RNA Oscillator: Limit Cycle Oscillations based on Artificial Biomolecular Reactions
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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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- 1.Alberts, B., Johnson, A., Lewis, J., Raff, M. and Roberts, K., Molecular Biology of the Cell, Garland Science, 2008.Google Scholar
- 7.Fall, C. P., Marland, E. S., Wagner, J. M. and Tyson, J. J., Computational Cell Biology, Springer, 2002.Google Scholar
- 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
- 13.Murray, J. D., Mathematical Biology I: An Introduction, 3rd ed., Springer, 2002.Google Scholar
- 14.Nicolis, G. and Prigogine, I., Self-Organization in Nonequilibrium Systems -From Dissipative Structures to Order through Fluctuations, John Wiley & Sons, 1977.Google Scholar
- 19.Strogatz, S. H., Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry, and Engineering, Westview Pr, 2001.Google Scholar
- 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.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.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
- 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