Modeling the Transcriptional Cascade

Negative cascade assembly and overview

A full description of the Transcriptional Cascade can be found here.

ODEs

The kinetic equations were written out in a Matlab script for both transcription and translation.

Sensitivity

Parameter Sweeps

1111 : parameter vs parameter 1111 : parameter vs parameter 1111 : parameter vs parameter 111 : parameter vs parameter 1111 : parameter vs parameter 111 : parameter vs parameter 1111 : parameter vs parameter 111 : parameter vs parameter

Stability

Jacobian

Design Recommendations

Based on the results of the simulations, a series of recommendations were given to the delay team to aid them in choosing parts which would maximize the delay time.

1. Significant transcription leakages greatly shorten the delay time. Attempt to minimize leakages. Leakage of λp is a far bigger problem than pTet leakage.
2. Use a weak promoter and a weak RBS on the last stage (λp) of the cascade.
3. A weak pLac promoters is favorable.
4. A strong pTet promoter is favorable.
5. A strong RBS on CI gene is favorable.
6. A weak RBS on TetR gene is favorable.
7. A weak RBS on the endonuclease is favorable although a strong RBS can be used for the GFP gene.
8. When choosing RBS and promoter strengths avoid the red areas on the stability plots.