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length unit: length
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notes: This is the model of the in vitro DNA oscillator called oligator with the optmized set of parameters described in the article: Programming an in vitro DNA oscillator using a molecular networking strategy. Montagne K, Plasson R, Sakai Y, Fujii T, Rondelez Y. Mol Syst Biol. 2011 Feb 1;7:466. PubmedID: 21283142 , Doi: 10.1038/msb.2010.120 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. The model reproduces the time courses in fig 2B. The parameter identifiers of the reaction constants are not the same as in the supplemental material, but are just called kXd and kXr for the forward and backwards constant of reaction X respectively. This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team. For more information see the terms of use . To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dhar…
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occurs in: http://identifiers.org/taxonomy/131567
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W3 CDTF: Thu Feb 17 01:23:22 GMT 2011

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value: 0.485802

800232
type: Reaction
kinetic law: 638108
reactant: 638083
fast: false
product: 638096
is: SBO:0000205
reversible: false
is version of: http://identifiers.org/ec-code/2.7.7.7
is version of: GO:0003887

638083
type: SpeciesReference
stoichiometry: 1.0
species: 800192

638096
type: SpeciesReference
stoichiometry: 1.0
species: 800197

W3 CDTF: Fri Apr 20 22:59:26 BST 2012

800323
type: Parameter
is: SBO:0000035
constant: true
units: 637865
value: 15.2

800276
type: Reaction
kinetic law: 639105
product: 639093
reactant: 639080
is version of: GO:0004527
is: SBO:0000179
fast: false
reversible: true

639093
type: SpeciesReference
stoichiometry: 1.0
species: 800225

639080
type: SpeciesReference
stoichiometry: 1.0
species: 800217

800364
type: Parameter
is: SBO:0000338
constant: true
units: 637865
value: 0.610714285714

800379
type: Parameter
is: SBO:0000039
constant: true
units: 637816
value: 4.15391351351E-5

800249
type: Reaction
kinetic law: 638510
product: 638498
reactant: 638486
is version of: GO:0004519
is: SBO:0000178
fast: false
reversible: false

638498
type: SpeciesReference
stoichiometry: 1.0
species: 800204

638486
type: SpeciesReference
stoichiometry: 1.0
species: 800209

800339
type: Parameter
is: SBO:0000339
constant: true
units: 637816
value: 0.0171

800356
type: Parameter
is: SBO:0000339
constant: true
units: 637816
value: 0.027

800380
type: Parameter
is: SBO:0000036
constant: true
units: 637816
value: 4.15391351351E-5

800260
type: Reaction
kinetic law: 638739
product: 638727
reactant: 638715
is version of: GO:0003677
is: SBO:0000205
fast: false
reversible: false

638727
type: SpeciesReference
stoichiometry: 1.0
species: 800221

638715
type: SpeciesReference
stoichiometry: 1.0
species: 800213

ORG:
  orgname: EMBL-EBI
n:
  given: Lukas
  family: Endler