Team:Waterloo/Notebook/Oligos

From 2009.igem.org

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|Amplifies RK2 oriT adds EcoRI site, adds attB site in the forward orientation (rev) || RK2E-R || ATGGAATTCCGCGCCCGGGGAGCCCAAGGGCACGCCCTGGCACCCCGGGCAGGATAGGTGAAGT || 64
|Amplifies RK2 oriT adds EcoRI site, adds attB site in the forward orientation (rev) || RK2E-R || ATGGAATTCCGCGCCCGGGGAGCCCAAGGGCACGCCCTGGCACCCCGGGCAGGATAGGTGAAGT || 64
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|ampifies RK2 oriT adds PstI site, adds attB in the reverse orientation (fwd) || RK2-FP || CATCTGCAGCGCGCCCGGGGAGCCCAAGGGCACGCCCTGGCACCCCGGCCAGCCTCGCAGAGCA || 64
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|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
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|BBa sequencing/Colony PCR primer (rev)  || VR || ATTACCGCCTTTGAGTGAGC || 20
|BBa sequencing/Colony PCR primer (rev)  || VR || ATTACCGCCTTTGAGTGAGC || 20
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|PmeIR ORF (fwd)  || PmeIR-F || ATCCGGAATTCGCGGCGCTTTCTAGATGACAACAAACTCCCCCTCAGACG || 50
 
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|PmeIR ORF (rev)  || PmelR-R || CGCAAAACTGCAGCGGCCGCTACTAGTATCAAACCGTACTTCGCCCCCGTTG || 52
 
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|pRecA oligo (sense strand; produces BioBrick-compatible EcoRI/SpeI overhangs when annealed to recAR)  || recAF || AATTCGCGGCCGCTTCTAGAGTACAAAACACTTGATACTGTATATATATACAGTATAATTGCTTCAACATA || 71
 
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|pRecA oligo (antisense strand; produces BioBrick-compatible EcoRI/SpeI overhangs when annealed to recAR)  || recAR || CTAGTATGTTGAAGCAATTATACTGTATATATATACAGTATCAAGTGTTTTGTACTCTAGAAGCGGCCGCG || 71
 
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|{B0034}-{T7gene6 ORF} (fwd; for adding {Prefix-RBS} onto the gene 6 ORF by PCR)  || RBST7g6-F || GAATTCCGGCCGCTTCTAGAGAAAGAGGAGAAATACTAGATGGCACTTCTTGACCTTAAAC || 61
 
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|T7gene6 ORF (rev)  || T7gs-R || CTGCAGCGGCCGCTACTAGTATTATTACGGTCTCCACAGGTAAATCTC || 48
 
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|T7gene6 ORF rev; for joining to PmeI with crossover PCR  || T7g6-RXO-RBS || CTAGTATTTCTCCTCTTTCTCTAGTATTATTACGGTCTCCACAGGTAAATCTC || 53
 
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|PmeI ORF (fwd; for adding prefix-RBS)  || RBSpmeI-F || GAATTCCGGCCGCTTCTAGAGAAAGAGGAGAAATACTAGATGACAACAAACTCCCCCTCAG || 61
 
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|PmeI ORF (fwd; for adding prefix-RBS and joining to T7gene6 by crossover PCR) || RBSpmeI-FXO || TACTAGAGAAAGAGGAGAAATACTAGATGACAACAAACTCCCCCTCAG || 48
 
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|PmeI ORF (rev; TAATAA stop codon-suffix)  || pmeI-R || CTGCAGCGGCCGCTACTAGTATTATTAAACCGTACTTCGCCCCCG || 45
 
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|Primer for part R0011 (Plac-PL hybrid promoter; fwd) || R0011-F || GAATTCCGGCCGCTTCTAGAGAATTGTGAGCGGATAAC || 38
 
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|Primer for part R0011 (Plac-PL hybrid promoter; rev for joining to ORFs with RBS by crossover PCR)|| R0011RBS-RXO || CTAGTATTTCTCCTCTTTCTCTAGTATGTGCTCAGTATCTTGTTATC || 47
 
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|CI ORF (fwd; prefix-RBS) || RBSC0051-F || GAATTCCGGCCGCTTCTAGAGAAAGAGGAGAAATACTAGATGAGCACAAAAAAGAAACC || 59
 
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|CI ORF (fwd; prefix-RBS for joining to R0011 promoter by crossover PCR) || RBSC0051-FXO || TACTAGAGAAAGAGGAGAAATACTAGATGAGCACAAAAAAGAAACC || 46
 
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|CI ORF (rev; suffix adapter)  || C0051-R || CTGCAGCGGCCGCTACTAGTATTATTAAGCTACTAAAGCG || 40
 
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|CI ORF (rev; for joining to transcriptional terminator (b0015) by crossover PCR)  || C0051-RXO || GATGCCTGGCTCTAGTATTATTAAGCTACTAAAGCG || 36
 
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|Transcriptional terminator (B0015; fwd; for joining to ORFs by crossover PCR)  || B0015-FXO || TAATAATACTAGAGCCAGGCATCAAATAAAACG || 33
 
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|Transcriptional terminator (B0015; rev)  || B0015-R || CTGCAGCGGCCGCTACTAGTATATAAACGCAGAAAGGCC || 39
 
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|RFP ORF (fwd; prefix-RBS)  || RFP-RBS-F || GAATTCCGGCCGCTTCTAGAGAAAGAGGAGAAATACTAGATGGCTTCCTCCGAAGACG || 58
 
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|RFP ORF (fwd; prefix-RBS for joining to transcriptional terminator by crossover PCR ) || RFP-RXO || GATGCCTGGCTCTAGTATTATTAAGCACCGGTGG || 34
 
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Revision as of 05:43, 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
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 - BBa sequencing/Colony PCR primer (fwd) VF2 TGCCACCTGACGTCTAAGAA 20
BBa sequencing/Colony PCR primer (rev) VR ATTACCGCCTTTGAGTGAGC 20
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