"
Team:Waterloo/Notebook/Oligos
From 2009.igem.org
(Difference between revisions)
| Line 5: | Line 5: | ||
|- | |- | ||
| - | |amplifies first half of E. coli alpha gal gene adds SalI REN site (fwd) || HI-SalI-F || CATGTCGACATGATGTCTGCACCCAAAATT || | + | |amplifies first half of E. coli alpha gal gene adds SalI REN site (fwd) || HI-SalI-F || CATGTCGACATGATGTCTGCACCCAAAATT || 30 |
|- | |- | ||
| - | |amplifies first half of alpha gal gene adds BamHI REN site (rev) || HI-BamHI-attP-R || ATGGGATCCCCCCCAACTGAGAGAACTCAAAGGTTACCCCAGTTGGGGGTAACGCAGCGTAGCTGG || | + | |amplifies first half of alpha gal gene adds BamHI REN site (rev) || HI-BamHI-attP-R || ATGGGATCCCCCCCAACTGAGAGAACTCAAAGGTTACCCCAGTTGGGGGTAACGCAGCGTAGCTGG || 66 |
|- | |- | ||
| - | |amplifies second half of alpha gal gene, adds KpnI site (fwd) || H2-KpnI-attP-F || CATGGTACCCCCCCAACTGAGAGAACTCAAAGGTTACCCCAGTTGGGGGCGTTTTACCTGGAGCTGG || | + | |amplifies second half of alpha gal gene, adds KpnI site (fwd) || H2-KpnI-attP-F || CATGGTACCCCCCCAACTGAGAGAACTCAAAGGTTACCCCAGTTGGGGGCGTTTTACCTGGAGCTGG || 67 |
|- | |- | ||
| - | |amplifies second half of alpha gal gene, adds XbaI site (rev) || H2-XbaI-R || ATGTCTAGAGGTCAGCAGCGTCTGT || | + | |amplifies second half of alpha gal 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 || | + | |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 || | + | |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 VF2 (fwd) || Prefix-RBS || GGCCGCTTCTAGAGAAAGAGG || 21 | ||
| Line 23: | Line 23: | ||
|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 | ||
|- | |- | ||
| - | |amplifies c31 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 || | + | |amplifies c31 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 c31 int, adds suffix, changes stop codon to double TAA (rev) || Int-DSC-R || CTGCAGCGGCCGCTACTAGTATTATTACGCCGCTACGTCTTCCGTG || | + | |amplifies c31 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) || | + | |amplifies T7 Gene 6 exonuclease, adds ATG start codon, adds BBa prefix (fwd2) || T7gene6-F2 || GAATTCGCGGCCGCTTCTAGATGGCACTTCTTGACCTTAAAC || 42 |
| - | GAATTCGCGGCCGCTTCTAGATGGCACTTCTTGACCTTAAAC || | + | |
|- | |- | ||
|does not add standard start codon (fwd) || T7gene6-F || CAATGGAATTCGCGGCCGCTTCTAGATGGCACTTCTTGACCTTAAA || 46 | |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 || | + | |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 | |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 || | + | |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 prefix (fwd) || T7gene5-F || CAATGGAATTCGCGGCCGCTTCTAGATGATCGTTTCTGACATCGAA || 46 | ||
|- | |- | ||
| - | |Amplifies T7 gene 5 exonuclease, a 3'-5' exonuclease, adds BBa suffix (rev) || T7gene5-R || | + | |Amplifies T7 gene 5 exonuclease, a 3'-5' exonuclease, adds BBa suffix (rev) || T7gene5-R || CAATTTCTGCAGCGGCCGCTACTAGTATCAGTGGCAAATCGCCCAATTAGG || 51 |
| - | CAATTTCTGCAGCGGCCGCTACTAGTATCAGTGGCAAATCGCCCAATTAGG || 51 | + | |
|- | |- | ||
|amplifies phbA (fwd) || phbA-F || GAATTCGCGGCCGCTTCTAGATGAGCAATCCCTCGATCG || 39 | |amplifies phbA (fwd) || phbA-F || GAATTCGCGGCCGCTTCTAGATGAGCAATCCCTCGATCG || 39 | ||
| Line 63: | Line 61: | ||
|amplifies PmeI from Pseudomonas mendocina NEB698, or our synthetic ORF (rev) || PmeIR-R || CTGCAGCGGCCGCTACTAGTATTATTAAACCGTACTTCGCCCCCG || 45 | |amplifies PmeI from Pseudomonas mendocina NEB698, or our synthetic ORF (rev) || PmeIR-R || CTGCAGCGGCCGCTACTAGTATTATTAAACCGTACTTCGCCCCCG || 45 | ||
|- | |- | ||
| - | |sense oligo for RecA lexA hybrid promoter (K093000) 5' EcoRI overhang (fwd) || recA-F || | + | |sense oligo for RecA lexA hybrid promoter (K093000) 5' EcoRI overhang (fwd) || recA-F || AATTCGCGGCCGCTTCTAGAGTACAAAACACTTGATACTGTATATATATACAGTATAATTGCTTCAACATA|| 71 |
| - | AATTCGCGGCCGCTTCTAGAGTACAAAACACTTGATACTGTATATATATACAGTATAATTGCTTCAACATA || 71 | + | |
|- | |- | ||
|sense oligo for RecA lexA hybrid promoter (K093000) 3' SpeI overhang (rev) || recA-R || CTAGTATGTTGAAGCAATTATACTGTATATATATACAGTATCAAGTGTTTTGTACTCTAGAAGCGGCCGCG || 71 | |sense oligo for RecA lexA hybrid promoter (K093000) 3' SpeI overhang (rev) || recA-R || CTAGTATGTTGAAGCAATTATACTGTATATATATACAGTATCAAGTGTTTTGTACTCTAGAAGCGGCCGCG || 71 | ||
| Line 78: | Line 75: | ||
|ampifies RK2 oriT adds PstI site, adds attB in the reverse orientation (fwd) || RK2-FP || CATCTGCAGCGCGCCCGGGGAGCCCAAGGGCACGCCCTGGCACCCCGGCCAGCCTCGCAGAGCA || 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 |- | + | |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 (fwd) || VF2 || TGCCACCTGACGTCTAAGAA || 20 | ||
|- | |- | ||
|BBa sequencing/Colony PCR primer (rev) || VR || ATTACCGCCTTTGAGTGAGC || 20 | |BBa sequencing/Colony PCR primer (rev) || VR || ATTACCGCCTTTGAGTGAGC || 20 | ||
|- | |- | ||
Revision as of 06:04, 21 October 2009
| Description | Oligo Name | Sequence | Length |
|---|---|---|---|
| amplifies first half of E. coli alpha gal gene adds SalI REN site (fwd) | HI-SalI-F | CATGTCGACATGATGTCTGCACCCAAAATT | 30 |
| amplifies first half of alpha gal gene adds BamHI REN site (rev) | HI-BamHI-attP-R | ATGGGATCCCCCCCAACTGAGAGAACTCAAAGGTTACCCCAGTTGGGGGTAACGCAGCGTAGCTGG | 66 |
| amplifies second half of alpha gal gene, adds KpnI site (fwd) | H2-KpnI-attP-F | CATGGTACCCCCCCAACTGAGAGAACTCAAAGGTTACCCCAGTTGGGGGCGTTTTACCTGGAGCTGG | 67 |
| amplifies second half of alpha gal 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 c31 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 c31 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 J23118 constitutive promoter (BBa_K093012) anneals to promoter sequence (fwd) | RFP-BamHI-F | CATGGATCCTTGACGGCTAGCTCAGTC | 27 |
| anneals to RFP ORF sequence adds TT (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 (K093000) 5' EcoRI overhang (fwd) | recA-F | AATTCGCGGCCGCTTCTAGAGTACAAAACACTTGATACTGTATATATATACAGTATAATTGCTTCAACATA | 71 |
| sense oligo for RecA lexA hybrid promoter (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 |
