Difference between revisions of "Team:TJU China/Model"

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                 transcription of smURFP.However,because the promoter $P_{arsR_{d}}$ has already bound with ArsR,as a result,RNAP
 
                 transcription of smURFP.However,because the promoter $P_{arsR_{d}}$ has already bound with ArsR,as a result,RNAP
 
                 can't bind with the promoter $P_{arsR_{d}}$. can’t bind with the promoter $P_{arsR_{d}}$.</div>
 
                 can't bind with the promoter $P_{arsR_{d}}$. can’t bind with the promoter $P_{arsR_{d}}$.</div>
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             <div class="word">However,at the presence of $As^{3+}$,it can bind with ArsR,then dissociate ArsR and $P_{arsR_{d}}$,which makes the combination of RNAP and $P_{arsR_{d}}$ possible.</div>
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             <div class="word">However,at the presence of $As^{3+}$,it can bind with ArsR,then dissociate ArsR and $P_{arsR_{d}}$ , which makes the combination of RNAP and $P_{arsR_{d}}$ possible.</div>
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            <div class="pic"><img src="https://static.igem.org/mediawiki/2018/4/4d/T--TJU_China--m3.png"></div>
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            <div class="word">We then take degradation into account: </div>
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Revision as of 18:41, 16 October 2018

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Dynamic Model of Heavy Metal Detection Biosensor
Minghui Yin,Sherry Dongqi Bao
TianJin University
October 15,2018
1 Introduction
Modeling is a powerful tool in synthetic biology. It provides us with a necessary engineering approach to characterize our pathways quantitatively and predict their performance,thus help us test and modify our design.Through the dynamic model of heavy-metal detection biosensor,we hope to gain insights into the characteristics of our whole circuit's dynamics.
2 Methods
2.1 Analysis of metabolic pathways
Figure 1: Metabolic pathways related to plasmid#1
At the beginning, on the plasmid#1, the promoter $P_{arsR}$ isn't bound with ArsR,thus it is active.ArsR and smURFP are transcribed and translated under the control of the promoters $P_{arsR_{u}}$ and $P_{arsR_{d}}$,with subscript u and d representing upstream and downstream separately.The subscript l of smURFP in the equation means leaky expression without the expression of $As^{3+}$.As ArsR is expressed gradually,it will bind with the promoter $P_{arsR}$ and make it inactive.[1]
On the plasmid#2,the fusion protein of dCas9 and RNAP(RNA polymerase) are produced after transcription and translation,and sgRNA is produced after transcription.
Figure 2: Metabolic pathways related to dCas9/RNAP
dCas9(*RNAP) can bind with its target DNA sequence without cutting, which is at the upstream of the promoter $P_{arsR_{d}}$.Simulataneously,dCas9 can lead RNAP to bind with the promoter $P_{arsR_{d}}$ and enhance the transcription of smURFP.However,because the promoter $P_{arsR_{d}}$ has already bound with ArsR,as a result,RNAP can't bind with the promoter $P_{arsR_{d}}$. can’t bind with the promoter $P_{arsR_{d}}$.
However,at the presence of $As^{3+}$,it can bind with ArsR,then dissociate ArsR and $P_{arsR_{d}}$ , which makes the combination of RNAP and $P_{arsR_{d}}$ possible.
We then take degradation into account: