Minnesota/24 June 2009

From 2009.igem.org

(Difference between revisions)
Line 5: Line 5:
|'''[[Minnesota/23 June 2009|Go to Previous Day (June 23)]]'''|| width=158|'''[[Minnesota/25 June 2009|Go to Next Day (June 25)]]'''
|'''[[Minnesota/23 June 2009|Go to Previous Day (June 23)]]'''|| width=158|'''[[Minnesota/25 June 2009|Go to Next Day (June 25)]]'''
|}
|}
 +
'''Patrick'''<br>
 +
 +
'''Ben'''<br>
Since there are several problems with the first TNN model, we are deciding to focus on them one at a time. The first thing to work on is the leakiness problem. In order to deal with this issue, we are including a reaction that allows for the binding of the RNA polymerase to the operator site even if the site is occupied by a tetR. This will allow for some expression at an aTc concentration of 0, because at this point tetR is almost always bound to the tetO operator.
Since there are several problems with the first TNN model, we are deciding to focus on them one at a time. The first thing to work on is the leakiness problem. In order to deal with this issue, we are including a reaction that allows for the binding of the RNA polymerase to the operator site even if the site is occupied by a tetR. This will allow for some expression at an aTc concentration of 0, because at this point tetR is almost always bound to the tetO operator.

Revision as of 21:40, 30 July 2009

Back to Notebook Home
Go to Previous Day (June 23)Go to Next Day (June 25)

Patrick

Ben
Since there are several problems with the first TNN model, we are deciding to focus on them one at a time. The first thing to work on is the leakiness problem. In order to deal with this issue, we are including a reaction that allows for the binding of the RNA polymerase to the operator site even if the site is occupied by a tetR. This will allow for some expression at an aTc concentration of 0, because at this point tetR is almost always bound to the tetO operator.

Here is the model we are working on:

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:aTc21E+081E-03
tetR2:aTc + tetO1 ↔ tetR2:tetO1:aTc1E+081
tetR2:aTc2 + tetO1 ↔ tetR2:tetO1:aTc21E+081E+05
tetR2:tetO1 + aTc ↔ tetR2:tetO1:aTc1E+081E-03
tetR2:tetO1:aTc + aTc ↔ tetR2:tetO1:aTc21E+081E-03
tetR2 -> Ø2.89E-04
tetR2:aTc -> aTc2.89E-04
tetR2:aTc2 -> 2 aTc2.89E-04
tetR2 + nsDNA ↔ tetR2:nsDNA10003.2409
tetR2:aTc + nsDNA ↔ tetR2:aTc:nsDNA10003.2409
tetR2:aTc:nsDNA -> aTc + nsDNA1.93E-04
tetR2:nsDNA -> nsDNA1.93E-04
Ø -> tetR21E-11
aTc_ext -> aTc3.3E-04
gfp_mRNA -> Ø1.16E-03
gfp -> Ø3.21E-05
RNAp + tetO1:tetR2 + lacP -> RNAp:lacP + tetR2311000
RNAp + tetO1:aTc:tetR2 + lacP -> RNAp:lacP + tetR2311000
RNAp + tetO1:aTc2:tetR2 + lacP -> RNAp:lacP + tetR2311000


Tnnatcvariesleaky3.jpgTnnexperiment.jpg

As you can see from the above graph, this model shows no response to aTc concentration. The gfp output is the same whether there are 0 or 260 molecules of aTc in the cell. Essentially this system is completely leaky, which is not what is needed. Also, the model still peaks and decreases, instead of plateauing.