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


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.


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


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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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