Rna oscillator: Limit cycle oscillations based on artificial biomolecular reactions

Masahiro Takinoue*, Daisuke Kiga, Koh Ichiroh Shohda, Akira Suyama

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

7 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)107-127
Number of pages21
JournalNew Generation Computing
Issue number2
Publication statusPublished - 2009 Feb
Externally publishedYes


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

ASJC Scopus subject areas

  • Software
  • Theoretical Computer Science
  • Hardware and Architecture
  • Computer Networks and Communications


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