Component | Description | Part/Accession # | Base Pairs | Plasmid | Resistance | Well |
RBS | Ribosomal Binding Site | BBa_B0034 | 12 | pSB1A2 | Ampicillin | plate 1, 2M |
Red Light Sensor | Description | BBa_I15010 | 2,238 | pSB2K3 | Kanamycin | N/A |
OmpR (E. coli) | description | NP_417864.1 | 720 | pSB1T3 | Tetracycline | N/A |
Terminator | Stops Transcription | BBa_B0015 | 129 | pSB1AK3 | Ampicillin and Kanamycin | plate 1, 23L |
OmpR + Terminator | description | sequence | 916 | pany-amp | Ampicillin | synthesized |
OmpC promoter | description | BBa_R0082 | 108 | pSB1A2 | Ampicillin | plate 1, 16K |
puc B/A | description | sequence | 375 | pSB1A3 | Ampicillin | N/A |
puc B | description | YP_353390 | 156 | ? | ? | N/A |
puc A | description | YP_353391 | 165 | ? | ? | N/A |
OmpC promoter+BA | description | sequence | 539 | pany-kana | Kanamycin | synthesized |
Light Response System | description | BBa_M30109 | 4,333 | ? | Ampicillin | N/A |
TetR repressible | description | BBa_J13002 | 74 | pSB1A2 | Ampicillin | plate 1, 13B |
Green Fluorescent Protein | Marker for characterization | BBa_E0240 | 976 | pSB1A2 | Ampicillin | plate 1, 12M |
The first part of our characterization begins with the puc promoter. The puc promoter is what turns on the entire system both naturally in Rhodobacter sphaeroides and in our modified system. It is important that we have a baseline to compare the two systems so that we can determine how much efficiency is gained with the modified system given equal transcription of the puc genes. By attaching Green Fluorescent Protein (GFP) to the promoter we can quantify the rate of transcription by measuring the emittance of green light using fluorescence spectrophotometer.
Modeling the Gene Regulatory Network
References
1. Alon, Uri. Introduction to systems biology and the design principles of biological networks. Boca Raton, FL: Chapman & Hall, 2006.
2. Bower, James M. Computational Modeling of Genetic and Biochemical Networks (Computational Molecular Biology). New York: M.I.T. PRESS, 2001.
3. System modeling in cellular biology from concepts to nuts and bolts. Cambridge, MA: MIT P, 2006.