Component | Description | Part/Accession # | Base Pairs | Plasmid | Resistance | Well |
RBS | Ribosomal Binding Site | [http://partsregistry.org/Part:BBa_B0034 BBa_B0034] | 12 | pSB1A2 | Ampicillin | plate 1, 2M |
Cph8 | Red Light sensor | [http://partsregistry.org/Part:BBa_I15010 BBa_I15010] | 2,238 | pSB2K3 | Kanamycin | N/A |
OmpR (E. coli) | description | [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=retrieve&dopt=full_report&list_uids=947913&log$=databasead&logdbfrom=protein NP_417864.1] | 720 | pSB1T3 | Tetracycline | N/A |
Terminator | Stops Transcription | [http://partsregistry.org/Part:BBa_B0015 BBa_B0015] | 129 | pSB1AK3 | Ampicillin and Kanamycin | plate 1, 23L |
OmpR + Terminator | description | sequence | 916 | pany-amp | Ampicillin | synthesized |
OmpC promoter | description | [http://partsregistry.org/Part:BBa_R0082 BBa_R0082] | 108 | pSB1A2 | Ampicillin | plate 1, 16K |
puc B/A | description | sequence | 375 | pSB1A3 | Ampicillin | N/A |
puc B | description | [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=retrieve&dopt=full_report&list_uids=3719170&log$=databasead&logdbfrom=nuccore YP_353390] | 156 | ? | ? | N/A |
puc A | description | [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=retrieve&dopt=full_report&list_uids=3719171&log$=databasead&logdbfrom=nuccore YP_353391] | 165 | ? | ? | N/A |
OmpC promoter+BA | description | sequence | 539 | pany-kana | Kanamycin | synthesized |
Light Response System | description | [http://partsregistry.org/Part:BBa_M30109 BBa_M30109] | 4,333 | ? | Ampicillin | N/A |
TetR repressible | description | [http://partsregistry.org/Part:BBa_J13002 BBa_J13002] | 74 | pSB1A2 | Ampicillin | plate 1, 13B |
Green Fluorescent Protein | Marker for characterization | [http://partsregistry.org/Part:BBa_E0240 BBa_E0240] | 876 | pSB1A2 | Ampicillin | plate 1, 12M |
Plasmids
Plasmid | Description | Base Pairs | Resistance | Copy Number | Cut Sites |
[http://partsregistry.org/Part:pSB1A2 pSB1A2] | BioBrick Vector | 2,079 | Ampicillin | high | |
[http://partsregistry.org/Part:pSB1K3 pSB1K3] | 2,206 | Kanamycin | high | ||
[http://partsregistry.org/Part:pSB1A3 pSB1A3] | Assembly plasmid | 2,157 | Ampicillin | high | |
[http://partsregistry.org/Part:pSB2K3 pSB2K3] | 4,425 | Kanamycin | variable | ||
[http://partsregistry.org/Part:pSB1T3 pSB1T3] | Assembly plasmid | 2,463 | Tetracycline | high | |
[http://partsregistry.org/Part:pSB1AK3 pSB1AK3] | Assembly Plasmid | 3,189 | Ampicillin and Kanamycin | high | |
pANY | |||||
pRKCBC3 | Tetracycline |
The first part of our characterization begins with the puc promoter. The puc promoter is what turns on the entire system naturally in Rhodobacter sphaeroides. The puc promoter is what ultimately controls the number of LH2 light harvesting complexes, which is how our system will yield an increase in photosynthetic efficiency. It is important that we are able to compare the transcription rate of the puc promoter in the two systems so that we can determine exactly how much efficiency is gained by adding a red light sensor. By attaching Green Fluorescent Protein (GFP) to the promoter we can quantify the rate of transcription by measuring the emittance of green light using a fluorescence spectrophotometer. We would expect to see more fluorescence with more transcription and vis versa.
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.