TY - JOUR
T1 - Rna oscillator
T2 - Limit cycle oscillations based on artificial biomolecular reactions
AU - Takinoue, Masahiro
AU - Kiga, Daisuke
AU - Shohda, Koh Ichiroh
AU - Suyama, Akira
N1 - Funding Information:
We thank Dr. Mitsunori Takano and Dr. Hiroshi Yoshida for helpful discussions. This work was supported by a grant for SENTAN (Development of Systems and Technology for Advanced Measurement and Analysis) from the Japan Science and Technology Agency (JST), and by a grant-in-aid for the 21st Century COE program “Research Center for Integrated Science” and for Science Research on the Priority Area “Molecular Programming” from the Ministry of Education, Culture, Sports, Science, and Technology of Japan. It was also supported by Research Fellowship of the Japan Society for the Promotion of Science for Young Scientists to Masahiro Takinoue.
Funding Information:
oMasahir akinoue,T .:Ph.D He is a biophysicist, and received a B.S. in Physics in 2002 and a Ph.D. in Biophysics in 2007 from the University of Tokyo. After serving as a postdoctoral fellow of Research Fellowship for Young Scientists of Japan Society for the Promotion of Science (JSPS), he has been a postdoctoral fellow of Kyoto University since 2008. His current research interests are DNA nanotechnology, DNA computing, and Nonlinear nonequilibrium phenomena in biophysical system.
PY - 2009/2
Y1 - 2009/2
N2 - 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.
AB - 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.
KW - Autonomous Nanomechanical Devices
KW - Bifurcation Analysis
KW - Limit Cycle Oscillation
KW - Molecular Reactions
KW - Nonlinear Nonequilibrium Open System
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U2 - 10.1007/s00354-008-0057-5
DO - 10.1007/s00354-008-0057-5
M3 - Article
AN - SCOPUS:70349581952
SN - 0288-3635
VL - 27
SP - 107
EP - 127
JO - New Generation Computing
JF - New Generation Computing
IS - 2
ER -