Difference between revisions of "Team:NYU Abu Dhabi/Model"
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$$ 6. Pr:D:S:P \to 2D + S + P + Pr + D $$ | $$ 6. Pr:D:S:P \to 2D + S + P + Pr + D $$ | ||
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| + | <h2>Based on the reaction model above, the following equations could be deduced: | ||
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| + | <img src="https://static.igem.org/mediawiki/2018/2/2a/T--NYU_Abu_Dhabi--equations2.JPG"class="center"> | ||
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Revision as of 21:23, 17 October 2018
Mathematical Modelling
The following species were used
Species Name |
Symbol Used |
|---|---|
Recombinase |
\(R\) |
Primer |
\(Pr\) |
DNA |
\(D\) |
DNA Polymerase |
\(P\) |
Single Strand Binding Protein (SSB) |
\(S\) |
A specific binding of recombinase to a primer to form a closed complex |
\(R:Pr\) |
A specific binding of recombinase and primer to the DNA to form a closed complex |
\(R:Pr:D\) |
A specific binding of recombinase, primer, SSB protein to the DNA to form a closed complex |
\(R:Pr:D:S\) |
A specific binding of recombinase, primer, SSB protein, DNA Polymerase to the DNA to form a closed complex |
\(R:Pr:D:S:P\) |
A specific binding of primer, SSB protein, DNA Polymerase to the DNA to form a closed complex |
\(Pr:D:S:P\) |
The following parameters were used
Parameter |
Variable Name |
|---|---|
Forward rate constant for the binding of Recombinase and Primer |
\(k1f\) |
Reverse rate constant for the binding of Recombinase and Primer |
\(k1r\) |
Forward rate constant for the binding of Recombinase, Primer to DNA |
\(k2f\) |
Reverse rate constant for the binding of Recombinase, Primer to DNA |
\(k2r\) |
Forward rate constant for the binding of Recombinase, Primer, DNA to SSB protein |
\(k3f\) |
Reverse rate constant for the binding of Recombinase, Primer, DNA to SSB protein |
\(k3r\) |
Forward rate constant for the binding of Recombinase, Primer, DNA, SSB protein to DNA Polymerase |
\(k4f\) |
Reverse rate constant for the binding of Recombinase, Primer, DNA, SSB protein to DNA Polymerase |
\(k4r\) |
Forward rate constant for the unbinding of Recombinase from the Recombinase, Primer, DNA, SSB protein, DNA Polymerase complex |
\(k5f\) |
Reverse rate constant for the unbinding of Recombinase from the Recombinase, Primer, DNA, SSB protein, DNA Polymerase complex |
\(k5r\) |
Rate constant for the replication of DNA with the complex consists of Primer, DNA, SSB Protein, DNA Polymerase |
\(kf\) |
$$ 1. R + Pr \leftrightharpoons R:Pr $$ $$ 2. R:Pr + D \leftrightharpoons R:Pr:D $$ $$ 3. R:Pr:D + S \leftrightharpoons R:Pr:D:S $$ $$ 4. R:Pr:D:S + P \leftrightharpoons R:Pr:D:S:P $$ $$ 5. R:Pr:D:S:P \leftrightharpoons R + Pr:D:S:P $$ $$ 6. Pr:D:S:P \to 2D + S + P + Pr + D $$
Based on the reaction model above, the following equations could be deduced:
