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) || T7G6-F2 ||
+
|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