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<p>By plotting the data into the prism and doing the following steps, the system can calculate automatically</p> | <p>By plotting the data into the prism and doing the following steps, the system can calculate automatically</p> | ||
+ | <p>Due to the aptamer has the ability to bind with non-specific site, thus we can add MX into the equation which lead to an increase in the affinity of the aptamer.</p> | ||
+ | <p>Using the data from the Aptamer experiments we can evaluate that the Kd of our aptamer is 1.806 μM, we also calculate the Kd from modeling experiment and the Kd of group 30mins, 60mins and 75mins are 0.05197,0.4477 and 0.2358 respectively.</p> | ||
+ | <p>However, the modeling experiment's Kd can't be defined in this way as the concentration is constant. Therefore the increase in Kd illustrate that liposome decomposed significantly under room temperature. And the data of 60mins group for modeling can't be used.</p> | ||
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<center> | <center> | ||
<img src="https://static.igem.org/mediawiki/2021/5/52/T--GreatBay_SCIE--Model_OApt_Kd.png" width="30%; height: auto;"> | <img src="https://static.igem.org/mediawiki/2021/5/52/T--GreatBay_SCIE--Model_OApt_Kd.png" width="30%; height: auto;"> |
Revision as of 00:13, 22 October 2021
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At first we planned to calculate Kd which can be derived from Hill equation
![](https://static.igem.org/mediawiki/2021/3/3c/T--GreatBay_SCIE--Dissociation.jpg)
But soon we found that it is impossible to calculate in this way as the seller of the ELISA kit can't tell us the concentration of the aptamer so we had to find another way.
This equation is derived from Michaelis–Menten kinetics
$$V=V_{max}\frac{[P]}{K_M\times{[P]}}$$
With slightly modification, we can obtain the following equation
$$Y=\frac{B_{max}\times X}{K_d+X}+M\times X$$
Where Bmax is the maximum specific binding in the same units as Y.
Kd is the equilibrium dissociation constant, in the same units as X. It is the radio-ligand concentration needed to achieve a half-maximum binding at equilibrium.
MX is the slope of nonspecific binding in Y units divided by X units.
By plotting the data into the prism and doing the following steps, the system can calculate automatically
Due to the aptamer has the ability to bind with non-specific site, thus we can add MX into the equation which lead to an increase in the affinity of the aptamer.
Using the data from the Aptamer experiments we can evaluate that the Kd of our aptamer is 1.806 μM, we also calculate the Kd from modeling experiment and the Kd of group 30mins, 60mins and 75mins are 0.05197,0.4477 and 0.2358 respectively.
However, the modeling experiment's Kd can't be defined in this way as the concentration is constant. Therefore the increase in Kd illustrate that liposome decomposed significantly under room temperature. And the data of 60mins group for modeling can't be used.
![](https://static.igem.org/mediawiki/2021/5/52/T--GreatBay_SCIE--Model_OApt_Kd.png)
![](https://static.igem.org/mediawiki/2021/2/2c/T--GreatBay_SCIE--Model_Kd_Graph.png)
![](https://static.igem.org/mediawiki/2021/3/3e/T--GreatBay_SCIE--Model_Kd_Graphs.png)
Reference
Equation: One site -- Specific binding https://www.graphpad.com/guides/prism/latest/curve-fitting/reg_one_site_specific.htm