Design and Numerical Analysis of RNA Oscillator

  • Masahiro Takinoue
  • Daisuke Kiga
  • Koh-ichiroh Shohda
  • Akira Suyama
Conference paper
Part of the Proceedings in Information and Communications Technology book series (PICT, volume 1)


In recent years, various types of DNA nanomachines driven by DNA hybridizations have been developed as one of remarkable applications of DNA computer for nanotechnology. Here, we propose an oscillator as a nanosystem to control the nanomachines. It was modeled after a circadian rhythm in life systems and utilized DNA/RNA and their molecular reactions. The molecular reactions were composed of nucleic-acid hybridization, RNA transcription, DNA extension, RNA degradation, and uracil-containing DNA degradation. Results of numerical analyses of rate equations for the reactions demonstrated that oscillatory condition of the system was decided by balance between RNA influx into the system and RNA degradation out of the system. The analytical results will provide much important information when the oscillator is constructed in in vitro experiments.


Bifurcation Diagram Stable Steady State Kinetic Simulation Unstable Steady State Oscillatory Reaction 
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Copyright information

© Springer Tokyo 2009

Authors and Affiliations

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

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