Team:Tsinghua-A/Modeling/Part1

From 2012.igem.org

Tsinghua-A::Modeling

Part1:Construction of DDE equation

The ara operon is regulated by the AraC protein. If arabinose is absent, the dimer AraC protein represses the structural gene by binding to araI 1 and araO 2 and the DNA forms a loop. The loop prevents RNA polymerase from binding to the promoter of the ara operon, thereby blocking transcription .When arabinose is present, arabinose binds AraC and prevents AraC from interacting. This breaks the DNA loop. The two AraC-arabinose complexes bind to the araI site which promotes transcription. When arabinose is present, AraC acts as an activator and promotes the translation of Cre. Then we use Cre-Loxp recombination, a site-specific recombinase technology to carry out inversions in the DNA of cells. The description of the system contains the above mass actions as well as some hill kinetics, Henri-Michaelis-Menten. Since concentration of protein is the integrals of its mRNA, we assume that it is proportional to concentration of mRNA in a previous time. readmore

Part2: Gillespie algorithm

readmore

Sensitivity Analysis

We analyze three parameters and the third parameter –the degradation rate of Cre protein –have an obvious effect on the final percent of the genes in different state.readmore

Feedforward

By introducing a feed forward to the system, we increase the percent of the genes flipping to the state we want.And the system is more stable.readmore

Reference

[1] MEGERLE J A, FRITZ G, GERLAND U, et al. Timing and dynamics of single cell gene expression in the arabinose utilization system [J]. Biophys J, 2008, 95(4): 2103-15.
[2] RUFER A, NEUENSCHWANDER P F, SAUER B. Analysis of Cre-loxP interaction by surface plasmon resonance: influence of spermidine on cooperativity [J]. Anal Biochem, 2002, 308(1): 90-9.
[3] VAN DUYNE G D. A structural view of cre-loxp site-specific recombination [J]. Annu Rev Biophys Biomol Struct, 2001, 30:87-104.
[4] BONNET J, SUBSOONTORN P, ENDY D. Rewritable digital data storage in live cells via engineered control of recombination directionality [J]. Proc Natl Acad Sci U S A, 2012, 109(23): 8884-9.
[5] ZHANG X, REEDER T, SCHLEIF R. Transcription activation parameters at ara pBAD [J]. J Mol Biol, 1996, 258(1): 14-24.
[6] BERNSTEIN D. Simulating mesoscopic reaction-diffusion systems using the Gillespie algorithm [J]. Phys Rev E Stat Nonlin Soft Matter Phys, 2005, 71(4 Pt 1): 041103.
[7] Danlel T. Gillespie. 1977. Exact Stochastic Simulation of Coupled Chemical Reactions. J. Phys. Chem., 1977, 81 (25):2340–2361.