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As is shown in the diagram, 2 Cre molecules bind with 1 loxP site successively, either on cDNA or P<sub>target</sub>. Four Cre molecules will form a Holliday junction, and thus starting the recombination reaction. Two pairs of loxP will work together and complete the strand exchange between cDNA and P<sub>target</sub>. After that, the recombined product is produced. What we are interested in is the percentage of recombined P<sub>target</sub> among all P<sub>target</sub>s in one E. coli. So, we turn to compute that percentage based on the model that we have established.<br /><br /> | As is shown in the diagram, 2 Cre molecules bind with 1 loxP site successively, either on cDNA or P<sub>target</sub>. Four Cre molecules will form a Holliday junction, and thus starting the recombination reaction. Two pairs of loxP will work together and complete the strand exchange between cDNA and P<sub>target</sub>. After that, the recombined product is produced. What we are interested in is the percentage of recombined P<sub>target</sub> among all P<sub>target</sub>s in one E. coli. So, we turn to compute that percentage based on the model that we have established.<br /><br /> | ||
− | Unfortunately, we found that the amount of substances is too small. For example, the concentration of is only 10 nM, which means there are only about 5 molecules of in one cell. These small numbers caused some computational problems in Matlab when we were using its ODE solver (ode15s). To address this problem, we converted the units of the amount of the substances from mole per litter (M) to molecule. The units of the kinetic parameters are also converted accordingly | + | Unfortunately, we found that the amount of substances is too small. For example, the concentration of is only 10 nM, which means there are only about 5 molecules of in one cell. These small numbers caused some computational problems in Matlab when we were using its ODE solver (ode15s). To address this problem, we converted the units of the amount of the substances from mole per litter (M) to molecule. The units of the kinetic parameters are also converted accordingly.<br /><br /> |
Now the recombination step is modeled under the initial condition of 5 molecules of non-mutated , 3228 molecules of Cre and 5 molecules of cDNA (<a href="#Fig4">Fig 4b</a>). The last two numbers are the outputs of previous models after going through some unit conversion steps. | Now the recombination step is modeled under the initial condition of 5 molecules of non-mutated , 3228 molecules of Cre and 5 molecules of cDNA (<a href="#Fig4">Fig 4b</a>). The last two numbers are the outputs of previous models after going through some unit conversion steps. | ||
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Revision as of 16:14, 20 October 2019