Team:Waterloo/Notebook/Oligos

From 2009.igem.org

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|cgtgcaacgtcagcatggcg
|cgtgcaacgtcagcatggcg
|-
|-
 +
|sequenceing c31 int gene anneals internally
 +
|Int seq2 R
 +
|cgccatgctgacgttgcacg
 +
|-
 +
|sequenceing c31 int gene anneals internally
 +
|Int seq3 R
 +
|caccaccaccggattacgtc
 +
|-
 +
|was designed to fix an error in another PCR primer that was thrown out. Could still amplify biobricked c31 int
 +
|Int RBS
 +
|GAATTCGCGGCCGCTTCTAGAGAAAGAGGAGAAATACTAGATGGAC
 +
|-
 +
|sequencing primer for pKNG101 derived vectors (pFB9XXXX)
 +
|pKNG101 F
 +
|CTACATATCACAACGTGCGTG
 +
|-
 +
|sequencing primer for pKNG101 derived vectors (pFB9XXXX)
 +
|pKNG101 R
 +
|CTCCGTCTACTGTACGATACAC
 +
|-
 +
|linker+ for synthetic attP cloning into pKNG101 derived vectors
 +
|FB attP BamHI F
 +
|CTCAGTTGGGGGG
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|-
 +
|linker- for synthetic attP cloning into pKNG101 derived vectors
 +
|FB attP BamHI R
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|GATCCCCC
 +
|-
 +
|linker+ for synthetic attP cloning into pKNG101 derived vectors
 +
|FB attP SalI F
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|TCGACCCC
 +
|-
 +
|linker- for synthetic attP cloning into pKNG101 derived vectors
 +
|FB attP SalI R
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|CCCAGTTGGGGG
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|-
 +
|Bba linker+ attB
 +
|BBa attB EcoRI F
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|AATTCGCGGCCGCTTCTAGAG
 +
|-
 +
|Bba linker- attB
 +
|BBa attB EcoRI R
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|CACCCTCTAGAAGCGGCCGCG
 +
|-
 +
|Bba linker+ attB
 +
|BBa attB PstI F
 +
|CGCGTACTAGTAGCGGCCGCTGCA
 +
|-
 +
|Bba linker- attB
 +
|BBa attB PstI R
 +
|GCGGCCGCTACTAGTA
 +
|-
 +
|BBa linker+ attP
 +
|BBa attP EcoRI fwd
 +
|aattcgcggccgcttctagagCCC
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|24
 +
|-
 +
|BBa linker- attP
 +
|BBa attP EcoRI rev
 +
|CCCAGTTGGGGctctagaagcggccgcg
 +
|-
 +
|BBa linker+ attP
 +
|BBa attP PstI fwd
 +
|CTCAGTTGGGGGGtactagtagcggccgctgca
 +
|33
 +
|-
 +
|BBa linker- attP
 +
|BBa attP PstI rev
 +
|gcggccgctactagtaCCCC
 +
|20
 +
|-
 +
|attB +strand
 +
|attB34 TG F
 +
|GGTGCCAGGGCGTGCCCTGGGGCTCCCCGGG
 +
|-
 +
|attB -strand
 +
|attB34 TG R
 +
|CGCGCCCGGGGAGCCCCAGGGCACGCCCTGG
 +
|-
 +
|attB +strand
 +
|attB34 CT F
 +
|GGTGCCAGGGCGTGCCCCTGGGCTCCCCGGG
 +
|-
 +
|attB -strand
 +
|attB34 CT R
 +
|CGCGCCCGGGGAGCCCAGGGGCACGCCCTGG
 +
|-
 +
|attB +strand
 +
|attB34 TT F
 +
|GGTGCCAGGGCGTGCCCTTGGGCTCCCCGGG
 +
|-
 +
|attB -strand
 +
|attB34 TT R
 +
|CGCGCCCGGGGAGCCCAAGGGCACGCCCTGG
 +
|-
 +
|attB +strand
 +
|attB 34 GA F
 +
|GGTGCCAGGGCGTGCCCGAGGGCTCCCCGGG
 +
|-
 +
|attB -strand
 +
|attB34 GA R
 +
|CGCGCCCGGGGAGCCCTCGGGCACGCCCTGG
 +
|-
 +
|attB +strand
 +
|attB34 AC F
 +
|GGTGCCAGGGCGTGCCCACGGGCTCCCCGGG
 +
|-
 +
|attB -strand
 +
|attB34 AC R
 +
|CGCGCCCGGGGAGCCCGTGGGCACGCCCTGG
 +
|-
 +
|attB +strand
 +
|attB34 GG F
 +
|GGTGCCAGGGCGTGCCCGGGGGCTCCCCGGG
 +
|-
 +
|attB -strand
 +
|attB34 GG R
 +
|CGCGCCCGGGGAGCCCCCGGGCACGCCCTGG
 +
|-
 +
|attP + strand
 +
|attP39 TG F
 +
|CAACTGGGGTAACCTTGGAGTTCT
 +
|-
 +
|attP - strand
 +
|attP39 TG R
 +
|CCAACTGAGAGAACTCCAAGGTTAC
 +
|-
 +
|attP + strand
 +
|attP39 CT F
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|CAACTGGGGTAACCTCTGAGTTCT
 +
|-
 +
|attP - strand
 +
|attP39 CT R
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|CCAACTGAGAGAACTCAGAGGTTAC
 +
|-
 +
|attP + strand
 +
|attP39 TT F
 +
|CAACTGGGGTAACCTTTGAGTTCT
 +
|-
 +
|attP - strand
 +
|attP39 TT R
 +
|CCAACTGAGAGAACTCAAAGGTTAC
 +
|-
 +
|attP + strand
 +
|attP39 GA F
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|CAACTGGGGTAACCTGAGAGTTCT
 +
|-
 +
|attP - strand
 +
|attP39 GA R
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|CCAACTGAGAGAACTCTCAGGTTAC
 +
|-
 +
|attP + strand
 +
|attP39 AC F
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|CAACTGGGGTAACCTACGAGTTCT
 +
|-
 +
|attP - strand
 +
|attP39 AC R
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|CCAACTGAGAGAACTCGTAGGTTAC
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|-
 +
|attP + strand
 +
|attP39 GG F
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|CAACTGGGGTAACCTGGGAGTTCT
 +
|-
 +
|attP - strand
 +
|attP39 GG R
 +
|CCAACTGAGAGAACTCCCAGGTTAC

Latest revision as of 02:57, 22 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
sequencing c31 int gene anneals internally Int seq F cgtgcaacgtcagcatggcg
sequenceing c31 int gene anneals internally Int seq2 R cgccatgctgacgttgcacg
sequenceing c31 int gene anneals internally Int seq3 R caccaccaccggattacgtc
was designed to fix an error in another PCR primer that was thrown out. Could still amplify biobricked c31 int Int RBS GAATTCGCGGCCGCTTCTAGAGAAAGAGGAGAAATACTAGATGGAC
sequencing primer for pKNG101 derived vectors (pFB9XXXX) pKNG101 F CTACATATCACAACGTGCGTG
sequencing primer for pKNG101 derived vectors (pFB9XXXX) pKNG101 R CTCCGTCTACTGTACGATACAC
linker+ for synthetic attP cloning into pKNG101 derived vectors FB attP BamHI F CTCAGTTGGGGGG
linker- for synthetic attP cloning into pKNG101 derived vectors FB attP BamHI R GATCCCCC
linker+ for synthetic attP cloning into pKNG101 derived vectors FB attP SalI F TCGACCCC
linker- for synthetic attP cloning into pKNG101 derived vectors FB attP SalI R CCCAGTTGGGGG
Bba linker+ attB BBa attB EcoRI F AATTCGCGGCCGCTTCTAGAG
Bba linker- attB BBa attB EcoRI R CACCCTCTAGAAGCGGCCGCG
Bba linker+ attB BBa attB PstI F CGCGTACTAGTAGCGGCCGCTGCA
Bba linker- attB BBa attB PstI R GCGGCCGCTACTAGTA
BBa linker+ attP BBa attP EcoRI fwd aattcgcggccgcttctagagCCC 24
BBa linker- attP BBa attP EcoRI rev CCCAGTTGGGGctctagaagcggccgcg
BBa linker+ attP BBa attP PstI fwd CTCAGTTGGGGGGtactagtagcggccgctgca 33
BBa linker- attP BBa attP PstI rev gcggccgctactagtaCCCC 20
attB +strand attB34 TG F GGTGCCAGGGCGTGCCCTGGGGCTCCCCGGG
attB -strand attB34 TG R CGCGCCCGGGGAGCCCCAGGGCACGCCCTGG
attB +strand attB34 CT F GGTGCCAGGGCGTGCCCCTGGGCTCCCCGGG
attB -strand attB34 CT R CGCGCCCGGGGAGCCCAGGGGCACGCCCTGG
attB +strand attB34 TT F GGTGCCAGGGCGTGCCCTTGGGCTCCCCGGG
attB -strand attB34 TT R CGCGCCCGGGGAGCCCAAGGGCACGCCCTGG
attB +strand attB 34 GA F GGTGCCAGGGCGTGCCCGAGGGCTCCCCGGG
attB -strand attB34 GA R CGCGCCCGGGGAGCCCTCGGGCACGCCCTGG
attB +strand attB34 AC F GGTGCCAGGGCGTGCCCACGGGCTCCCCGGG
attB -strand attB34 AC R CGCGCCCGGGGAGCCCGTGGGCACGCCCTGG
attB +strand attB34 GG F GGTGCCAGGGCGTGCCCGGGGGCTCCCCGGG
attB -strand attB34 GG R CGCGCCCGGGGAGCCCCCGGGCACGCCCTGG
attP + strand attP39 TG F CAACTGGGGTAACCTTGGAGTTCT
attP - strand attP39 TG R CCAACTGAGAGAACTCCAAGGTTAC
attP + strand attP39 CT F CAACTGGGGTAACCTCTGAGTTCT
attP - strand attP39 CT R CCAACTGAGAGAACTCAGAGGTTAC
attP + strand attP39 TT F CAACTGGGGTAACCTTTGAGTTCT
attP - strand attP39 TT R CCAACTGAGAGAACTCAAAGGTTAC
attP + strand attP39 GA F CAACTGGGGTAACCTGAGAGTTCT
attP - strand attP39 GA R CCAACTGAGAGAACTCTCAGGTTAC
attP + strand attP39 AC F CAACTGGGGTAACCTACGAGTTCT
attP - strand attP39 AC R CCAACTGAGAGAACTCGTAGGTTAC
attP + strand attP39 GG F CAACTGGGGTAACCTGGGAGTTCT
attP - strand attP39 GG R CCAACTGAGAGAACTCCCAGGTTAC
Retrieved from "http://2009.igem.org/Team:Waterloo/Notebook/Oligos"