Rna oscillator: Limit cycle oscillations based on artificial biomolecular reactions

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

Research output: Contribution to journalArticle

7 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)107-127
Number of pages21
JournalNew Generation Computing
Volume27
Issue number2
DOIs
Publication statusPublished - 2009 Feb
Externally publishedYes

Fingerprint

Limit Cycle
RNA
DNA
Oscillation
Degradation
Nucleic acids
Circadian Rhythm
Nanotechnology
Rate Equations
Transcription
Engine
Engines
Demonstrate
Experiment
Experiments

Keywords

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

ASJC Scopus subject areas

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

Cite this

Rna oscillator : Limit cycle oscillations based on artificial biomolecular reactions. / Takinoue, Masahiro; Kiga, Daisuke; Shohda, Koh Ichiroh; Suyama, Akira.

In: New Generation Computing, Vol. 27, No. 2, 02.2009, p. 107-127.

Research output: Contribution to journalArticle

Takinoue, Masahiro ; Kiga, Daisuke ; Shohda, Koh Ichiroh ; Suyama, Akira. / Rna oscillator : Limit cycle oscillations based on artificial biomolecular reactions. In: New Generation Computing. 2009 ; Vol. 27, No. 2. pp. 107-127.
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