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Team:Waterloo/Notebook/Oligos
From 2009.igem.org
(Difference between revisions)
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CAATTTCTGCAGCGGCCGCTACTAGTATCAGTGGCAAATCGCCCAATTAGG || 51 | 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 | ||
|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 | ||
|- | |- | ||
| - | |||
| - | |||
| - | |||
| - | |||
|PmeIR ORF (fwd) || PmeIR-F || ATCCGGAATTCGCGGCGCTTTCTAGATGACAACAAACTCCCCCTCAGACG || 50 | |PmeIR ORF (fwd) || PmeIR-F || ATCCGGAATTCGCGGCGCTTTCTAGATGACAACAAACTCCCCCTCAGACG || 50 | ||
Revision as of 05:36, 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 | |||||
| amplifies first half of alpha gal gene adds BamHI REN site (rev) | HI-BamHI-attP-R | ATGGGATCCCCCCCAACTGAGAGAACTCAAAGGTTACCCCAGTTGGGGGTAACGCAGCGTAGCTGG | |||||
| amplifies second half of alpha gal gene, adds KpnI site (fwd) | H2-KpnI-attP-F | CATGGTACCCCCCCAACTGAGAGAACTCAAAGGTTACCCCAGTTGGGGGCGTTTTACCTGGAGCTGG | |||||
| amplifies second half of alpha gal gene, adds XbaI site (rev) | H2-XbaI-R | ATGTCTAGAGGTCAGCAGCGTCTGT | |||||
| 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 (rev) | Suffix-EcoRV-R | ATCCTGCAGCGGCCGCTACTAGTA | |||||
| 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 | |||||
| amplifies c31 int, adds suffix, changes stop codon to double TAA (rev) | Int-DSC-R | CTGCAGCGGCCGCTACTAGTATTATTACGCCGCTACGTCTTCCGTG | |||||
| amplifies T7 Gene 6 exonuclease, adds ATG start codon, adds BBa prefix (fwd2) | T7G6-F2 |
GAATTCGCGGCCGCTTCTAGATGGCACTTCTTGACCTTAAAC || | |||||
| 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 | |||||
| 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 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 | BBa sequencing/Colony PCR primer (fwd) | VF2 | TGCCACCTGACGTCTAAGAA | 20 |
| BBa sequencing/Colony PCR primer (rev) | VR | ATTACCGCCTTTGAGTGAGC | 20 | ||||
| PmeIR ORF (fwd) | PmeIR-F | ATCCGGAATTCGCGGCGCTTTCTAGATGACAACAAACTCCCCCTCAGACG | 50 | ||||
| PmeIR ORF (rev) | PmelR-R | CGCAAAACTGCAGCGGCCGCTACTAGTATCAAACCGTACTTCGCCCCCGTTG | 52 | ||||
| pRecA oligo (sense strand; produces BioBrick-compatible EcoRI/SpeI overhangs when annealed to recAR) | recAF | AATTCGCGGCCGCTTCTAGAGTACAAAACACTTGATACTGTATATATATACAGTATAATTGCTTCAACATA | 71 | ||||
| pRecA oligo (antisense strand; produces BioBrick-compatible EcoRI/SpeI overhangs when annealed to recAR) | recAR | CTAGTATGTTGAAGCAATTATACTGTATATATATACAGTATCAAGTGTTTTGTACTCTAGAAGCGGCCGCG | 71 | ||||
| {B0034}-{T7gene6 ORF} (fwd; for adding {Prefix-RBS} onto the gene 6 ORF by PCR) | RBST7g6-F | GAATTCCGGCCGCTTCTAGAGAAAGAGGAGAAATACTAGATGGCACTTCTTGACCTTAAAC | 61 | ||||
| T7gene6 ORF (rev) | T7gs-R | CTGCAGCGGCCGCTACTAGTATTATTACGGTCTCCACAGGTAAATCTC | 48 | ||||
| T7gene6 ORF rev; for joining to PmeI with crossover PCR | T7g6-RXO-RBS | CTAGTATTTCTCCTCTTTCTCTAGTATTATTACGGTCTCCACAGGTAAATCTC | 53 | ||||
| PmeI ORF (fwd; for adding prefix-RBS) | RBSpmeI-F | GAATTCCGGCCGCTTCTAGAGAAAGAGGAGAAATACTAGATGACAACAAACTCCCCCTCAG | 61 | ||||
| PmeI ORF (fwd; for adding prefix-RBS and joining to T7gene6 by crossover PCR) | RBSpmeI-FXO | TACTAGAGAAAGAGGAGAAATACTAGATGACAACAAACTCCCCCTCAG | 48 | ||||
| PmeI ORF (rev; TAATAA stop codon-suffix) | pmeI-R | CTGCAGCGGCCGCTACTAGTATTATTAAACCGTACTTCGCCCCCG | 45 | ||||
| Primer for part R0011 (Plac-PL hybrid promoter; fwd) | R0011-F | GAATTCCGGCCGCTTCTAGAGAATTGTGAGCGGATAAC | 38 | ||||
| Primer for part R0011 (Plac-PL hybrid promoter; rev for joining to ORFs with RBS by crossover PCR) | R0011RBS-RXO | CTAGTATTTCTCCTCTTTCTCTAGTATGTGCTCAGTATCTTGTTATC | 47 | ||||
| CI ORF (fwd; prefix-RBS) | RBSC0051-F | GAATTCCGGCCGCTTCTAGAGAAAGAGGAGAAATACTAGATGAGCACAAAAAAGAAACC | 59 | ||||
| CI ORF (fwd; prefix-RBS for joining to R0011 promoter by crossover PCR) | RBSC0051-FXO | TACTAGAGAAAGAGGAGAAATACTAGATGAGCACAAAAAAGAAACC | 46 | ||||
| CI ORF (rev; suffix adapter) | C0051-R | CTGCAGCGGCCGCTACTAGTATTATTAAGCTACTAAAGCG | 40 | ||||
| CI ORF (rev; for joining to transcriptional terminator (b0015) by crossover PCR) | C0051-RXO | GATGCCTGGCTCTAGTATTATTAAGCTACTAAAGCG | 36 | ||||
| Transcriptional terminator (B0015; fwd; for joining to ORFs by crossover PCR) | B0015-FXO | TAATAATACTAGAGCCAGGCATCAAATAAAACG | 33 | ||||
| Transcriptional terminator (B0015; rev) | B0015-R | CTGCAGCGGCCGCTACTAGTATATAAACGCAGAAAGGCC | 39 | ||||
| RFP ORF (fwd; prefix-RBS) | RFP-RBS-F | GAATTCCGGCCGCTTCTAGAGAAAGAGGAGAAATACTAGATGGCTTCCTCCGAAGACG | 58 | ||||
| RFP ORF (fwd; prefix-RBS for joining to transcriptional terminator by crossover PCR ) | RFP-RXO | GATGCCTGGCTCTAGTATTATTAAGCACCGGTGG | 34 |
