Team:Waterloo/Notebook/Oligos
From 2009.igem.org
(Difference between revisions)
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- | |amplifies first half of E. coli | + | |amplifies first half of ''E. coli'' α-galactosidase gene adds SalI site (fwd) || HI-SalI-F || CATGTCGACATGATGTCTGCACCCAAAATT || 30 |
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- | |amplifies first half of | + | |amplifies first half of α-galactosidase gene adds BamHI site (rev) || HI-BamHI-attP-R || ATGGGATCCCCCCCAACTGAGAGAACTCAAAGGTTACCCCAGTTGGGGGTAACGCAGCGTAGCTGG || 66 |
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- | |amplifies second half of | + | |amplifies second half of α-galactosidase gene, adds KpnI site (fwd) || H2-KpnI-attP-F || CATGGTACCCCCCCAACTGAGAGAACTCAAAGGTTACCCCAGTTGGGGGCGTTTTACCTGGAGCTGG || 67 |
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- | |amplifies second half of | + | |amplifies second half of α-galactosidase gene, adds XbaI site (rev) || H2-XbaI-R || ATGTCTAGAGGTCAGCAGCGTCTGT || 25 |
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|Amplifes any biobrick, adds EcoRV end for ligation into EcoRV blunt ends (fwd) || Prefix-EcoRV-F || ATCGAATTCGCGGCCGCTTCTAG || 23 | |Amplifes any biobrick, adds EcoRV end for ligation into EcoRV blunt ends (fwd) || Prefix-EcoRV-F || ATCGAATTCGCGGCCGCTTCTAG || 23 | ||
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|ordered to add Plac and RBS to the cI ORF (project 2008) || Plac-RBS-F || GAATTCGCGGCCGCTTCTAGAGAATTGTGAGCGGATAACAATTGACATTGTGAGCGGATAA CAAGATACTGAGCACATACTAGAGAAAGAGGAGAAATACTAG || 103 | |ordered to add Plac and RBS to the cI ORF (project 2008) || Plac-RBS-F || GAATTCGCGGCCGCTTCTAGAGAATTGTGAGCGGATAACAATTGACATTGTGAGCGGATAA CAAGATACTGAGCACATACTAGAGAAAGAGGAGAAATACTAG || 103 | ||
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- | |amplifies | + | |amplifies ΦC31 int, adds RBS, Prefix, changes start codon to ATG, changes G to A maintaining glutamic acid codon and eliminating EcoRI site (fwd) || Int-BBa-F || GAATTCGCGGCCGCTTCTAGAGAAAGAGGAGAAATACTAGATGGACACGTACGCGGGTGCTT ACGACCGTCAGTCGCGCGAGCGCGAAAATTCG || 94 |
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- | |amplifies | + | |amplifies ΦC31 int, adds suffix, changes stop codon to double TAA (rev) || Int-DSC-R || CTGCAGCGGCCGCTACTAGTATTATTACGCCGCTACGTCTTCCGTG || 46 |
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|amplifies T7 Gene 6 exonuclease, adds ATG start codon, adds BBa prefix (fwd2) || T7gene6-F2 || GAATTCGCGGCCGCTTCTAGATGGCACTTCTTGACCTTAAAC || 42 | |amplifies T7 Gene 6 exonuclease, adds ATG start codon, adds BBa prefix (fwd2) || T7gene6-F2 || GAATTCGCGGCCGCTTCTAGATGGCACTTCTTGACCTTAAAC || 42 | ||
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|does not add standard stop codon (rev) || T7gene6-R || CAATTTCTGCAGCGGCCGCTACTAGTACTACGGTCTCCACAGG || 43 | |does not add standard stop codon (rev) || T7gene6-R || CAATTTCTGCAGCGGCCGCTACTAGTACTACGGTCTCCACAGG || 43 | ||
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- | |amplifies T7 G6 makes product for cross over PCR with | + | |amplifies T7 G6 makes product for cross over PCR with ''pmeI'' cross over PCR product || T7g6-RXO-RBS || CTAGTATTTCTCCTCTTTCTCTAGTATTATTACGGTCTCCACAGGTAAATCTC || 53 |
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- | |Amplifies T7 gene 5 exonuclease, a | + | |Amplifies T7 gene 5 exonuclease, a 3′-5′ exonuclease, adds BBa prefix (fwd) || T7gene5-F || CAATGGAATTCGCGGCCGCTTCTAGATGATCGTTTCTGACATCGAA || 46 |
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- | |Amplifies T7 gene 5 exonuclease, a | + | |Amplifies T7 gene 5 exonuclease, a 3′-5′ exonuclease, adds BBa suffix (rev) || T7gene5-R || CAATTTCTGCAGCGGCCGCTACTAGTATCAGTGGCAAATCGCCCAATTAGG || 51 |
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|amplifies phbA (fwd) || phbA-F || GAATTCGCGGCCGCTTCTAGATGAGCAATCCCTCGATCG || 39 | |amplifies phbA (fwd) || phbA-F || GAATTCGCGGCCGCTTCTAGATGAGCAATCCCTCGATCG || 39 | ||
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|amplifies phbC, non standard stop codon (rev) || phbC-R || CTGCAGCGGCCGCTACTAGTATCAGGCGCGCACGCGCACGTAGG || 44 | |amplifies phbC, non standard stop codon (rev) || phbC-R || CTGCAGCGGCCGCTACTAGTATCAGGCGCGCACGCGCACGTAGG || 44 | ||
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- | | | + | |amplifes RFP with [http://partsregistry.org/Part:BBa_J23118 BBa_J23118] constitutive promoter ([http://partsregistry.org/Part:BBa_K093012 BBa_K093012]) anneals to promoter sequence (fwd) || RFP-BamHI-F || CATGGATCCTTGACGGCTAGCTCAGTC || 27 |
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- | |anneals to RFP ORF sequence adds TT ( | + | |anneals to RFP ORF sequence adds TT ([http://partsregistry.org/Part:BBa_B1002 BBa_B1002]) adds KpnI site, but don't use it to clone, the ORF contains other KpnI sites || RFP-KpnII-TT-R (rev) || ATGGGTACCAAAAAAAAACCCCGCCGAAGCGGGGTTTTTTTTTCTCTAGTAGCGATCTACACTAGCACTATCA || 73 |
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- | |amplifies | + | |amplifies ''pmeI'' from ''Pseudomonas mendocina'' NEB698, used to amplify synthetic ORF to add RBS (fwd)|| PmeIR-F || GAATTCCGGCCGCTTCTAGAGAAAGAGGAGAAATACTAGATGACAACAAACTCCCCCTCAG || 61 |
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- | |amplifies | + | |amplifies ''pmeI'' from ''Pseudomonas mendocina'' NEB698, or our synthetic ORF (rev) || PmeIR-R || CTGCAGCGGCCGCTACTAGTATTATTAAACCGTACTTCGCCCCCG || 45 |
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- | |sense oligo for RecA lexA hybrid promoter ( | + | |sense oligo for RecA-lexA hybrid promoter ([http://partsregistry.org/Part:BBa_K093000 BBa_K093000]) 5' EcoRI overhang (fwd) || recA-F || AATTCGCGGCCGCTTCTAGAGTACAAAACACTTGATACTGTATATATATACAGTATAATTGCTTCAACATA|| 71 |
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- | |sense oligo for RecA lexA hybrid promoter ( | + | |sense oligo for RecA lexA hybrid promoter ([http://partsregistry.org/Part:BBa_K093000 BBa_K093000]) 3' SpeI overhang (rev) || recA-R || CTAGTATGTTGAAGCAATTATACTGTATATATATACAGTATCAAGTGTTTTGTACTCTAGAAGCGGCCGCG || 71 |
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|amplifies RFP ORF adds RBS (fwd) || RFP-RBS-F || GAATTCCGGCCGCTTCTAGAGAAAGAGGAGAAATACTAGATGGCTTCCTCCGAAGACG || 58 | |amplifies RFP ORF adds RBS (fwd) || RFP-RBS-F || GAATTCCGGCCGCTTCTAGAGAAAGAGGAGAAATACTAGATGGCTTCCTCCGAAGACG || 58 | ||
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|amplifes RK2 oriT adds Mph1103I site (compatible end with PstI) (rev) || RK2-RP || ATGATGCATCCGGGCAGGATAGGTGAAGT || 29 | |amplifes RK2 oriT adds Mph1103I site (compatible end with PstI) (rev) || RK2-RP || ATGATGCATCCGGGCAGGATAGGTGAAGT || 29 | ||
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- | |BBa sequencing/ | + | |BBa sequencing/colony PCR primer (fwd) || VF2 || TGCCACCTGACGTCTAAGAA || 20 |
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- | |BBa sequencing/ | + | |BBa sequencing/colony PCR primer (rev) || VR || ATTACCGCCTTTGAGTGAGC || 20 |
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Revision as of 22:59, 21 October 2009
Description | Oligo Name | Sequence | Length |
---|---|---|---|
amplifies first half of E. coli α-galactosidase gene adds SalI site (fwd) | HI-SalI-F | CATGTCGACATGATGTCTGCACCCAAAATT | 30 |
amplifies first half of α-galactosidase gene adds BamHI site (rev) | HI-BamHI-attP-R | ATGGGATCCCCCCCAACTGAGAGAACTCAAAGGTTACCCCAGTTGGGGGTAACGCAGCGTAGCTGG | 66 |
amplifies second half of α-galactosidase gene, adds KpnI site (fwd) | H2-KpnI-attP-F | CATGGTACCCCCCCAACTGAGAGAACTCAAAGGTTACCCCAGTTGGGGGCGTTTTACCTGGAGCTGG | 67 |
amplifies second half of α-galactosidase gene, adds XbaI site (rev) | H2-XbaI-R | ATGTCTAGAGGTCAGCAGCGTCTGT | 25 |
Amplifes any biobrick, adds EcoRV end for ligation into EcoRV blunt ends (fwd) | Prefix-EcoRV-F | ATCGAATTCGCGGCCGCTTCTAG | 23 |
Amplifes any biobrick, adds EcoRV end for ligation into EcoRV blunt ends (rev) | Suffix-EcoRV-R | ATCCTGCAGCGGCCGCTACTAGTA | 24 |
B0034 RBS primer, use with VF2 (fwd) | Prefix-RBS | GGCCGCTTCTAGAGAAAGAGG | 21 |
B0034 RBS primer, use with VR (rev) | Suffix-RBS | TTTCTCCTCTTTCTCTAGATGCGG | 24 |
ordered to add Plac and RBS to the cI ORF (project 2008) | Plac-RBS-F | GAATTCGCGGCCGCTTCTAGAGAATTGTGAGCGGATAACAATTGACATTGTGAGCGGATAA CAAGATACTGAGCACATACTAGAGAAAGAGGAGAAATACTAG | 103 |
amplifies ΦC31 int, adds RBS, Prefix, changes start codon to ATG, changes G to A maintaining glutamic acid codon and eliminating EcoRI site (fwd) | Int-BBa-F | GAATTCGCGGCCGCTTCTAGAGAAAGAGGAGAAATACTAGATGGACACGTACGCGGGTGCTT ACGACCGTCAGTCGCGCGAGCGCGAAAATTCG | 94 |
amplifies ΦC31 int, adds suffix, changes stop codon to double TAA (rev) | Int-DSC-R | CTGCAGCGGCCGCTACTAGTATTATTACGCCGCTACGTCTTCCGTG | 46 |
amplifies T7 Gene 6 exonuclease, adds ATG start codon, adds BBa prefix (fwd2) | T7gene6-F2 | GAATTCGCGGCCGCTTCTAGATGGCACTTCTTGACCTTAAAC | 42 |
does not add standard start codon (fwd) | T7gene6-F | CAATGGAATTCGCGGCCGCTTCTAGATGGCACTTCTTGACCTTAAA | 46 |
amplifies T7 Gene 6 exonuclease, adds double TAA stop codon, adds BBa suffix (rev2) | T7G6-R2 | CTGCAGCGGCCGCTACTAGTATTATTACGGTCTCCACAGGTAAATCTC | 48 |
does not add standard stop codon (rev) | T7gene6-R | CAATTTCTGCAGCGGCCGCTACTAGTACTACGGTCTCCACAGG | 43 |
amplifies T7 G6 makes product for cross over PCR with pmeI cross over PCR product | T7g6-RXO-RBS | CTAGTATTTCTCCTCTTTCTCTAGTATTATTACGGTCTCCACAGGTAAATCTC | 53 |
Amplifies T7 gene 5 exonuclease, a 3′-5′ exonuclease, adds BBa prefix (fwd) | T7gene5-F | CAATGGAATTCGCGGCCGCTTCTAGATGATCGTTTCTGACATCGAA | 46 |
Amplifies T7 gene 5 exonuclease, a 3′-5′ exonuclease, adds BBa suffix (rev) | T7gene5-R | CAATTTCTGCAGCGGCCGCTACTAGTATCAGTGGCAAATCGCCCAATTAGG | 51 |
amplifies phbA (fwd) | phbA-F | GAATTCGCGGCCGCTTCTAGATGAGCAATCCCTCGATCG | 39 |
amplifies phbA, non standard stop codon (rev) | phbB-R | CTGCAGCGGCCGCTACTAGTATTACAGGCGTTCCACGCACATGG | 44 |
amplifies phbB (fwd) | phbB-F | GAATTCGCGGCCGCTTCTAGATGAGCAGGGTAGCACTGG | 39 |
amplifies phbB, non standard stop codon (rev) | phbB-R | CTGCAGCGGCCGCTACTAGTA TCAGGCGAAGTACTGGCCGC | 41 |
amplifies phbC (fwd) | phbC-F | GAATTCGCGGCCGCTTCTAGATGACAGCAGAGAAGGCTGAGG | 42 |
amplifies phbC, non standard stop codon (rev) | phbC-R | CTGCAGCGGCCGCTACTAGTATCAGGCGCGCACGCGCACGTAGG | 44 |
amplifes RFP with [http://partsregistry.org/Part:BBa_J23118 BBa_J23118] constitutive promoter ([http://partsregistry.org/Part:BBa_K093012 BBa_K093012]) anneals to promoter sequence (fwd) | RFP-BamHI-F | CATGGATCCTTGACGGCTAGCTCAGTC | 27 |
anneals to RFP ORF sequence adds TT ([http://partsregistry.org/Part:BBa_B1002 BBa_B1002]) adds KpnI site, but don't use it to clone, the ORF contains other KpnI sites | RFP-KpnII-TT-R (rev) | ATGGGTACCAAAAAAAAACCCCGCCGAAGCGGGGTTTTTTTTTCTCTAGTAGCGATCTACACTAGCACTATCA | 73 |
amplifies pmeI from Pseudomonas mendocina NEB698, used to amplify synthetic ORF to add RBS (fwd) | PmeIR-F | GAATTCCGGCCGCTTCTAGAGAAAGAGGAGAAATACTAGATGACAACAAACTCCCCCTCAG | 61 |
amplifies pmeI from Pseudomonas mendocina NEB698, or our synthetic ORF (rev) | PmeIR-R | CTGCAGCGGCCGCTACTAGTATTATTAAACCGTACTTCGCCCCCG | 45 |
sense oligo for RecA-lexA hybrid promoter ([http://partsregistry.org/Part:BBa_K093000 BBa_K093000]) 5' EcoRI overhang (fwd) | recA-F | AATTCGCGGCCGCTTCTAGAGTACAAAACACTTGATACTGTATATATATACAGTATAATTGCTTCAACATA | 71 |
sense oligo for RecA lexA hybrid promoter ([http://partsregistry.org/Part:BBa_K093000 BBa_K093000]) 3' SpeI overhang (rev) | recA-R | CTAGTATGTTGAAGCAATTATACTGTATATATATACAGTATCAAGTGTTTTGTACTCTAGAAGCGGCCGCG | 71 |
amplifies RFP ORF adds RBS (fwd) | RFP-RBS-F | GAATTCCGGCCGCTTCTAGAGAAAGAGGAGAAATACTAGATGGCTTCCTCCGAAGACG | 58 |
amplifies RFP ORF, creates product for crossover PCR | RFP-RXO | GATGCCTGGCTCTAGTATTATTAAGCACCGGTGG | 34 |
Amplifies RK2 oriT adds MunI site (compatible end with EcoRI) (fwd) | RK2E-F | CATCAATTGCCGGCCAGCCTCGCAGAGCA | 29 |
Amplifies RK2 oriT adds EcoRI site, adds attB site in the forward orientation (rev) | RK2E-R | ATGGAATTCCGCGCCCGGGGAGCCCAAGGGCACGCCCTGGCACCCCGGGCAGGATAGGTGAAGT | 64 |
ampifies RK2 oriT adds PstI site, adds attB in the reverse orientation (fwd) | RK2-FP | CATCTGCAGCGCGCCCGGGGAGCCCAAGGGCACGCCCTGGCACCCCGGCCAGCCTCGCAGAGCA | 64 |
amplifes RK2 oriT adds Mph1103I site (compatible end with PstI) (rev) | RK2-RP | ATGATGCATCCGGGCAGGATAGGTGAAGT | 29 |
BBa sequencing/colony PCR primer (fwd) | VF2 | TGCCACCTGACGTCTAAGAA | 20 |
BBa sequencing/colony PCR primer (rev) | VR | ATTACCGCCTTTGAGTGAGC | 20 |