Minnesota/8 June 2009

From 2009.igem.org

(Difference between revisions)
Line 20: Line 20:
|RNA:lacP -> RNAp:lacP* || .01 ||
|RNA:lacP -> RNAp:lacP* || .01 ||
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|RNAp:lacP* -> lacP + lacO1 + RNAp:DNAgfp||30||
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|RNAp:DNAgfp -> RNAp + gfp_mRNA||30||
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|gfp_mRNA + rib -> rib:gfp_mRNA||100000||
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|rib:gfp_mRNA -> rib:gfp_mRNA_1 + gfp_mRNA||33||
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|-
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|rib:gfp_mRNA_1 -> rib + gfp||33||
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|tetR2 + aTc ↔ tetR2:aTc||2E+09||4E-04
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|tetR2:aTc + aTc  ↔ tetR2:aTc2|| number||
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|tetR2:aTc + tetO1 ↔ tetR2:tetO1:aTc||n||
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|tetR2:aTc2 + tetO1 ↔ tetR2:tetO1:aTc2||n||
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|tetR2:tetO1 + aTc ↔ tetR2:tetO1:aTc||n|| 
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|}
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k = .01
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RNAp:lacP* -> lacP + lacO1 + RNAp:DNAgfp k = 30
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RNAp:DNAgfp -> RNAp + gfp_mRNA k = 30
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gfp_mRNA + rib -> rib:gfp_mRNA     k = 100000
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rib:gfp_mRNA -> rib:gfp_mRNA_1 + gfp_mRNA  k = 33
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rib:gfp_mRNA_1 -> rib + gfp k = 33
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tetR2 + aTc  ↔ tetR2:aTc kf = 2E+09        kr = 4E-04
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tetR2:aTc + aTc  ↔ tetR2:aTc2
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tetR2:aTc + tetO1 ↔ tetR2:tetO1:aTc
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tetR2:aTc2 + tetO1 ↔ tetR2:tetO1:aTc2
+
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tetR2:tetO1 + aTc ↔ tetR2:tetO1:aTc
+
tetR2:tetO1:aTc + aTc ↔ tetR2:tetO1:aTc2
tetR2:tetO1:aTc + aTc ↔ tetR2:tetO1:aTc2
tetR2 -> Ø
tetR2 -> Ø

Revision as of 20:41, 28 July 2009

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Today the first model of the TNN system was created. In order to do this, the previous work of the Kaznessis group was used to provide a basis for a a lot of the reactions. This allowed us to easily obtain reasonable kinetic constants for almost all the reactions in the model. Here is the first incarnation of the model (many future models will simply change this one):

Reaction Forward Kinetic Constant Reverse Kinetic Constant
RNAp + lacP + lacI4:lacO1 -> RNAp:lacP6.23E+05
RNAp + lacP + lacO1 ↔ RNAp:lacP1E+07 1
RNA:lacP -> RNAp:lacP* .01
RNAp:lacP* -> lacP + lacO1 + RNAp:DNAgfp30
RNAp:DNAgfp -> RNAp + gfp_mRNA30
gfp_mRNA + rib -> rib:gfp_mRNA100000
rib:gfp_mRNA -> rib:gfp_mRNA_1 + gfp_mRNA33
rib:gfp_mRNA_1 -> rib + gfp33
tetR2 + aTc ↔ tetR2:aTc2E+094E-04
tetR2:aTc + aTc ↔ tetR2:aTc2 number
tetR2:aTc + tetO1 ↔ tetR2:tetO1:aTcn
tetR2:aTc2 + tetO1 ↔ tetR2:tetO1:aTc2n
tetR2:tetO1 + aTc ↔ tetR2:tetO1:aTcn


tetR2:tetO1:aTc + aTc ↔ tetR2:tetO1:aTc2 tetR2 -> Ø tetR2:aTc -> aTc tetR2:aTc2 -> 2 aTc tetR2 + nsDNA ↔ tetR2:nsDNA tetR2:aTc + nsDNA ↔ tetR2:aTc:nsDNA tetR2:aTc:nsDNA -> aTc + nsDNA tetR2:nsDNA -> nsDNA Ø -> tetR2 aTc -> Ø Ø -> aTc gfp_mRNA -> Ø k = 1.16E-03 gfp -> Ø k = 3.21E-05