title: Programming an in vitro DNA oscillator using a molecular networking strategy.
abstract: Living organisms perform and control complex behaviours by using webs of chemical reactions organized in precise networks. This powerful system concept, which is at the very core of biology, has recently become a new foundation for bioengineering. Remarkably, however, it is still extremely difficult to rationally create such network architectures in artificial, non-living and well-controlled settings. We introduce here a method for such a purpose, on the basis of standard DNA biochemistry. This approach is demonstrated by assembling de novo an efficient chemical oscillator: we encode the wiring of the corresponding network in the sequence of small DNA templates and obtain the predicted dynamics. Our results show that the rational cascading of standard elements opens the possibility to implement complex behaviours in vitro. Because of the simple and well-controlled environment, the corresponding chemical network is easily amenable to quantitative mathematical analysis. These synthetic systems may thus accelerate our understanding of the underlying principles of biological dynamic modules.
authors.affiliation: LIMMS/CNRS-IIS, Institute of Industrial Science, University of Tokyo, Meguro-ku, Tokyo, Japan.
authors.forename: Kevin
authors.initials: K
authors.lastname: Montagne
authors.forename: Raphael
authors.initials: R
authors.lastname: Plasson
authors.forename: Yasuyuki
authors.initials: Y
authors.lastname: Sakai
authors.forename: Teruo
authors.initials: T
authors.lastname: Fujii
authors.forename: Yannick
authors.initials: Y
authors.lastname: Rondelez
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D025461:Feedback, Physiological; D053263:Gene Regulatory Networks; D007700:Kinetics; D008957:Models, Genetic; D016133:Polymerase Chain Reaction; D058615:Synthetic Biology; D049490:Systems Biology / Q000379:methods; D013816:Thermodynamics
chemical_list: D004247:DNA