Team:Waterloo/Notebook/Oligos

{| width="100%" border="1" cellpadding="2" ! 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 BBa_J23118 constitutive promoter (BBa_K093012) anneals to promoter sequence (fwd) || RFP-BamHI-F || CATGGATCCTTGACGGCTAGCTCAGTC || 27
 * anneals to RFP ORF sequence adds TT (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 (BBa_K093000) 5' EcoRI overhang (fwd) || recA-F || AATTCGCGGCCGCTTCTAGAGTACAAAACACTTGATACTGTATATATATACAGTATAATTGCTTCAACATA|| 71
 * sense oligo for RecA lexA hybrid promoter (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
 * 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
 * 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
 * CAACTGGGGTAACCTGGGAGTTCT
 * attP - strand
 * attP39 GG R
 * CCAACTGAGAGAACTCCCAGGTTAC
 * CCAACTGAGAGAACTCCCAGGTTAC