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● Expression leakage is a phenomenon where the reporter (i.e. Red Fluorescent Protein in our project) is expressed in the absence of trigger RNA. The level of leakage can be measured as: | ● Expression leakage is a phenomenon where the reporter (i.e. Red Fluorescent Protein in our project) is expressed in the absence of trigger RNA. The level of leakage can be measured as: | ||
− | <p><center><img src="https://static.igem.org/mediawiki/2017/3/32/CUHK_leakage.png" width=" | + | <p><center><img src="https://static.igem.org/mediawiki/2017/3/32/CUHK_leakage.png" width="30%" height="auto" class=" igem-logo"></center></p> |
<p style="font-family: roboto;font-size:115%;"> | <p style="font-family: roboto;font-size:115%;"> | ||
To activate toehold switch, an amount of energy is needed to open the toehold switch hairpin. The Switch MFE reflects the difficulty for the toehold switch unwinding process. We assume that the more negative the Switch MFE, the harder for the unwinding to take place, and hence a lower leakage. | To activate toehold switch, an amount of energy is needed to open the toehold switch hairpin. The Switch MFE reflects the difficulty for the toehold switch unwinding process. We assume that the more negative the Switch MFE, the harder for the unwinding to take place, and hence a lower leakage. | ||
</p> | </p> | ||
<br> | <br> | ||
− | + | <b><p style="font-family: roboto;font-size:125%;color:blue">Assumption 2: ΔG<sub>RBS-Linker</sub> correlates with the duplex expression</p></b> | |
<p style="font-family: roboto;font-size:115%;"> | <p style="font-family: roboto;font-size:115%;"> | ||
● ΔG<sub>RBS-Linker</sub> is the Gibbs free energy of the RNA sequence starting from the RBS to the linker in the switch-trigger duplex.<br> | ● ΔG<sub>RBS-Linker</sub> is the Gibbs free energy of the RNA sequence starting from the RBS to the linker in the switch-trigger duplex.<br> | ||
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<br><br> | <br><br> | ||
− | + | <b><p style="font-family: roboto;font-size:125%;color:blue">Assumption 3: ΔMFE correlates with the duplex expression</b></p> | |
<p style="font-family: roboto;font-size:115%;"> | <p style="font-family: roboto;font-size:115%;"> | ||
● ΔMFE is defined as MFE of the switch-trigger duplex RNA minus (switch RNA MFE + trigger RNA MFE). | ● ΔMFE is defined as MFE of the switch-trigger duplex RNA minus (switch RNA MFE + trigger RNA MFE). | ||
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Therefore, we assume that the more negative the MFE difference is, the higher the switch-trigger duplex RNA concentration compared to that of the switch RNA when in equilibrium. | Therefore, we assume that the more negative the MFE difference is, the higher the switch-trigger duplex RNA concentration compared to that of the switch RNA when in equilibrium. | ||
<br> | <br> | ||
− | <center>Switch RNA+Trigger RNA↔Duplex RNA</center> | + | <p style="font-family: roboto;font-size:115%;"><center>Switch RNA+Trigger RNA↔Duplex RNA</center></p> |
<br> | <br> | ||
<p style="font-family: roboto;font-size:115%;"> | <p style="font-family: roboto;font-size:115%;"> |
Revision as of 02:26, 2 November 2017