,no. 4, pp. 315-318, 2002.zbMATHMathSciNetCrossRefGoogle Scholar
  16. 16.
    J. Liphardt, B. Onoa, S. B. Smith, I. Tinoco, Jr., and C. Bustamante, “Reversible unfolding of single RNA molecules by mechanical force,” Science, vol. 292,no. 5517, pp. 733-737, 2001.CrossRefGoogle Scholar
  17. 17.
    C. D. Mao, T. H. LaBean, J. H. Reif, and N. C. Seeman, “Logical computation using algorithmic self-assembly of DNA triple-crossover molecules,” Nature, vol. 407,no. 6803, pp. 493-496, 2000.CrossRefGoogle Scholar
  18. 18.
    C. D. Mao, W. Q. Sun, and N. C. Seeman, “Assembly of Borromean rings from DNA,” Nature, vol. 386,no. 6621, pp. 137-138, 1997.CrossRefGoogle Scholar
  19. 19.
    C. D. Mao, W. Q. Sun, Z. Y. Shen, and N. C. Seeman, “A nanomechanical device based on the B-Z transition of DNA,” Nature, vol. 397,no. 6715, pp. 144-146, 1999.CrossRefGoogle Scholar
  20. 20.
    J. C. Mitchell and B. Yurke, “DNA Scissors,” in DNA Computing, N. Jonoska and N. C. Seeman (eds.), 7th International Workshop on DNA-Based Computers, DNA7 Tampa, FL, USA, June 10–13, 2001, Springer, 2002, pp. 263-268.Google Scholar
  21. 21.
    L. E. Morrison, T. C. Halder, and L. M. Stols, “Solution-phase detection of polynucleotides using interacting fluorescent labels and competitive hybridization,” Anal. Biochem., vol. 183,no. 2, pp. 231-244, 1989.CrossRefGoogle Scholar
  22. 22.
    L. E. Morrison and L. M. Stols, “Sensitive fluorescence-based thermodynamic and kinetic measurements of DNA hybridization in solution,” Biochemistry, vol. 32,no. 12, pp. 3095-3104, 1993.CrossRefGoogle Scholar
  23. 23.
    C.M. Niemeyer and M. Adler, “Nanomechanical Devices Based on DNA,” Angew. Chem. Int. Ed., vol. 41,no. 20, pp. 3779-3783, 2002.CrossRefGoogle Scholar
  24. 24.
    N. Paul and G. F. Joyce, “A self-replicating ligase ribozyme,” Proc. Natl. Acad. Sci. USA, vol. 99,no. 20, pp. 12733-12740, 2002.CrossRefGoogle Scholar
  25. 25.
    C. M. Radding, K. L. Beattie, W. K. Holloman, and R. C. Wiegand, “Uptake of homologous single-stranded fragments by superhelical DNA: IV branch migration,” J. Mol. Biol., vol. 116,no. 4, pp. 825-839, 1977.CrossRefGoogle Scholar
  26. 26.
    M. Rief, H. Clausen-Schaumann, and H.E. Gaub, “Sequence-dependent mechanics of single DNA molecules,” Nat. Struct. Biol., vol. 6,no. 4, pp. 346-349, 1999.CrossRefGoogle Scholar
  27. 27.
    J. SantaLucia, Jr., “A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics,” Proc. Natl. Acad. Sci. USA, vol. 95,no. 4, pp. 1460-1465, 1998.CrossRefGoogle Scholar
  28. 28.
    D. Sievers and G. von Kiedrowski, “Self replication of complementary nucleotide-based oligomers,” Nature, vol. 369,no. 6477, pp. 221-224, 1994.CrossRefGoogle Scholar
  29. 29.
    F. C. Simmel and B. Yurke, “Using DNA to construct and power a nanoactuator,” Phys. Rev. E, vol. 63,no. 4, art. no. 041913, 2001.Google Scholar
  30. 30.
    F. C. Simmel and B. Yurke, “A DNA-based molecular device switchable between three distinct mechanical states,” Appl. Phys. Lett., vol. 80,no. 5, pp. 883-885, 2002.CrossRefGoogle Scholar
  31. 31.
    S. B. Smith, Y. J. Cui, and C. Bustamante, “Overstretching B-DNA: The elastic response of individual double-stranded and single-stranded DNA molecules,” Science, vol. 271,no. 5250, pp. 795-799, 1996.Google Scholar
  32. 32.
    B. Tinland, A. Pluen, J. Sturm, and G. Weill, “Persistence length of single-stranded DNA,” Macromolecules, vol. 30,no. 19, pp. 5763-5765, 1997.CrossRefGoogle Scholar
  33. 33.
    A.J. Turberfield, B. Yurke, and A.P. Mills, Jr., “DNA hybridization catalysts and molecular tweezers,” in DNA Based Computers V, E. Winfree and D.K. Gifford (eds.), DLMACS Series in Discrete Mathematics and Theoretical Computer Science, vol. 54, 2000, pp. 171-182.Google Scholar
  34. 34.
    J.G. Wetmur and N. Davidson, “Kinetics of Renaturation of DNA,” J. Mol. Biol., vol. 31,no. 3, pp. 349-370, 1968.CrossRefGoogle Scholar
  35. 35.
    E. Winfree, F. R. Lui, L. A. Wenzler, and N. C. Seeman, “Design and self-assembly of two-dimensional DNA crystals,” Nature, vol. 394,no. 6693, pp. 539-544, 1998.CrossRefGoogle Scholar
  36. 36.
    H. Yan, X. P. Zhang, Z. Y. Shen, and N. C. Seeman, “A robust DNA mechanical device controlled by hybridization topology,” Nature, vol. 415,no. 6867, pp. 62-65, 2002.CrossRefGoogle Scholar
  37. 37.
    B. Yurke, A. J. Turberfield, A. P. Mills, Jr., F. C. Simmel, and J. L. Neumann, “A DNA-fuelled molecular machine made of DNA,” Nature, vol. 406,no. 6796, pp. 605-608, 2000.CrossRefGoogle Scholar
  38. 38.
    Y. W. Zhang and N. C. Seeman, “Construction of a DNA-truncated Octahedron,” J. Am. Chem. Soc., vol. 116,no. 5, pp. 1661-1669, 1994.CrossRefGoogle Scholar

Copyright information

© Kluwer Academic Publishers 2003

Authors and Affiliations

  • Bernard Yurke
    • 1
  • Allen P. MillsJr.
    • 2
  1. 1.Bell LaboratoriesLucent TechnologiesMurray Hill
  2. 2.Department of PhysicsUniversity of CaliforniaRiverside

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