Team:Peking/Modeling/Luminesensor/Orthogonality

Orthogonal Test in silico

Our Luminesensor is expected to be orthogonal to endogenous SOS pathway. In order to remove this obstacle on the application prospects of our Luminesensor, we used LexA408 instead of wild-type LexA DNA Binding domain. LexA408 and LexA are bio-orthogonal with each other since the sequence of the binding sites have variations (See Characterization).
By adding several nodes into the network, we constructed modeling for orthogonality in silica simulation(Figure 1):

Figure 1. Kinetic Network for Orthogonal Analysis

where

• L denotes Luminesensor
• I denotes the inner wild LexA
• D_L denotes the specific DNA binding site to Luminesensor
• D_I denotes the specific DNA binding site to wild LexA

The parameters are estimated as following:

Figure 2. Orthogonality Simulation Result.

The result(Figure 2) shows that the contrast is highly related to the orthogonality. As our Luminesensor is orthogonal to the endogerous LexA system, our system still works well in bacteria with endogenously expressed LexA (See Characterization).