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Team:Gifu/Modeling
From 2014.igem.org
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<p>If you choose to create a model during your project, please write about it here. Modeling is not an essential part of iGEM, but we encourage any and all teams to model some aspect of their project. See previous "Best Model" awards for more information.</p>--> | <p>If you choose to create a model during your project, please write about it here. Modeling is not an essential part of iGEM, but we encourage any and all teams to model some aspect of their project. See previous "Best Model" awards for more information.</p>--> | ||
<h1 id="theme">Modeling</h1> | <h1 id="theme">Modeling</h1> | ||
| + | <h1 id="theme3">Summary</h1> | ||
<p> | <p> | ||
We examined the efficiency of circularization of mRNA in E. coli. The mRNA synthesized by transcription of induced plasmid may be considered that there are mainly 3 shape patterns in the process of circularization (fig.1). In this experiment, we carried out reverse transcription of RNA of Escherichia coli, and calculated the abundance ratio of each shape pattern by detecting specific sequences by using MPN-PCR (Most Probable Number-PCR). | We examined the efficiency of circularization of mRNA in E. coli. The mRNA synthesized by transcription of induced plasmid may be considered that there are mainly 3 shape patterns in the process of circularization (fig.1). In this experiment, we carried out reverse transcription of RNA of Escherichia coli, and calculated the abundance ratio of each shape pattern by detecting specific sequences by using MPN-PCR (Most Probable Number-PCR). | ||
</p> | </p> | ||
<p> | <p> | ||
| - | By examining the abundance ratio of sequence A, B or C, D , and B / A shows the probability that the reaction doesn’t start (step | + | By examining the abundance ratio of sequence A, B or C, D , and B / A shows the probability that the reaction doesn’t start (step Ⅰ). Also, we can calculate the probability that RNA will cyclize (step Ⅱ,Ⅲ) by C, D. |
By examining these, we investigated the rate-limiting step in the process of cyclization or probability to cyclization of the RNA. | By examining these, we investigated the rate-limiting step in the process of cyclization or probability to cyclization of the RNA. | ||
</p> | </p> | ||
| + | <h1 id="theme3">Experiment</h1> | ||
| + | <p> | ||
| + | We extracted total RNA from E. coli and then carried out the reverse transcription. This time we used the two types of primer; oligo dt primer and random primer. And we carried out reverse transcription with them. We serially diluted obtained cDNA, and calculated abundance rate by using MPN-PCR. | ||
| + | </p> | ||
| + | <h2> | ||
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| + | <p id="space"></p> | ||
</div> | </div> | ||
</body> | </body> | ||
</html> | </html> | ||
Revision as of 19:56, 17 October 2014
Modeling
Summary
We examined the efficiency of circularization of mRNA in E. coli. The mRNA synthesized by transcription of induced plasmid may be considered that there are mainly 3 shape patterns in the process of circularization (fig.1). In this experiment, we carried out reverse transcription of RNA of Escherichia coli, and calculated the abundance ratio of each shape pattern by detecting specific sequences by using MPN-PCR (Most Probable Number-PCR).
By examining the abundance ratio of sequence A, B or C, D , and B / A shows the probability that the reaction doesn’t start (step Ⅰ). Also, we can calculate the probability that RNA will cyclize (step Ⅱ,Ⅲ) by C, D. By examining these, we investigated the rate-limiting step in the process of cyclization or probability to cyclization of the RNA.
Experiment
We extracted total RNA from E. coli and then carried out the reverse transcription. This time we used the two types of primer; oligo dt primer and random primer. And we carried out reverse transcription with them. We serially diluted obtained cDNA, and calculated abundance rate by using MPN-PCR.
