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New Generation Computing

, Volume 27, Issue 2, pp 107–127 | Cite as

RNA Oscillator: Limit Cycle Oscillations based on Artificial Biomolecular Reactions

  • Masahiro TakinoueEmail author
  • Daisuke Kiga
  • Koh-ichiroh Shohda
  • Akira Suyama
Article

Abstract

In recent years, various DNA nanomachines driven by DNA hybridizations have been developed as a remarkable application of DNA computers for nanotechnology. Here, we propose an oscillatory reaction system as a nano-sized nucleic acid engine to control the nanomachines. It utilizes DNA/RNA and their molecular reactions, and is modeled after the circadian rhythm in life systems. The molecular reactions consist of nucleic acid hybridization, RNA transcription, DNA extension, RNA degradation, and uracil-containing DNA degradation. Numerical analyses of rate equations for the reactions demonstrate that oscillatory conditions of the reaction system are determined by the balance between RNA influx into the system and RNA degradation out of the system. The analytical results will provide important information when the oscillator is constructed in in vitro experiments.

Keywords:

Limit Cycle Oscillation Nonlinear Nonequilibrium Open System Autonomous Nanomechanical Devices Molecular Reactions Bifurcation Analysis 

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References

  1. 1.
    Alberts, B., Johnson, A., Lewis, J., Raff, M. and Roberts, K., Molecular Biology of the Cell, Garland Science, 2008.Google Scholar
  2. 2.
    Atkinson, M. R., Savageau, M. A., Myers, J. T. and Ninfa, A. J., “Development of Genetic Circuitry Exhibiting Toggle Switch or Oscillatory Behavior in Escherichia coli,” Cell, 113, pp. 597–607, 2003.CrossRefGoogle Scholar
  3. 3.
    Chen, Y. and Mao, C., “Putting a Brake on an Autonomous DNA Nanomotor,” J. Am. Chem. Soc., 126, pp. 8626–8627, 2004.CrossRefGoogle Scholar
  4. 4.
    Dittmer, W. U., Kempter, S., Radler, J. O. and Simmel, F. C., “Using Gene Regulation to Program DNA-Based Molecular Devices,” Small, 1, pp. 709–712, 2005.CrossRefGoogle Scholar
  5. 5.
    Dittmer, W. U. and Simmel, F. C., “Transcriptional Control of DNA-Based Nanomachines,” Nano Lett., 4, pp. 689–691, 2004.CrossRefGoogle Scholar
  6. 6.
    Elowitz, M. B. and Leibler, S., “A synthetic oscillatory network of transcriptional regulators,” Nature, 403, pp. 335–338, 2000.CrossRefGoogle Scholar
  7. 7.
    Fall, C. P., Marland, E. S., Wagner, J. M. and Tyson, J. J., Computational Cell Biology, Springer, 2002.Google Scholar
  8. 8.
    Field, R. J. and Noyes, R. M., “Oscillations in chemical systems. IV. Limit cycle behavior in a model of a real chemical reaction,” J. Chem. Phys., 60, pp. 1877–1884, 1974.Google Scholar
  9. 9.
    Fung, E., Wong, W. W., Suen, J. K., Bulter, T., Lee, S.-g. and Liao, J. C., “A synthetic gene-metabolic oscillator,” Nature, 435, pp. 118–122, 2005.CrossRefGoogle Scholar
  10. 10.
    Hirano, N., Haruki, M., Morikawa, M. and Kanaya, S., “Enhancement of the Enzymatic Activity of Ribonuclease HI from Thermus thermophilus HB8 with a Suppressor Mutation Method,” Biochemistry, 39, pp. 13285–13294, 2000.CrossRefGoogle Scholar
  11. 11.
    Mao, C., Sun, W., Shen, Z. and Seeman, N. C., “A nanomechanical device based on the B-Z transition of DNA,” Nature, 397, pp. 144–146, 1999.CrossRefGoogle Scholar
  12. 12.
    Martint, C. T. and Coleman, J. E., “Kinetic Analysis of T7 RNA Polymerase-Promoter Interactions with Small Synthetic Promoters,” Biochemistry, 26, pp. 2690–2696, 1987.CrossRefGoogle Scholar
  13. 13.
    Murray, J. D., Mathematical Biology I: An Introduction, 3rd ed., Springer, 2002.Google Scholar
  14. 14.
    Nicolis, G. and Prigogine, I., Self-Organization in Nonequilibrium Systems -From Dissipative Structures to Order through Fluctuations, John Wiley & Sons, 1977.Google Scholar
  15. 15.
    Seelig, G., Yurke, B. and Winfree, E., “Catalyzed Relaxation of a Metastable DNA Fuel,” J. Am. Chem. Soc., 128, pp. 12211–12220, 2006.CrossRefGoogle Scholar
  16. 16.
    Sherman, W. B. and Seeman, N. C., “A Precisely Controlled DNA Biped Walking Device,” Nano Lett., 4, pp. 1203–1207, 2004.CrossRefGoogle Scholar
  17. 17.
    Shin, J.-S. and Pierce, N. A., “A Synthetic DNA Walker for Molecular Transport,” J. Am. Chem. Soc., 126, pp. 10834–10835, 2004.CrossRefGoogle Scholar
  18. 18.
    Simmel, F. C. and Dittmer, W. U., “DNA Nanodevices,” Small, 1, pp. 284–299, 2005.CrossRefGoogle Scholar
  19. 19.
    Strogatz, S. H., Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry, and Engineering, Westview Pr, 2001.Google Scholar
  20. 20.
    Takinoue, M., Kiga, D., Shohda, K.-i. and Suyama, A., “Design and numerical analysis of RNA oscillator,” Proceedings in Information and Communications Technology: Natural Computing, 1, pp. 201–212, 2008.Google Scholar
  21. 21.
    Takinoue, M., Kiga, D., Shohda, K.-i. and Suyama, A., “Experiments and simulation models of a basic computation element of an autonomous molecular computing system,” Phys. Rev. E., 78, article no. 041921, 2008.Google Scholar
  22. 22.
    Tian, Y., He, Y., Chen, Y., Yin, P. and Mao, C., “A DNAzyme That Walks Processively and Autonomously along a One-Dimensional Track,” Angew. Chem. Int. Ed., 44, pp. 2–5, 2005.Google Scholar
  23. 23.
    Tian, Y. and Mao, C., “Molecular Gears: A Pair of DNA Circles Continuously Rolls against Each,” J. Am. Chem. Soc., 126, pp. 11410–11411, 2004.CrossRefGoogle Scholar
  24. 24.
    Turberfield, A. J., Mitchell, J. C., Yurke, B., Mills Jr., A. P., Blakey, M. I. and Simmel, F. C., “DNA Fuel for Free-Running Nanomachines”, Phys. Rev. Lett., 90, article no. 118102, 2003.Google Scholar
  25. 25.
    Varshney, U. and Sande, J. H. v. d., “Specificities and Kinetics of Uracil Excision from Uracil-Containing DNA Oligomers by Escherichia coli Uracil DNA Glycosylase,” Biochemistry, 30, pp. 4055–4061, 1991.CrossRefGoogle Scholar
  26. 26.
    Yan, H., Zhang, X., Shen, Z. and Seeman, N. C., “A robust DNA mechanical device controlled by hybridization topology,” Nature, 415, pp. 62–65, 2002.CrossRefGoogle Scholar
  27. 27.
    Yin, P., Yan, H., Daniell, X. G., Turberfield, A. J. and Reif, J. H., “A Unidirectional DNAWalker That Moves Autonomously along a Track,” Angew. Chem. Int. Ed., 43, pp. 4906–4911, 2004.CrossRefGoogle Scholar
  28. 28.
    Yurke, B., Turberfield, A. J., Mills Jr., A. P., Simmel, F. C. and Neumann, J. L., “A DNA-fuelled molecular machine made of DNA,” Nature, 406, pp. 605–608, 2000.CrossRefGoogle Scholar

Copyright information

© Ohmsha and Springer Japan jointly hold copyright of the journal. 2009

Authors and Affiliations

  • Masahiro Takinoue
    • 1
    Email author
  • Daisuke Kiga
    • 2
  • Koh-ichiroh Shohda
    • 3
  • Akira Suyama
    • 3
  1. 1.Department of Life Sciences and Institute of PhysicsThe University of TokyoTokyoJapan
  2. 2.Department of Computational Intelligence and System ScienceTokyo Institute of TechnologyYokohamaJapan
  3. 3.Department of Life Sciences and Institute of PhysicsThe University of TokyoTokyoJapan

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