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<p style="font-family: quicksand;font-size:130%;">Assumptions and Definition:</p><br> | <p style="font-family: quicksand;font-size:130%;">Assumptions and Definition:</p><br> | ||
− | <p style="font-family: roboto;font-size: | + | <p style="font-family: roboto;font-size:110%;"><u><b>Assumption: Switch MFE ∝ leakage</p></b></u> |
− | < | + | <p style="font-family: roboto;font-size:100%;"> |
− | + | ||
>> Switch MFE is the Gibbs free energy of a toehold switch folded in the most stable structure.<br> | >> Switch MFE is the Gibbs free energy of a toehold switch folded in the most stable structure.<br> | ||
>> Leakage is the level of reporter expression when switch is not activated by trigger.<br> | >> Leakage is the level of reporter expression when switch is not activated by trigger.<br> | ||
To activate toehold switch, an amount of energy is needed to open the toehold switch hairpin. Switch MFE reflects the difficulty for the toehold switch activation process. We assume that the more negative the Switch MFE, the harder for the activation to take place, and hence a lower leakage. </p> | To activate toehold switch, an amount of energy is needed to open the toehold switch hairpin. Switch MFE reflects the difficulty for the toehold switch activation process. We assume that the more negative the Switch MFE, the harder for the activation to take place, and hence a lower leakage. </p> | ||
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− | <u><b>Assumption:∆ G RBS-Linker ∝ Dynamic range</ | + | <u><b><p style="font-family: roboto;font-size:110%;">Assumption:∆ G RBS-Linker ∝ Dynamic range</p></b></u> |
>> ∆ G RBS-Linker is the Gibbs free energy of the sequence starting from the RBS to the linker(Figure).<br> | >> ∆ G RBS-Linker is the Gibbs free energy of the sequence starting from the RBS to the linker(Figure).<br> | ||
>> Dynamic range is the ratio of reporter expression between non- activated switch and trigger- activated switch. | >> Dynamic range is the ratio of reporter expression between non- activated switch and trigger- activated switch. | ||
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After the trigger opened the toehold switch hairpin, ribosome need to unwind the RBS- linker region to translate the RFP reporter gene. ∆ G RBS-linker reflects the difficulty for the unwinding process. It is assumed that the more negative the ∆ G RBS-linker , the harder for the translation to take place, and hence a lower dynamic range. It had already demonstrated that the ∆ G RBS-linker is correlated with the dynamic range in the original paper.<br><br> | After the trigger opened the toehold switch hairpin, ribosome need to unwind the RBS- linker region to translate the RFP reporter gene. ∆ G RBS-linker reflects the difficulty for the unwinding process. It is assumed that the more negative the ∆ G RBS-linker , the harder for the translation to take place, and hence a lower dynamic range. It had already demonstrated that the ∆ G RBS-linker is correlated with the dynamic range in the original paper.<br><br> | ||
− | <u><b>Assumption: MFE Difference ∝ Switch-trigger formation</b></u>< | + | <u><b><p style="font-family: roboto;font-size:110%;">Assumption: MFE Difference ∝ Switch-trigger formation</b></u></p> |
>> MFE difference is defined as the difference between switch MFE and MFE of the dimner.<br> | >> MFE difference is defined as the difference between switch MFE and MFE of the dimner.<br> | ||
Since ∆ G = -RTlnK, MFE difference(∆ G) is proportional to equilibrium concentration (K). Therefore, we assume that the higher the MFE difference, the higher the dimer concentration and hence the expression level. | Since ∆ G = -RTlnK, MFE difference(∆ G) is proportional to equilibrium concentration (K). Therefore, we assume that the higher the MFE difference, the higher the dimer concentration and hence the expression level. |
Revision as of 14:07, 24 October 2017