IGEM:Stanford/2009/Project Homeostasis/Primer: Difference between revisions
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==Anti-Immunosuppression Device == | ==Anti-Immunosuppression Device == | ||
*[http://openwetware.org/wiki/IGEM:Stanford/2009/Project_Homeostasis/Primer/Primersdoc Finalized Primers] | |||
Primers | Primers | ||
'''HlyB (from E. coli str. CFT073)''' | |||
[OPTIONAL]: Primers to use GTT TCT TC instead of TATA in front? I.e. | |||
GTTTCTTCgaattcgcggccgcttctagATGGTTTGCTTTTTTTTACCTGCCA | |||
Instead of: | |||
TATA gaattcgcggccgcttctagATGGTTTGCTTTTTTTTACCTGCCA | |||
*'''HlyC (from E. coli str. CFT073)''' | |||
Forward: TATAgaattcgcggccgcttctagagTTGGTTTGCTTTTTTTTACCTGCC | |||
Reverse: '''''TATA tactagtagcggccgctgcagTTAACCTGTTAATGAAAAATTGAAATC''''' | |||
untire sequence: http://www.ncbi.nlm.nih.gov/nuccore/NC_004431.1/?from=3418210&to=3418884&report=fasta | |||
Added 7/1/09 - ''Mark'' | |||
*'''HlyC (from E. coli str. CFT073)''' | |||
''Forward'': TATAgaattcgcggccgcttctagagTTGGTTTGCTTTTTTTTACCTGCCACC | |||
''Reverse'': '''''TATAtactagtagcggccgctgcagCTCTTAACCTGTTAATG''''' | |||
*'''HlyB (from E. coli str. CFT073)''' | |||
''Forward'': TATAgaattcgcggccgcttctagagGGAGTCATAATGGATTCTTGTC | ''Forward'': TATAgaattcgcggccgcttctagagGGAGTCATAATGGATTCTTGTC | ||
''Reverse'': TATAtactagtagcggccgctgcagGTTAGTCTGACTGTAACTG | ''Reverse'': '''''TATAtactagtagcggccgctgcagGTTAGTCTGACTGTAACTG''''' | ||
'''HlyD (from E. coli str. CFT073)''' | *'''HlyD (from E. coli str. CFT073)''' | ||
''Forward'': TATAgaattcgcggccgcttctagATGAAAACATGGTTAATGGGGTTCAGCG | ''Forward'': TATAgaattcgcggccgcttctagATGAAAACATGGTTAATGGGGTTCAGCG | ||
''Reverse'': TATAtactagtagcggccgctgcagCTCTGAGACTTAACGCTCATG | ''Reverse'': '''''TATAtactagtagcggccgctgcagCTCTGAGACTTAACGCTCATG''''' | ||
'''TolC (from E. coli str. CFT073)''' | *'''TolC (from E. coli str. CFT073)''' | ||
''Forward'': TATAgaattcgcggccgcttctagagGCAAATGAAGAAATTGCTCC | ''Forward'': TATAgaattcgcggccgcttctagagGCAAATGAAGAAATTGCTCC | ||
''Reverse'': TATAtactagtagcggccgctgcagCGTCATCAGTTACGGAAAGGG | ''Reverse'': '''''TATAtactagtagcggccgctgcagCGTCATCAGTTACGGAAAGGG''''' | ||
Added 7/1/09 - ''Ming'' | |||
*'''HlyB (from CFT073)''' | |||
"Forward": TATAgaattcgcggccgcttctag ATGGATTCTTGTCATAAAATTG | |||
"Reverse": '''''TATAtactagtagcggccgctgcag TTAGTCTGACTGTAACTG''''' | |||
*'''HlyD (from CFT073)''' | |||
"Forward":TATA gaattcgcggccgcttctag ATGAAAACATGGTTAATG | |||
"Reverse": '''''TATAtactagtagcggccgctgcag TTAACGCTCATGTAAACTTTC''''' | |||
*'''TolC''' | |||
"Forward": TATAgaattcgcggccgcttctagATGAAGAAATTGCTCCCCATTC | |||
"Reverse": '''''TATAtactagtagcggccgctgcagTCAGTTACGGAAAGGGTTATG'''''' | |||
*'''HlyA''' | |||
complete genome: [http://www.ncbi.nlm.nih.gov/nuccore/NC_004431.1/?from=3418896&to=3421970&report=fasta] | |||
'' | Added 6/28/09 - ''Robert, Ariana'' | ||
*'''IL-6 fusion gene''' | |||
"Forward": TATAGAATTCGCGGCCGCTTCTAGAGGGATGCATCACCGGTTCCGC | |||
"Reverse": '''''ATATTACTAGTAGCGGCCGCTGCAGGGATGCATTCATTTGACGAAGAG''''' | |||
''' | *'''New IL-6 fusion gene (Joe 7-5)''' | ||
"Forward: TATAgaattcgcggccgcttctagATGCCAACAATAACCACTGC | |||
"Reverse": TATAtactagtagcggccgctgcagTTATGCTGATGCTGTCAAAG | |||
Added 7/1/09 - ''Anusuya'' | |||
*'''TrpR''' ''(E. coli str. IAI1)'' | |||
''Forward'': TATAgaattcgcggccgcttctagATGGCCCAACAATCACCCTATTCAGC | |||
''Reverse'': ''''''TATAtactagtagcggccgctgcagTCAATCGCTTTTCAGCAACACCTCTTCCAGCCACTGGC''''' | |||
*'''Trp Promoter and Operator''' ''(E. coli: no specified strain )'' | |||
''Forward:'' TATAgaattcgcggccgcttctagagCTCAAGGCGCACTCCCGTTCTG | |||
''Reverse:'' TATAtactagtagcggccgctgcagTCGATACCCTTTTTACGTGAACTTGCGTACTAG | |||
*Protease-binding sequence? | |||
Gene Sequences | Gene Sequences | ||
'''HylB''' | *'''trp-operon (promoter-operator) sequence''' | ||
5' CTCAAGGCGCACTCCCGTTCTGGATAATGTTTTTTGCGCCGACATCATAACGGTTCTGGCAAATATTCTGAAATGACCTGTTGACAATTAATCATCGAACTAGTTAACTAGTACGCAAGTTCACGTAAAAAGGGTATCCA 3' | |||
(Nucleotide Sequence of the Promoter- Operator Region of the Tryptophan Operon of Escherichia coli By G. N. BENNETT, M. E. SCHW~,INGRUB~.R~, K. D. BROW~: | |||
C. SQUIRES § AND C. ¥'ANOFSKY ) | |||
*'''HylB''' | |||
ATGATCATCAATAAATTTTCCCTTAAATGGATGTTGGCTATTGCCGTCGCCATCCCTGCGATAGCACTGTTGTTTGTGGCTTTCACCAGTCTAAACACCATGTCAGTGATGCAAGCGCAGTCCAACAGCTTGTATGCCAACACGGCTGCACCAATGCGTGCCATGGCTGAAGCAACCTCACGTATTCCTCGGATGCGTGTCGGTATCGATATGATGCTACTGCAAGAAACGGCGCTCAAAGATGCGAAAGGGGTCCTCAAACGAGTCGAAGAGGCAAGAACCGAAGATATCCCAGAAATGCGTCAAGCAATGCAAGTTGCGGTTGATTCTCAGGTTAATCCGGAACTCAAAGAGCAGGCACGCAAACTTCAAGCTCGTTTTGAACAAATGGTACGTGAAGAGTTAGAGCCTATGCTGCAAGCCTTCGCCAATAACGATATGACCACGGCACAAAACATTTACCGCGATAAATACGCGCCGACCTATGGTGAAATGCGTAAACAAGCCAACCAGATCCTCGATACGCTTTTGCAGCAAGCGGAGCAGCAAAACCATGCCAGTGTGGAAAGCTTCGAAGCAGGACGCACCAAGCAAATGGTGATCATTGCAGCAGGCTTGATCATTTCATTCATCACTTCACTGGTTATCATAACGAACTTACGTAGCCGAGTGGCTTACCTGAAAGATCGTATGAGTTCTGCGGCGGCGAATCTTTCACTGCGTACTCGATTGGAGTTGGATGGTAACGATGAACTGTGTGACATCGGTAAAAGCTTCAATGCGTTCATTGATAAAGTGCATCACTCGATTGAAGAAGTGGCAGAAAACTCAAAAGAGCTGGCGACGATGGCCTCTAGTGTGTCGCAGCGCGCGCACATGACGCAATCTAACTGTGCTTCGCAGCGAGATAGAACAGTGCAAGTTGCGACGGCGATTCATGAGCTTGGTGCCACCGTATCCGAAATCGCTTCCAATGCGGCCATGGCTGCCGATGTCGCGAAGCAAGCGACGCTGCATTCTGGTGAAGGGAAAAAAGTGGTAGGCGAAGTGCAAAATCGGATCCAAACACTGGTCAATGAACTCGATAATGCCACTCAAGTTGTCTCATCACTGGCGACCCAAATTAACGGTATTAGCTCAACACTTGATACCATTCGCAGTATTTCTGAGCAAACGAACCTATTGGCGCTCAACGCTGCGATTGAAGCTGCGCGAGCGGGTGAACAAGGTCGTGGTTTTGCGGTGGTGGCGGATGAAGTTCGCACATTAGCAAGTCGTTCAGCGGCATCGACGGAAGAGATCCAGCAAGTCATTAATCGCCTTCAAACGGAGTCAACTCGCGCAGTAGAAGCAATGGAAAAAGGTCGCTCGCAAAGTGATGTGGTGGTTGAGTTTTCCGCTAAAGCGAACCAATCTCTCACAGAGATCAACAGCCAAATTGATCAGATTAATGATCAAAATATTCAAGTTGCGACCGCGACAGAGGAACAATCAACCGTGGTGGAAGACATTAATCGCAACGTTGAAGACATCAACCAACTGACGACAGAAACCTCGCATGTTGCGGATGAGTTAAGCCGAGCCAGTGCAAGCTTGCAACGTCTCTCTTCGCAACTGGATAAACTGGTGGGCAGTTTTGAACTTTAA | ATGATCATCAATAAATTTTCCCTTAAATGGATGTTGGCTATTGCCGTCGCCATCCCTGCGATAGCACTGTTGTTTGTGGCTTTCACCAGTCTAAACACCATGTCAGTGATGCAAGCGCAGTCCAACAGCTTGTATGCCAACACGGCTGCACCAATGCGTGCCATGGCTGAAGCAACCTCACGTATTCCTCGGATGCGTGTCGGTATCGATATGATGCTACTGCAAGAAACGGCGCTCAAAGATGCGAAAGGGGTCCTCAAACGAGTCGAAGAGGCAAGAACCGAAGATATCCCAGAAATGCGTCAAGCAATGCAAGTTGCGGTTGATTCTCAGGTTAATCCGGAACTCAAAGAGCAGGCACGCAAACTTCAAGCTCGTTTTGAACAAATGGTACGTGAAGAGTTAGAGCCTATGCTGCAAGCCTTCGCCAATAACGATATGACCACGGCACAAAACATTTACCGCGATAAATACGCGCCGACCTATGGTGAAATGCGTAAACAAGCCAACCAGATCCTCGATACGCTTTTGCAGCAAGCGGAGCAGCAAAACCATGCCAGTGTGGAAAGCTTCGAAGCAGGACGCACCAAGCAAATGGTGATCATTGCAGCAGGCTTGATCATTTCATTCATCACTTCACTGGTTATCATAACGAACTTACGTAGCCGAGTGGCTTACCTGAAAGATCGTATGAGTTCTGCGGCGGCGAATCTTTCACTGCGTACTCGATTGGAGTTGGATGGTAACGATGAACTGTGTGACATCGGTAAAAGCTTCAATGCGTTCATTGATAAAGTGCATCACTCGATTGAAGAAGTGGCAGAAAACTCAAAAGAGCTGGCGACGATGGCCTCTAGTGTGTCGCAGCGCGCGCACATGACGCAATCTAACTGTGCTTCGCAGCGAGATAGAACAGTGCAAGTTGCGACGGCGATTCATGAGCTTGGTGCCACCGTATCCGAAATCGCTTCCAATGCGGCCATGGCTGCCGATGTCGCGAAGCAAGCGACGCTGCATTCTGGTGAAGGGAAAAAAGTGGTAGGCGAAGTGCAAAATCGGATCCAAACACTGGTCAATGAACTCGATAATGCCACTCAAGTTGTCTCATCACTGGCGACCCAAATTAACGGTATTAGCTCAACACTTGATACCATTCGCAGTATTTCTGAGCAAACGAACCTATTGGCGCTCAACGCTGCGATTGAAGCTGCGCGAGCGGGTGAACAAGGTCGTGGTTTTGCGGTGGTGGCGGATGAAGTTCGCACATTAGCAAGTCGTTCAGCGGCATCGACGGAAGAGATCCAGCAAGTCATTAATCGCCTTCAAACGGAGTCAACTCGCGCAGTAGAAGCAATGGAAAAAGGTCGCTCGCAAAGTGATGTGGTGGTTGAGTTTTCCGCTAAAGCGAACCAATCTCTCACAGAGATCAACAGCCAAATTGATCAGATTAATGATCAAAATATTCAAGTTGCGACCGCGACAGAGGAACAATCAACCGTGGTGGAAGACATTAATCGCAACGTTGAAGACATCAACCAACTGACGACAGAAACCTCGCATGTTGCGGATGAGTTAAGCCGAGCCAGTGCAAGCTTGCAACGTCTCTCTTCGCAACTGGATAAACTGGTGGGCAGTTTTGAACTTTAA | ||
http://www.ncbi.nlm.nih.gov/nuccore/NC_012583.1/?from=274978&to=276624&report=fasta NCBI Reference Sequence: NC_012583.1 from Vibrio cholerae O395 chromosome II, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/NC_012583.1/?from=274978&to=276624&report=fasta NCBI Reference Sequence: NC_012583.1 from Vibrio cholerae O395 chromosome II, complete genome | ||
''' | ''' | ||
HylD''' | |||
*HylD''' | |||
ATGGCTGCGTTCGGACAAGACGTCTTCAGGCGCTTCGGCACGGTCACCGAACGCTTCTCCGGCACCGGCGGCAAACTCTTCGGCGGCCTGCTCGCGCGCCTGTCGAGCGTGGAGCGCGACGACAGCCTGGACTGGGCGAGCGACGCCGACTGGGCGCGCCTGCAGCAGGAGCCGCTGCGCGCGCGCGCGGTACTCAAGGTCAGCGCGATCGCGCTGCTGGTGCTGCTCGGCTGGGCCGCGGTGGCGCATGTGGACGAGGTGACCAAGGGCGACGGCAAGGTGATCCCGTCCAGCCAGCTGCAGATCATCCAGTCGGTCGATGGCGGCGTGGTGGAGTCGATCGCGGTGCGCGAGGGCGAGGTGGTCGAGGCCGGGCAGCTGCTGCTCAAGGTCGATCCCACCCGTTTCATGTCCTCGCTGCTGGAAAACCGCGCCGAGTTCCTCGCGCTGGAAATCAAGCGCCGGCGGCTCGAGGCGCTGACCCAGGGGACGCCGTTCTCGGTGCCGGCCGAGCTGGAGAAGGAGGCGGCGGACATCGCCGCCCACGAGCGCCGGCTGTATGAATCCAGCCGCGCCGAGATGGACGCGCAGCAGTCGATCGCGCGCGACCAGCTGCGCCAGCGCGAGCAGGAACTCAACGAGGTGCGCGCCCGCAGTGAGAACGCCGCCCGCGCCTACGAACTGGTGCAGCAGGAACTCAAGGTCACCAAGCCGCTCGCGGCCTCCGGCGCGGTATCCGAGGTCGAGCTGCTGCGTCTGGAGCGCGACGTGTCGCGCTTGCGCGGCGAGCGCGAGCAGAGCGCGGCGCAGATTTCGCGCATCCAGTCGGCCATCGCCGAATCCACGCGCAAGATCCAGGAGATCGAGCTGACGGTGCGCAACCAGCTGCGCAACGAGCTTTCGGACACCATGGCGCGGCTGGGCAGCCTGACCCAGGGCAGCCGCATGCTGGCCGACCGCGTCAAGCACGCCGAAATCCGCGCGCCGATGCGCGGCACGGTCAAGCGCATCCTCGTCAACACCGTGGGTGGCGTGGTCCAGCCGGGCAAGGAAGTGGCCGAGATCGTGCCGCTCGACGACGCGCTGATCCTCGAAGCGCAGGTCAAGCCGAGCGACATCGCCTTCCTGCGCCCGGGTCAGTCGGCGCTGGTCAAGTTCTCCGCGTACGACTTCTCGATCTACGGCGGCCTGGAGGCGGTCGTGGACCAGATTTCCGCCGACACCGTGGTCGATGCAAAGGGTTCCGCGTTCTACGTGGTGCGGGTGCGCACGCTGCATTCCTCTCTGGGTGAAAACCTGCCGATCATTCCGGGCATGGTGGCCGAAGTGGACATCCTGACCGGCAAGAAGACCATCCTCTCCTACCTGCTGAAGCCCGTGCTGCGGGCCAAGGCCAACGCACTGTCCGAACGATGA | ATGGCTGCGTTCGGACAAGACGTCTTCAGGCGCTTCGGCACGGTCACCGAACGCTTCTCCGGCACCGGCGGCAAACTCTTCGGCGGCCTGCTCGCGCGCCTGTCGAGCGTGGAGCGCGACGACAGCCTGGACTGGGCGAGCGACGCCGACTGGGCGCGCCTGCAGCAGGAGCCGCTGCGCGCGCGCGCGGTACTCAAGGTCAGCGCGATCGCGCTGCTGGTGCTGCTCGGCTGGGCCGCGGTGGCGCATGTGGACGAGGTGACCAAGGGCGACGGCAAGGTGATCCCGTCCAGCCAGCTGCAGATCATCCAGTCGGTCGATGGCGGCGTGGTGGAGTCGATCGCGGTGCGCGAGGGCGAGGTGGTCGAGGCCGGGCAGCTGCTGCTCAAGGTCGATCCCACCCGTTTCATGTCCTCGCTGCTGGAAAACCGCGCCGAGTTCCTCGCGCTGGAAATCAAGCGCCGGCGGCTCGAGGCGCTGACCCAGGGGACGCCGTTCTCGGTGCCGGCCGAGCTGGAGAAGGAGGCGGCGGACATCGCCGCCCACGAGCGCCGGCTGTATGAATCCAGCCGCGCCGAGATGGACGCGCAGCAGTCGATCGCGCGCGACCAGCTGCGCCAGCGCGAGCAGGAACTCAACGAGGTGCGCGCCCGCAGTGAGAACGCCGCCCGCGCCTACGAACTGGTGCAGCAGGAACTCAAGGTCACCAAGCCGCTCGCGGCCTCCGGCGCGGTATCCGAGGTCGAGCTGCTGCGTCTGGAGCGCGACGTGTCGCGCTTGCGCGGCGAGCGCGAGCAGAGCGCGGCGCAGATTTCGCGCATCCAGTCGGCCATCGCCGAATCCACGCGCAAGATCCAGGAGATCGAGCTGACGGTGCGCAACCAGCTGCGCAACGAGCTTTCGGACACCATGGCGCGGCTGGGCAGCCTGACCCAGGGCAGCCGCATGCTGGCCGACCGCGTCAAGCACGCCGAAATCCGCGCGCCGATGCGCGGCACGGTCAAGCGCATCCTCGTCAACACCGTGGGTGGCGTGGTCCAGCCGGGCAAGGAAGTGGCCGAGATCGTGCCGCTCGACGACGCGCTGATCCTCGAAGCGCAGGTCAAGCCGAGCGACATCGCCTTCCTGCGCCCGGGTCAGTCGGCGCTGGTCAAGTTCTCCGCGTACGACTTCTCGATCTACGGCGGCCTGGAGGCGGTCGTGGACCAGATTTCCGCCGACACCGTGGTCGATGCAAAGGGTTCCGCGTTCTACGTGGTGCGGGTGCGCACGCTGCATTCCTCTCTGGGTGAAAACCTGCCGATCATTCCGGGCATGGTGGCCGAAGTGGACATCCTGACCGGCAAGAAGACCATCCTCTCCTACCTGCTGAAGCCCGTGCTGCGGGCCAAGGCCAACGCACTGTCCGAACGATGA | ||
http://www.ncbi.nlm.nih.gov/nuccore/NC_008702.1/?from=674498&to=675913&report=fasta NCBI Reference Sequence: NC_008702.1 from Azoarcus sp. BH72, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/NC_008702.1/?from=674498&to=675913&report=fasta NCBI Reference Sequence: NC_008702.1 from Azoarcus sp. BH72, complete genome | ||
'''TolC''' | *'''TolC''' | ||
ATGAAGAAATTGCTCCCCATTCTTATCGGCCTGAGCCTTTCTGGGTTCAGTTCGTTGAGCCAGGCCGAGAACCTGATGCAAGTTTATCAGCAAGCACGCCTTAGTAACCCGGAATTGCGTAAGTCTGCCGCCGATCGTGATGCTGCCTTTGAAAAAATTAATGAAGCGCGCAGTCCATTACTGCCACAGCTAGGTTTAGGTGCAGATTACACCTATAGCAACGGCTACCGCGACGCGAACGGCATCAACTCTAACGCGACCAGTGCGTCCTTGCAGTTAACTCAATCCATTTTTGATATGTCGAAATGGCGTGCGTTAACGCTGCAGGAAAAAGCAGCAGGGATTCAGGACGTCACGTATCAGACCGATCAGCAAACCTTGATCCTCAACACCGCGACCGCTTATTTCAACGTGTTGAATGCTATTGACGTTCTTTCCTATACACAGGCACAAAAAGAAGCGATCTACCGTCAATTAGATCAAACCACCCAACGTTTTAACGTGGGCCTGGTAGCGATCACCGACGTGCAGAACGCCCGCGCACAGTACGATACCGTGCTGGCGAACGAAGTGACCGCACGTAATAACCTTGATAACGCGGTAGAGCAGCTGCGCCAGATCACCGGTAACTACTATCCGGAACTGGCTGCGCTGAATGTCGAAAACTTTAAAACCGACAAACCACAGCCGGTTAACGCGCTGCTGAAAGAAGCCGAAAAACGCAACCTGTCGCTGTTACAGGCACGCTTGAGCCAGGACCTGGCGCGCGAGCAAATTCGCCAGGCGCAGGATGGTCACTTACCGACTCTGGATTTAACGGCTTCTACCGGGATTTCTGACACCTCTTATAGCGGTTCGAAAACCCGTGGTGCCGCTGGTACCCAGTATGACGATAGCAATATGGGCCAGAACAAAGTTGGCCTGAGCTTCTCGCTGCCGATTTATCAGGGCGGAATGGTTAACTCGCAGGTGAAACAGGCACAGTACAACTTTGTCGGTGCCAGCGAGCAACTGGAAAGTGCCCATCGTAGCGTCGTGCAGACCGTGCGTTCCTCCTTCAACAACATTAATGCATCTATCAGTAGCATTAACGCCTACAAACAAGCCGTAGTTTCCGCTCAAAGCTCATTAGACGCGATGGAAGCGGGCTACTCGGTCGGTACGCGTACCATTGTTGATGTGTTGGATGCGACCACCACGTTGTACAACGCCAAGCAAGAGCTGGCGAATGCGCGTTATAACTACCTGATTAATCAGCTGAATATTAAGTCAGCTCTGGGTACGTTGAACGAGCAGGATCTGCTGGCACTGAACAATGCGCTGAGCAAACCGGTTTCCACTAATCCGGAAAACGTTGCACCGCAAACGCCGGAACAGAATGCTATTGCTGATGGTTATGCGCCTGATAGCCCGGCACCAGTCGTTCAGCAAACATCCGCACGCACTACCACCAGTAACGGTCATAACCCTTTCCGTAACTGA | ATGAAGAAATTGCTCCCCATTCTTATCGGCCTGAGCCTTTCTGGGTTCAGTTCGTTGAGCCAGGCCGAGAACCTGATGCAAGTTTATCAGCAAGCACGCCTTAGTAACCCGGAATTGCGTAAGTCTGCCGCCGATCGTGATGCTGCCTTTGAAAAAATTAATGAAGCGCGCAGTCCATTACTGCCACAGCTAGGTTTAGGTGCAGATTACACCTATAGCAACGGCTACCGCGACGCGAACGGCATCAACTCTAACGCGACCAGTGCGTCCTTGCAGTTAACTCAATCCATTTTTGATATGTCGAAATGGCGTGCGTTAACGCTGCAGGAAAAAGCAGCAGGGATTCAGGACGTCACGTATCAGACCGATCAGCAAACCTTGATCCTCAACACCGCGACCGCTTATTTCAACGTGTTGAATGCTATTGACGTTCTTTCCTATACACAGGCACAAAAAGAAGCGATCTACCGTCAATTAGATCAAACCACCCAACGTTTTAACGTGGGCCTGGTAGCGATCACCGACGTGCAGAACGCCCGCGCACAGTACGATACCGTGCTGGCGAACGAAGTGACCGCACGTAATAACCTTGATAACGCGGTAGAGCAGCTGCGCCAGATCACCGGTAACTACTATCCGGAACTGGCTGCGCTGAATGTCGAAAACTTTAAAACCGACAAACCACAGCCGGTTAACGCGCTGCTGAAAGAAGCCGAAAAACGCAACCTGTCGCTGTTACAGGCACGCTTGAGCCAGGACCTGGCGCGCGAGCAAATTCGCCAGGCGCAGGATGGTCACTTACCGACTCTGGATTTAACGGCTTCTACCGGGATTTCTGACACCTCTTATAGCGGTTCGAAAACCCGTGGTGCCGCTGGTACCCAGTATGACGATAGCAATATGGGCCAGAACAAAGTTGGCCTGAGCTTCTCGCTGCCGATTTATCAGGGCGGAATGGTTAACTCGCAGGTGAAACAGGCACAGTACAACTTTGTCGGTGCCAGCGAGCAACTGGAAAGTGCCCATCGTAGCGTCGTGCAGACCGTGCGTTCCTCCTTCAACAACATTAATGCATCTATCAGTAGCATTAACGCCTACAAACAAGCCGTAGTTTCCGCTCAAAGCTCATTAGACGCGATGGAAGCGGGCTACTCGGTCGGTACGCGTACCATTGTTGATGTGTTGGATGCGACCACCACGTTGTACAACGCCAAGCAAGAGCTGGCGAATGCGCGTTATAACTACCTGATTAATCAGCTGAATATTAAGTCAGCTCTGGGTACGTTGAACGAGCAGGATCTGCTGGCACTGAACAATGCGCTGAGCAAACCGGTTTCCACTAATCCGGAAAACGTTGCACCGCAAACGCCGGAACAGAATGCTATTGCTGATGGTTATGCGCCTGATAGCCCGGCACCAGTCGTTCAGCAAACATCCGCACGCACTACCACCAGTAACGGTCATAACCCTTTCCGTAACTGA | ||
http://www.ncbi.nlm.nih.gov/nuccore/NC_000913.2/?from=3176137&to=3177618&report=fasta NCBI Reference Sequence: NC_000913.2 from Escherichia coli str. K-12 substr. MG1655, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/NC_000913.2/?from=3176137&to=3177618&report=fasta NCBI Reference Sequence: NC_000913.2 from Escherichia coli str. K-12 substr. MG1655, complete genome | ||
*Protease-binding sequence? | |||
==Anti-Inflammatory Device== | ==Anti-Inflammatory Device== | ||
Line 82: | Line 174: | ||
'''SoxR''' (Escherichia coli E24377A) | '''SoxR''' (Escherichia coli E24377A) | ||
Forward: TATAgaattcgcggccgcttctagATGGAAAAGAAATTACCCCGC | |||
Reverse: '''''TATAtactagtagcggccgctgcagTTAGTTTTGTTCATCTTCCAGCAAGCGTG''''' | |||
complete gene sequence: [http://www.ncbi.nlm.nih.gov/nuccore/NC_009801.1/?from=4616553&to=4617017&report=fasta] | |||
'''SoxS promoter''' (Joe 7-5) | |||
Forward: TATAgaattcgcggccgcttctagagAATCGCTTTACCTCAAGTTAACTTG | |||
Reverse: TATAtactagtagcggccgctgcagCAGTTCGTTAATTCATCTGTTGGG | |||
Added 7/1/09 - ''Anusuya'' | |||
'''CrtB''' ''(Erwinia Uredovora)'' | '''CrtB''' ''(Erwinia Uredovora)'' | ||
TATAgaattcgcggccgcttctagATGGCAGTTGGCTCGAAAAG | ''Forward'': TATAgaattcgcggccgcttctagATGGCAGTTGGCTCGAAAAG | ||
'''''TATAtactagtagcggccgctgcagCTAGAGCGGGCGCTGCCAG''''' | ''Reverse'': '''''TATAtactagtagcggccgctgcagCTAGAGCGGGCGCTGCCAG''''' | ||
'''CrtE''' ''(Erwinia Uredovora)'' | '''CrtE''' ''(Erwinia Uredovora)'' | ||
TATAgaattcgcggccgcttctagATGACGGTCTGCGCAAAAAAAC | ''Forward'': TATAgaattcgcggccgcttctagATGACGGTCTGCGCAAAAAAAC | ||
'''''TATAtactagtagcggccgctgcagTTAACTGACGGCAGCGAGTTTTTTG''''' | ''Reverse'': '''''TATAtactagtagcggccgctgcagTTAACTGACGGCAGCGAGTTTTTTG''''' | ||
'''CrtI''' ''(Erwinia Uredovora)'' | '''CrtI''' ''(Erwinia Uredovora)'' | ||
TATAgaattcgcggccgcttctag ATGAAACCAACTACGGTAATTGGTGC | ''Forward'': TATAgaattcgcggccgcttctag ATGAAACCAACTACGGTAATTGGTGC | ||
TATAtactagtagcggccgctgcag TGATTGAGTAACGACGG | ''Reverse'': '''''TATAtactagtagcggccgctgcag TGATTGAGTAACGACGG''''' | ||
'''CrtY''' ''(Erwinia Uredovora)'' | '''CrtY''' ''(Erwinia Uredovora)'' | ||
TATAgaattcgcggccgcttctag ATGCAACCGCATTATGATCTG | ''Forward'': TATAgaattcgcggccgcttctag ATGCAACCGCATTATGATCTG | ||
TATAtactagtagcggccgctgcag TTAACGATGAGTCGTCATAATGGC | ''Reverse'': '''''TATAtactagtagcggccgctgcag TTAACGATGAGTCGTCATAATGGC''''' | ||
Line 118: | Line 220: | ||
'''Blh''' ''( | '''Blh''' ''(uncultured marine bacterium 66A03)'' | ||
''Forward'': TATAgaattcgcggccgcttctagATGGGTCTGATGCTGATTG | |||
''Reverse'': TATAtactagtagcggccgctgcagTCAGTTTTTGATTTTGATACGGG | |||
''''' | '''RalDH(II)''' ''(Rattus Norvegicus*)'' | ||
''Forward'': TATAgaattcgcggccgcttctagATGCCCGGCGAGGTGAAGGC | |||
''' | ''Reverse'': '''''TATAtactagtagcggccgctgcagTTAGGAGTTCTTCTGGGGGATC''''' | ||
*Originally from Rattus Norvegicus but sequence was modified | |||
'''HlyR''': Since HlyR is not a protein. This sequence is sequenced as a chunk with HlyA,HlyB, HlyC. Thus only one primer is needed. | |||
primer: TATAtactagtagcggccgctgcagGAATTCCAAGCGAAGTCC | |||
check paper for RalDH(II) http://www.jbc.org/cgi/content/abstract/271/27/16288 | |||
Gene sequences: | Gene sequences: | ||
SoxR | '''SoxR''' | ||
ATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGCGATATAAACGTGATGTGTTGCGATATGTTGCAATTATCAAAATTGCTCAGCGTATTGGCATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTGGATCGGCGCATTCATACCTTAGTGGCGCTGCGTGACGAACTGGACGGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAA | ATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGCGATATAAACGTGATGTGTTGCGATATGTTGCAATTATCAAAATTGCTCAGCGTATTGGCATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTGGATCGGCGCATTCATACCTTAGTGGCGCTGCGTGACGAACTGGACGGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAA | ||
http://www.ncbi.nlm.nih.gov/nuccore/NC_009801.1/?from=4616553&to=4617017&report=fasta | http://www.ncbi.nlm.nih.gov/nuccore/NC_009801.1/?from=4616553&to=4617017&report=fasta | ||
(NCBI Reference Sequence: NC_009801.1 from Escherichia coli E24377A, complete genome) | (NCBI Reference Sequence: NC_009801.1 from Escherichia coli E24377A, complete genome) | ||
'''SoxS''' | |||
AATCGCTTTACCTCAAGTTAACTTGAGGAATTATACTCCCCAACAGATGAATTAACGAACTG | |||
Crt genes | Crt genes | ||
Line 146: | Line 260: | ||
Kim et al. In vitro characterization of a recombinant Blh protein from an uncultured marine bacterium as a beta-carotene 15,15'-dioxygenase. J Biol Chem. 2009 Jun 5;284(23):15781-93. (supplementary material; 15,15'-Dioxygenase, product of Blh gene, codon-optimized and expressed in E. coli, forms a 64k protein of two 32 kDa dimers) | Kim et al. In vitro characterization of a recombinant Blh protein from an uncultured marine bacterium as a beta-carotene 15,15'-dioxygenase. J Biol Chem. 2009 Jun 5;284(23):15781-93. (supplementary material; 15,15'-Dioxygenase, product of Blh gene, codon-optimized and expressed in E. coli, forms a 64k protein of two 32 kDa dimers) | ||
RALDH | RALDH | ||
HlyR: | |||
sequence: GAATTCCAAGCGAAGTCCATCCCCCTCCCTCTTGATTACAAGGGTGATAATTATTATTCGCATTTGTGTG | |||
GTAATGGGATAGAAAGGAATGGATAGAAAAAGAACAAAATTAGTATAGCAATAGATATGCCCACTGCATT | |||
GAATACTTACAGGGCATTATTTTATTATGTTTAAATTGAAGTGGTCTCTGGTTTGATTTATTTGTTATTC | |||
AAGGGGGCTGTTTGGAGATCGGAAAATTCTGTACGTTAAGTGTATTATTTAACCAGTTTCGATGCGTAAC | |||
AGATTGATTTTGCTCAGCGGTTATCGCTTTTAAGTTGTTGCTCTTGGCTATCGCGTTTAGGTTATCCGAT | |||
TAAAGTCAAATTTCCTGAAAATGCTGTATAGCGCGGGAGTGCACCTTATAGCTGTAGGTAAGTATGTTCA | |||
AAAAATAGTCTTGCCGTACAATAATTTTCCATATCCAAACTCACTCCTTCAAGATTCTGGTCCCGGTTTA | |||
CGGGTAGTTTCCGGAAGGGCGGTAGCATGCTGATTCAAACTGCAAGATGAAACATTGTCGGAGTTGGATG | |||
GAATTAAGTCATGGCTATAGCATTTGGGCGTGCATAACAAAATTGGTCCTCATATTTTAGAGTATGATTG | |||
CATATTCACTAATATTTTTACTTTCTGATGCGTGGTGGCATCATGCTTTATGAGATAAACAATCCTGG | |||
blh | |||
ATGGGTCTGATGCTGATTGATTGGTGTGCACTGGCTCTGGTTGTTTTCATTGGCCTGCCGCACGGCGCG | |||
CTGGATGCTGCCATTTCTTTTTCTATGATCTCTTCTGCAAAACGCATTGCTCGTCTGGCTGGTATTCTG | |||
CTGATCTATCTGCTGCTGGCGACCGCGTTCTTCCTGATCTGGTATCAGCTGCCAGCGTTTAGCCTGCTG | |||
ATCTTCCTGCTGATCTCCATTATCCACTTTGGTATGGCAGACTTCAACGCGTCCCCAAGCAAACTGAAA | |||
TGGCCGCATATCATCGCCCACGGCGGTGTTGTTACTGTTTGGCTGCCGCTGATCCAGAAAAACGAAGTA | |||
ACTAAACTGTTTAGCATCCTGACTAACGGTCCGACTCCGATCCTGTGGGACATCCTGCTGATTTTCTTC | |||
CTGTGTTGGTCTATTGGCGTGTGTCTGCACACGTACGAAACCCTGCGCTCTAAACATTACAACATCGCC | |||
TTTGAACTGATCGGTCTGATTTTCCTGGCGTGGTATGCGCCGCCTCTGGTTACGTTTGCCACTTACTTC | |||
TGCTTCATTCATTCCCGTCGCCACTTCTCCTTTGTGTGGAAGCAGCTGCAACACATGTCTTCCAAAAAG | |||
ATGATGATTGGCAGCGCGATTATCCTGTCCTGTACCTCTTGGCTGATCGGCGGTGGTATCTATTTCTTC | |||
CTGAACTCCAAAATGATCGCCTCTGAGGCTGCGCTACAAACTGTGTTCATCGGTCTGGCGGCACTGACC | |||
GTGCCGCACATGATTCTGATCGACTTCATCTTCCGTCCGCACTCTTCCCGTATCAAAATCAAAAACTGA | |||
RALDH II | |||
ATGCCCGGCGAGGTGAAGGCCGACCCCGCCGCGCTCATGGCCTCGCTGCAGCTCCTGCCG | |||
TCACCCACGCCCAACCTCGAGATCAAGTACACCAAGATCTTTATTAACAATGAATGGCAG | |||
AACTCAGAGAGTGGGAGAGTGTTCCCTGTCTGTAATCCAGCCACAGGAGAGCAAGTGTGT | |||
GAAGTTCAAGAAGCAGACAAGGTGGATATAGACAAGGCAGTGCAGGCGGCCCGCCTGGCC | |||
TTCTCTCTTGGTTCTGTGTGGAGAAGGATGGACGCTTCTGAAAGAGGACGTCTGCTGGAC | |||
AAGCTTGCAGACTTGGTGGAACGGGACAGGGCAACTCTTGCAACTATGGAATCACTAAAT | |||
GGCGGTAAGCCATTCCTGCAAGCTTTTTACATCGATTTGCAGGGAGTCATCAAAACCCTG | |||
AGGTATTATGCAGGCTGGGCTGATAAAATTCACGGAATGACCATTCCTGTAGATGGAGAC | |||
TATTTTACCTTCACGAGACATGAGCCCATCGGAGTGTGTGGACAGATTATCCCGTGGAAT | |||
TTCCCCCTGCTGATGTTCACCTGGAAAATTGCTCCCGCACTGTGCTGTGGTAACACTGTG | |||
GTCATCAAGCCTGCAGAGCAGACACCACTCAGTGCACTGTATATGGGAGCCCTCATCAAG | |||
GAGGCTGGCTTTCCACCCGGGGTCGTCAACATTCTGCCAGGGTATGGGCCAACAGCAGGG | |||
GCAGCAATAGCGTCTCACATTGGCATAGACAAGATTGCATTCACAGGCTCTACTGAGGTT | |||
GGAAAGCTTATTCAAGAAGCAGCTGGAAGAAGTAATTTGAAGAGAGTAACTCTGGAACTT | |||
GGAGGGAAAAGCCCTAATATTATTTTTGCAGATGCTGACTTGGACTACGCTGTGGAGCAG | |||
GCTCACCAGGGTGTGTTCTTCAACCAAGGCCAGTGCTGCACTGCGGGGTCTCGAATCTTT | |||
GTGGAGGAGTCCATCTATGAGGAATTTGTGAAAAGAAGTGTGGAAAGAGCCAAGAGGCGC | |||
ATTGTGGGGAGCCCCTTTGATCCCACTACTGAGCAGGGTCCTCAGATTGATAAGAAGCAA | |||
TACAACAAAATCCTGGAGCTCATCCAGAGCGGTGTGGCCGAGGGCGCCAAGCTCGAGTGT | |||
GGAGGCAAAGGACTGGGAAGGAAGGGCTTCTTCATTGAGCCTACCGTGTTCTCCAACGTT | |||
ACAGATGACATGCGGATCGCCAAGGAGGAGATCTTTGGTCCTGTCCAGGAAATTTTGAGG | |||
TTTAAGACTATGGATGAAGTTATAGAAAGAGCCAATAACTCAGACTTCGGGCTTGTAGCG | |||
GCTGTCTTCACTAATGACATCAACAAGGCTCTCATGGTGTCCTCTGCAATGCAAGCTGGG | |||
ACAGTTTGGATCAATTGTTACAACGCCTTAAATGCTCAGAGCCCCTTCGGGGGGTTCAAG | |||
ATGTCTGGAAATGGGAGAGAAATGGGTGAGTTTGGCTTACGGGAGTACTCAGAAGTAAAG | |||
ACCGTGACGGTGAAGATCCCCCAGAAGAACTCCTAA | |||
==Comments== | |||
*For gene sequencing, I would suggest genedesigner | |||
*For primer design and selection I would suggest APE and oligo 6.87 |
Latest revision as of 10:53, 21 August 2009
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Project |
Research Proposal |
Systems Overview |
Cloning Plan |
Sequences & Primers |
Anti-Inflammation |
Device Overview |
Parts Design |
Challenges |
Results |
Anti-Immunosuppression |
Device Overview |
Parts Design |
Challenges |
Results |
Protocols |
Modeling |
Overview |
Notebook |
Results |
Future Work |
Archived Work |
Anti-Immunosuppression Device
Primers
[OPTIONAL]: Primers to use GTT TCT TC instead of TATA in front? I.e.
GTTTCTTCgaattcgcggccgcttctagATGGTTTGCTTTTTTTTACCTGCCA
Instead of:
TATA gaattcgcggccgcttctagATGGTTTGCTTTTTTTTACCTGCCA
- HlyC (from E. coli str. CFT073)
Forward: TATAgaattcgcggccgcttctagagTTGGTTTGCTTTTTTTTACCTGCC
Reverse: TATA tactagtagcggccgctgcagTTAACCTGTTAATGAAAAATTGAAATC
untire sequence: http://www.ncbi.nlm.nih.gov/nuccore/NC_004431.1/?from=3418210&to=3418884&report=fasta
Added 7/1/09 - Mark
- HlyC (from E. coli str. CFT073)
Forward: TATAgaattcgcggccgcttctagagTTGGTTTGCTTTTTTTTACCTGCCACC
Reverse: TATAtactagtagcggccgctgcagCTCTTAACCTGTTAATG
- HlyB (from E. coli str. CFT073)
Forward: TATAgaattcgcggccgcttctagagGGAGTCATAATGGATTCTTGTC
Reverse: TATAtactagtagcggccgctgcagGTTAGTCTGACTGTAACTG
- HlyD (from E. coli str. CFT073)
Forward: TATAgaattcgcggccgcttctagATGAAAACATGGTTAATGGGGTTCAGCG
Reverse: TATAtactagtagcggccgctgcagCTCTGAGACTTAACGCTCATG
- TolC (from E. coli str. CFT073)
Forward: TATAgaattcgcggccgcttctagagGCAAATGAAGAAATTGCTCC
Reverse: TATAtactagtagcggccgctgcagCGTCATCAGTTACGGAAAGGG
Added 7/1/09 - Ming
- HlyB (from CFT073)
"Forward": TATAgaattcgcggccgcttctag ATGGATTCTTGTCATAAAATTG
"Reverse": TATAtactagtagcggccgctgcag TTAGTCTGACTGTAACTG
- HlyD (from CFT073)
"Forward":TATA gaattcgcggccgcttctag ATGAAAACATGGTTAATG
"Reverse": TATAtactagtagcggccgctgcag TTAACGCTCATGTAAACTTTC
- TolC
"Forward": TATAgaattcgcggccgcttctagATGAAGAAATTGCTCCCCATTC
"Reverse": TATAtactagtagcggccgctgcagTCAGTTACGGAAAGGGTTATG'
- HlyA
complete genome: [1]
Added 6/28/09 - Robert, Ariana
- IL-6 fusion gene
"Forward": TATAGAATTCGCGGCCGCTTCTAGAGGGATGCATCACCGGTTCCGC
"Reverse": ATATTACTAGTAGCGGCCGCTGCAGGGATGCATTCATTTGACGAAGAG
- New IL-6 fusion gene (Joe 7-5)
"Forward: TATAgaattcgcggccgcttctagATGCCAACAATAACCACTGC
"Reverse": TATAtactagtagcggccgctgcagTTATGCTGATGCTGTCAAAG
Added 7/1/09 - Anusuya
- TrpR (E. coli str. IAI1)
Forward: TATAgaattcgcggccgcttctagATGGCCCAACAATCACCCTATTCAGC
Reverse: 'TATAtactagtagcggccgctgcagTCAATCGCTTTTCAGCAACACCTCTTCCAGCCACTGGC
- Trp Promoter and Operator (E. coli: no specified strain )
Forward: TATAgaattcgcggccgcttctagagCTCAAGGCGCACTCCCGTTCTG
Reverse: TATAtactagtagcggccgctgcagTCGATACCCTTTTTACGTGAACTTGCGTACTAG
- Protease-binding sequence?
Gene Sequences
- trp-operon (promoter-operator) sequence
5' CTCAAGGCGCACTCCCGTTCTGGATAATGTTTTTTGCGCCGACATCATAACGGTTCTGGCAAATATTCTGAAATGACCTGTTGACAATTAATCATCGAACTAGTTAACTAGTACGCAAGTTCACGTAAAAAGGGTATCCA 3'
(Nucleotide Sequence of the Promoter- Operator Region of the Tryptophan Operon of Escherichia coli By G. N. BENNETT, M. E. SCHW~,INGRUB~.R~, K. D. BROW~: C. SQUIRES § AND C. ¥'ANOFSKY )
- HylB
ATGATCATCAATAAATTTTCCCTTAAATGGATGTTGGCTATTGCCGTCGCCATCCCTGCGATAGCACTGTTGTTTGTGGCTTTCACCAGTCTAAACACCATGTCAGTGATGCAAGCGCAGTCCAACAGCTTGTATGCCAACACGGCTGCACCAATGCGTGCCATGGCTGAAGCAACCTCACGTATTCCTCGGATGCGTGTCGGTATCGATATGATGCTACTGCAAGAAACGGCGCTCAAAGATGCGAAAGGGGTCCTCAAACGAGTCGAAGAGGCAAGAACCGAAGATATCCCAGAAATGCGTCAAGCAATGCAAGTTGCGGTTGATTCTCAGGTTAATCCGGAACTCAAAGAGCAGGCACGCAAACTTCAAGCTCGTTTTGAACAAATGGTACGTGAAGAGTTAGAGCCTATGCTGCAAGCCTTCGCCAATAACGATATGACCACGGCACAAAACATTTACCGCGATAAATACGCGCCGACCTATGGTGAAATGCGTAAACAAGCCAACCAGATCCTCGATACGCTTTTGCAGCAAGCGGAGCAGCAAAACCATGCCAGTGTGGAAAGCTTCGAAGCAGGACGCACCAAGCAAATGGTGATCATTGCAGCAGGCTTGATCATTTCATTCATCACTTCACTGGTTATCATAACGAACTTACGTAGCCGAGTGGCTTACCTGAAAGATCGTATGAGTTCTGCGGCGGCGAATCTTTCACTGCGTACTCGATTGGAGTTGGATGGTAACGATGAACTGTGTGACATCGGTAAAAGCTTCAATGCGTTCATTGATAAAGTGCATCACTCGATTGAAGAAGTGGCAGAAAACTCAAAAGAGCTGGCGACGATGGCCTCTAGTGTGTCGCAGCGCGCGCACATGACGCAATCTAACTGTGCTTCGCAGCGAGATAGAACAGTGCAAGTTGCGACGGCGATTCATGAGCTTGGTGCCACCGTATCCGAAATCGCTTCCAATGCGGCCATGGCTGCCGATGTCGCGAAGCAAGCGACGCTGCATTCTGGTGAAGGGAAAAAAGTGGTAGGCGAAGTGCAAAATCGGATCCAAACACTGGTCAATGAACTCGATAATGCCACTCAAGTTGTCTCATCACTGGCGACCCAAATTAACGGTATTAGCTCAACACTTGATACCATTCGCAGTATTTCTGAGCAAACGAACCTATTGGCGCTCAACGCTGCGATTGAAGCTGCGCGAGCGGGTGAACAAGGTCGTGGTTTTGCGGTGGTGGCGGATGAAGTTCGCACATTAGCAAGTCGTTCAGCGGCATCGACGGAAGAGATCCAGCAAGTCATTAATCGCCTTCAAACGGAGTCAACTCGCGCAGTAGAAGCAATGGAAAAAGGTCGCTCGCAAAGTGATGTGGTGGTTGAGTTTTCCGCTAAAGCGAACCAATCTCTCACAGAGATCAACAGCCAAATTGATCAGATTAATGATCAAAATATTCAAGTTGCGACCGCGACAGAGGAACAATCAACCGTGGTGGAAGACATTAATCGCAACGTTGAAGACATCAACCAACTGACGACAGAAACCTCGCATGTTGCGGATGAGTTAAGCCGAGCCAGTGCAAGCTTGCAACGTCTCTCTTCGCAACTGGATAAACTGGTGGGCAGTTTTGAACTTTAA http://www.ncbi.nlm.nih.gov/nuccore/NC_012583.1/?from=274978&to=276624&report=fasta NCBI Reference Sequence: NC_012583.1 from Vibrio cholerae O395 chromosome II, complete genome
- HylD
ATGGCTGCGTTCGGACAAGACGTCTTCAGGCGCTTCGGCACGGTCACCGAACGCTTCTCCGGCACCGGCGGCAAACTCTTCGGCGGCCTGCTCGCGCGCCTGTCGAGCGTGGAGCGCGACGACAGCCTGGACTGGGCGAGCGACGCCGACTGGGCGCGCCTGCAGCAGGAGCCGCTGCGCGCGCGCGCGGTACTCAAGGTCAGCGCGATCGCGCTGCTGGTGCTGCTCGGCTGGGCCGCGGTGGCGCATGTGGACGAGGTGACCAAGGGCGACGGCAAGGTGATCCCGTCCAGCCAGCTGCAGATCATCCAGTCGGTCGATGGCGGCGTGGTGGAGTCGATCGCGGTGCGCGAGGGCGAGGTGGTCGAGGCCGGGCAGCTGCTGCTCAAGGTCGATCCCACCCGTTTCATGTCCTCGCTGCTGGAAAACCGCGCCGAGTTCCTCGCGCTGGAAATCAAGCGCCGGCGGCTCGAGGCGCTGACCCAGGGGACGCCGTTCTCGGTGCCGGCCGAGCTGGAGAAGGAGGCGGCGGACATCGCCGCCCACGAGCGCCGGCTGTATGAATCCAGCCGCGCCGAGATGGACGCGCAGCAGTCGATCGCGCGCGACCAGCTGCGCCAGCGCGAGCAGGAACTCAACGAGGTGCGCGCCCGCAGTGAGAACGCCGCCCGCGCCTACGAACTGGTGCAGCAGGAACTCAAGGTCACCAAGCCGCTCGCGGCCTCCGGCGCGGTATCCGAGGTCGAGCTGCTGCGTCTGGAGCGCGACGTGTCGCGCTTGCGCGGCGAGCGCGAGCAGAGCGCGGCGCAGATTTCGCGCATCCAGTCGGCCATCGCCGAATCCACGCGCAAGATCCAGGAGATCGAGCTGACGGTGCGCAACCAGCTGCGCAACGAGCTTTCGGACACCATGGCGCGGCTGGGCAGCCTGACCCAGGGCAGCCGCATGCTGGCCGACCGCGTCAAGCACGCCGAAATCCGCGCGCCGATGCGCGGCACGGTCAAGCGCATCCTCGTCAACACCGTGGGTGGCGTGGTCCAGCCGGGCAAGGAAGTGGCCGAGATCGTGCCGCTCGACGACGCGCTGATCCTCGAAGCGCAGGTCAAGCCGAGCGACATCGCCTTCCTGCGCCCGGGTCAGTCGGCGCTGGTCAAGTTCTCCGCGTACGACTTCTCGATCTACGGCGGCCTGGAGGCGGTCGTGGACCAGATTTCCGCCGACACCGTGGTCGATGCAAAGGGTTCCGCGTTCTACGTGGTGCGGGTGCGCACGCTGCATTCCTCTCTGGGTGAAAACCTGCCGATCATTCCGGGCATGGTGGCCGAAGTGGACATCCTGACCGGCAAGAAGACCATCCTCTCCTACCTGCTGAAGCCCGTGCTGCGGGCCAAGGCCAACGCACTGTCCGAACGATGA http://www.ncbi.nlm.nih.gov/nuccore/NC_008702.1/?from=674498&to=675913&report=fasta NCBI Reference Sequence: NC_008702.1 from Azoarcus sp. BH72, complete genome
- TolC
ATGAAGAAATTGCTCCCCATTCTTATCGGCCTGAGCCTTTCTGGGTTCAGTTCGTTGAGCCAGGCCGAGAACCTGATGCAAGTTTATCAGCAAGCACGCCTTAGTAACCCGGAATTGCGTAAGTCTGCCGCCGATCGTGATGCTGCCTTTGAAAAAATTAATGAAGCGCGCAGTCCATTACTGCCACAGCTAGGTTTAGGTGCAGATTACACCTATAGCAACGGCTACCGCGACGCGAACGGCATCAACTCTAACGCGACCAGTGCGTCCTTGCAGTTAACTCAATCCATTTTTGATATGTCGAAATGGCGTGCGTTAACGCTGCAGGAAAAAGCAGCAGGGATTCAGGACGTCACGTATCAGACCGATCAGCAAACCTTGATCCTCAACACCGCGACCGCTTATTTCAACGTGTTGAATGCTATTGACGTTCTTTCCTATACACAGGCACAAAAAGAAGCGATCTACCGTCAATTAGATCAAACCACCCAACGTTTTAACGTGGGCCTGGTAGCGATCACCGACGTGCAGAACGCCCGCGCACAGTACGATACCGTGCTGGCGAACGAAGTGACCGCACGTAATAACCTTGATAACGCGGTAGAGCAGCTGCGCCAGATCACCGGTAACTACTATCCGGAACTGGCTGCGCTGAATGTCGAAAACTTTAAAACCGACAAACCACAGCCGGTTAACGCGCTGCTGAAAGAAGCCGAAAAACGCAACCTGTCGCTGTTACAGGCACGCTTGAGCCAGGACCTGGCGCGCGAGCAAATTCGCCAGGCGCAGGATGGTCACTTACCGACTCTGGATTTAACGGCTTCTACCGGGATTTCTGACACCTCTTATAGCGGTTCGAAAACCCGTGGTGCCGCTGGTACCCAGTATGACGATAGCAATATGGGCCAGAACAAAGTTGGCCTGAGCTTCTCGCTGCCGATTTATCAGGGCGGAATGGTTAACTCGCAGGTGAAACAGGCACAGTACAACTTTGTCGGTGCCAGCGAGCAACTGGAAAGTGCCCATCGTAGCGTCGTGCAGACCGTGCGTTCCTCCTTCAACAACATTAATGCATCTATCAGTAGCATTAACGCCTACAAACAAGCCGTAGTTTCCGCTCAAAGCTCATTAGACGCGATGGAAGCGGGCTACTCGGTCGGTACGCGTACCATTGTTGATGTGTTGGATGCGACCACCACGTTGTACAACGCCAAGCAAGAGCTGGCGAATGCGCGTTATAACTACCTGATTAATCAGCTGAATATTAAGTCAGCTCTGGGTACGTTGAACGAGCAGGATCTGCTGGCACTGAACAATGCGCTGAGCAAACCGGTTTCCACTAATCCGGAAAACGTTGCACCGCAAACGCCGGAACAGAATGCTATTGCTGATGGTTATGCGCCTGATAGCCCGGCACCAGTCGTTCAGCAAACATCCGCACGCACTACCACCAGTAACGGTCATAACCCTTTCCGTAACTGA http://www.ncbi.nlm.nih.gov/nuccore/NC_000913.2/?from=3176137&to=3177618&report=fasta NCBI Reference Sequence: NC_000913.2 from Escherichia coli str. K-12 substr. MG1655, complete genome
- Protease-binding sequence?
Anti-Inflammatory Device
Primers:
SoxR (Escherichia coli E24377A)
Forward: TATAgaattcgcggccgcttctagATGGAAAAGAAATTACCCCGC
Reverse: TATAtactagtagcggccgctgcagTTAGTTTTGTTCATCTTCCAGCAAGCGTG
complete gene sequence: [2]
SoxS promoter (Joe 7-5)
Forward: TATAgaattcgcggccgcttctagagAATCGCTTTACCTCAAGTTAACTTG
Reverse: TATAtactagtagcggccgctgcagCAGTTCGTTAATTCATCTGTTGGG
Added 7/1/09 - Anusuya
CrtB (Erwinia Uredovora)
Forward: TATAgaattcgcggccgcttctagATGGCAGTTGGCTCGAAAAG
Reverse: TATAtactagtagcggccgctgcagCTAGAGCGGGCGCTGCCAG
CrtE (Erwinia Uredovora)
Forward: TATAgaattcgcggccgcttctagATGACGGTCTGCGCAAAAAAAC
Reverse: TATAtactagtagcggccgctgcagTTAACTGACGGCAGCGAGTTTTTTG
CrtI (Erwinia Uredovora)
Forward: TATAgaattcgcggccgcttctag ATGAAACCAACTACGGTAATTGGTGC
Reverse: TATAtactagtagcggccgctgcag TGATTGAGTAACGACGG
CrtY (Erwinia Uredovora)
Forward: TATAgaattcgcggccgcttctag ATGCAACCGCATTATGATCTG
Reverse: TATAtactagtagcggccgctgcag TTAACGATGAGTCGTCATAATGGC
Soxs: primer dimers
Blh (uncultured marine bacterium 66A03)
Forward: TATAgaattcgcggccgcttctagATGGGTCTGATGCTGATTG
Reverse: TATAtactagtagcggccgctgcagTCAGTTTTTGATTTTGATACGGG
RalDH(II) (Rattus Norvegicus*)
Forward: TATAgaattcgcggccgcttctagATGCCCGGCGAGGTGAAGGC
Reverse: TATAtactagtagcggccgctgcagTTAGGAGTTCTTCTGGGGGATC
- Originally from Rattus Norvegicus but sequence was modified
HlyR: Since HlyR is not a protein. This sequence is sequenced as a chunk with HlyA,HlyB, HlyC. Thus only one primer is needed. primer: TATAtactagtagcggccgctgcagGAATTCCAAGCGAAGTCC
check paper for RalDH(II) http://www.jbc.org/cgi/content/abstract/271/27/16288
Gene sequences: SoxR ATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGCGATATAAACGTGATGTGTTGCGATATGTTGCAATTATCAAAATTGCTCAGCGTATTGGCATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTGGATCGGCGCATTCATACCTTAGTGGCGCTGCGTGACGAACTGGACGGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAA http://www.ncbi.nlm.nih.gov/nuccore/NC_009801.1/?from=4616553&to=4617017&report=fasta (NCBI Reference Sequence: NC_009801.1 from Escherichia coli E24377A, complete genome)
SoxS
AATCGCTTTACCTCAAGTTAACTTGAGGAATTATACTCCCCAACAGATGAATTAACGAACTG
Crt genes
GenBank accession no. D90087—should we do as the entire cluster (in this case how should we design primers) or in parts?
Blh ATGGGTCTGATGCTGATTGATTGGTGTGCACTGGCTCTGGTTGTTTTCATTGGCCTGCCGCACGGCGCGCTGGATGCTGCCATTTCTTTTTCTATGATCTCTTCTGCAAAACGCATTGCTCGTCTGGCTGGTATTCTGCTGATCTATCTGCTGCTGGCGACCGCGTTCTTCCTGATCTGGTATCAGCTGCCAGCGTTTAGCCTGCTGATCTTCCTGCTGATCTCCATTATCCACTTTGGTATGGCAGACTTCAACGCGTCCCCAAGCAAACTGAAATGGCCGCATATCATCGCCCACGGCGGTGTTGTTACTGTTTGGCTGCCGCTGATCCAGAAAAACGAAGTAACTAAACTGTTTAGCATCCTGACTAACGGTCCGACTCCGATCCTGTGGGACATCCTGCTGATTTTCTTCCTGTGTTGGTCTATTGGCGTGTGTCTGCACACGTACGAAACCCTGCGCTCTAAACATTACAACATCGCCTTTGAACTGATCGGTCTGATTTTCCTGGCGTGGTATGCGCCGCCTCTGGTTACGTTTGCCACTTACTTCTGCTTCATTCATTCCCGTCGCCACTTCTCCTTTGTGTGGAAGCAGCTGCAACACATGTCTTCCAAAAAGATGATGATTGGCAGCGCGATTATCCTGTCCTGTACCTCTTGGCTGATCGGCGGTGGTATCTATTTCTTCCTGAACTCCAAAATGATCGCCTCTGAGGCTGCGCTGCAGACTGTGTTCATCGGTCTGGCGGCACTGACCGTGCCGCACATGATTCTGATCGACTTCATCTTCCGTCCGCACTCTTCCCGTATCAAAATCAAAAACTGA
Kim et al. In vitro characterization of a recombinant Blh protein from an uncultured marine bacterium as a beta-carotene 15,15'-dioxygenase. J Biol Chem. 2009 Jun 5;284(23):15781-93. (supplementary material; 15,15'-Dioxygenase, product of Blh gene, codon-optimized and expressed in E. coli, forms a 64k protein of two 32 kDa dimers)
RALDH
HlyR:
sequence: GAATTCCAAGCGAAGTCCATCCCCCTCCCTCTTGATTACAAGGGTGATAATTATTATTCGCATTTGTGTG GTAATGGGATAGAAAGGAATGGATAGAAAAAGAACAAAATTAGTATAGCAATAGATATGCCCACTGCATT GAATACTTACAGGGCATTATTTTATTATGTTTAAATTGAAGTGGTCTCTGGTTTGATTTATTTGTTATTC AAGGGGGCTGTTTGGAGATCGGAAAATTCTGTACGTTAAGTGTATTATTTAACCAGTTTCGATGCGTAAC AGATTGATTTTGCTCAGCGGTTATCGCTTTTAAGTTGTTGCTCTTGGCTATCGCGTTTAGGTTATCCGAT TAAAGTCAAATTTCCTGAAAATGCTGTATAGCGCGGGAGTGCACCTTATAGCTGTAGGTAAGTATGTTCA AAAAATAGTCTTGCCGTACAATAATTTTCCATATCCAAACTCACTCCTTCAAGATTCTGGTCCCGGTTTA CGGGTAGTTTCCGGAAGGGCGGTAGCATGCTGATTCAAACTGCAAGATGAAACATTGTCGGAGTTGGATG GAATTAAGTCATGGCTATAGCATTTGGGCGTGCATAACAAAATTGGTCCTCATATTTTAGAGTATGATTG CATATTCACTAATATTTTTACTTTCTGATGCGTGGTGGCATCATGCTTTATGAGATAAACAATCCTGG
blh
ATGGGTCTGATGCTGATTGATTGGTGTGCACTGGCTCTGGTTGTTTTCATTGGCCTGCCGCACGGCGCG CTGGATGCTGCCATTTCTTTTTCTATGATCTCTTCTGCAAAACGCATTGCTCGTCTGGCTGGTATTCTG CTGATCTATCTGCTGCTGGCGACCGCGTTCTTCCTGATCTGGTATCAGCTGCCAGCGTTTAGCCTGCTG ATCTTCCTGCTGATCTCCATTATCCACTTTGGTATGGCAGACTTCAACGCGTCCCCAAGCAAACTGAAA TGGCCGCATATCATCGCCCACGGCGGTGTTGTTACTGTTTGGCTGCCGCTGATCCAGAAAAACGAAGTA ACTAAACTGTTTAGCATCCTGACTAACGGTCCGACTCCGATCCTGTGGGACATCCTGCTGATTTTCTTC CTGTGTTGGTCTATTGGCGTGTGTCTGCACACGTACGAAACCCTGCGCTCTAAACATTACAACATCGCC TTTGAACTGATCGGTCTGATTTTCCTGGCGTGGTATGCGCCGCCTCTGGTTACGTTTGCCACTTACTTC TGCTTCATTCATTCCCGTCGCCACTTCTCCTTTGTGTGGAAGCAGCTGCAACACATGTCTTCCAAAAAG ATGATGATTGGCAGCGCGATTATCCTGTCCTGTACCTCTTGGCTGATCGGCGGTGGTATCTATTTCTTC CTGAACTCCAAAATGATCGCCTCTGAGGCTGCGCTACAAACTGTGTTCATCGGTCTGGCGGCACTGACC GTGCCGCACATGATTCTGATCGACTTCATCTTCCGTCCGCACTCTTCCCGTATCAAAATCAAAAACTGA
RALDH II
ATGCCCGGCGAGGTGAAGGCCGACCCCGCCGCGCTCATGGCCTCGCTGCAGCTCCTGCCG TCACCCACGCCCAACCTCGAGATCAAGTACACCAAGATCTTTATTAACAATGAATGGCAG AACTCAGAGAGTGGGAGAGTGTTCCCTGTCTGTAATCCAGCCACAGGAGAGCAAGTGTGT GAAGTTCAAGAAGCAGACAAGGTGGATATAGACAAGGCAGTGCAGGCGGCCCGCCTGGCC TTCTCTCTTGGTTCTGTGTGGAGAAGGATGGACGCTTCTGAAAGAGGACGTCTGCTGGAC AAGCTTGCAGACTTGGTGGAACGGGACAGGGCAACTCTTGCAACTATGGAATCACTAAAT GGCGGTAAGCCATTCCTGCAAGCTTTTTACATCGATTTGCAGGGAGTCATCAAAACCCTG AGGTATTATGCAGGCTGGGCTGATAAAATTCACGGAATGACCATTCCTGTAGATGGAGAC TATTTTACCTTCACGAGACATGAGCCCATCGGAGTGTGTGGACAGATTATCCCGTGGAAT TTCCCCCTGCTGATGTTCACCTGGAAAATTGCTCCCGCACTGTGCTGTGGTAACACTGTG GTCATCAAGCCTGCAGAGCAGACACCACTCAGTGCACTGTATATGGGAGCCCTCATCAAG GAGGCTGGCTTTCCACCCGGGGTCGTCAACATTCTGCCAGGGTATGGGCCAACAGCAGGG GCAGCAATAGCGTCTCACATTGGCATAGACAAGATTGCATTCACAGGCTCTACTGAGGTT GGAAAGCTTATTCAAGAAGCAGCTGGAAGAAGTAATTTGAAGAGAGTAACTCTGGAACTT GGAGGGAAAAGCCCTAATATTATTTTTGCAGATGCTGACTTGGACTACGCTGTGGAGCAG GCTCACCAGGGTGTGTTCTTCAACCAAGGCCAGTGCTGCACTGCGGGGTCTCGAATCTTT GTGGAGGAGTCCATCTATGAGGAATTTGTGAAAAGAAGTGTGGAAAGAGCCAAGAGGCGC ATTGTGGGGAGCCCCTTTGATCCCACTACTGAGCAGGGTCCTCAGATTGATAAGAAGCAA TACAACAAAATCCTGGAGCTCATCCAGAGCGGTGTGGCCGAGGGCGCCAAGCTCGAGTGT GGAGGCAAAGGACTGGGAAGGAAGGGCTTCTTCATTGAGCCTACCGTGTTCTCCAACGTT ACAGATGACATGCGGATCGCCAAGGAGGAGATCTTTGGTCCTGTCCAGGAAATTTTGAGG TTTAAGACTATGGATGAAGTTATAGAAAGAGCCAATAACTCAGACTTCGGGCTTGTAGCG GCTGTCTTCACTAATGACATCAACAAGGCTCTCATGGTGTCCTCTGCAATGCAAGCTGGG ACAGTTTGGATCAATTGTTACAACGCCTTAAATGCTCAGAGCCCCTTCGGGGGGTTCAAG ATGTCTGGAAATGGGAGAGAAATGGGTGAGTTTGGCTTACGGGAGTACTCAGAAGTAAAG ACCGTGACGGTGAAGATCCCCCAGAAGAACTCCTAA
Comments
- For gene sequencing, I would suggest genedesigner
- For primer design and selection I would suggest APE and oligo 6.87