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

From OpenWetWare

Jump to: navigation, search
Project name Main project page
Previous entry      

Modeling and measurements for flipper operation

  • Insert content here...

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)

  • Bulk GFP signal readout
  • Bulk b-gal activity readout
  • Bulk Restriction Digestion
  • Bulk PCR
  • Single-cell GFP readout

(Not available in our lab yet)

  • 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


Personal tools