User:Pakpoom Subsoontorn/Notebook/Genetically Encoded Memory/2009/03/29

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Modeling and measurements for flipper operation

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Detail Mechanism

 * Inducer IPTG diffuse into a cell
 * Mechanism: IPTG diffuses across E.coli cell membrane and cytosol and binds to lacI
 * Rate
 * Diffusion rate of IPTG across cell membrane
 * Diffusion rate of IPTG in cytosol
 * IPTG-lacI binding rate
 * Number
 * number of lacI in a single cell
 * lacI-IPTG leaves the promoter
 * Mechanism: lacI-IPTG has much lower affinity toward Lac operator than lacI and likely to dissociate
 * Rate
 * Dissociation rate of lacI-IPTG from the lac operon
 * Number
 * Transcription of Flipper
 * Mechanism: RNAP bind to the promoter, transcribing mRNA of the flipper out
 * Rate
 * Estimated transcription rate
 * promoter occupancy of our promoter
 * Number
 * Size of the gene
 * number of RNAP molecules
 * Translation of Flipper
 * Mechanism
 * Rate
 * Number
 * Flipper localizes at Flippee
 * Mechanism
 * Rate
 * Number
 * DNA inversion
 * Mechanism
 * Rate
 * Number
 * Transcription of reporter
 * Mechanism
 * Rate
 * Number
 * Translation of reporter
 * Mechanism
 * Rate
 * Number
 * Maturation of reporter
 * Mechanism
 * Rate
 * Number
 * Detection
 * Mechanism
 * Rate
 * Number

Measurement
(Currently available in our lab) (Not available in our lab yet)
 * Bulk GFP signal readout
 * Bulk b-gal activity readout
 * Bulk Restriction Digestion
 * Bulk PCR
 * Single-cell GFP readout
 * IPTG diffusion
 * Bulk Flipper transcription
 * Single-cell fipper transcription
 * Bulk Flipper translation
 * Single-cell flipper translation
 * Flipper localizes on the flippee
 * in vivo single cell DNA inversion
 * Bulk Flippee transcription
 * Single-cell Flippee translation


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