Team:Waterloo/Notebook/Oligos

From 2009.igem.org

(Difference between revisions)
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|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 ||
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|amplifies T7 Gene 6 exonuclease, adds ATG start codon, adds BBa prefix (fwd2) || T7G6-F2 || GAATTCGCGGCCGCTTCTAGATGGCACTTCTTGACCTTAAAC ||
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|amplifies T7 Gene 6 exonuclease, adds ATG start codon, adds BBa prefix (fwd2) || T7G6-F2 ||
 +
GAATTCGCGGCCGCTTCTAGATGGCACTTCTTGACCTTAAAC ||
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|does not add standard start codon (fwd) || T7gene6-F || CAATGGAATTCGCGGCCGCTTCTAGATGGCACTTCTTGACCTTAAA || 46
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|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 ||
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|does not add standard stop codon (rev) || T7gene6-R || CAATTTCTGCAGCGGCCGCTACTAGTACTACGGTCTCCACAGG || 43
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|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 ||
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|Amplifies T7 gene 5 exonuclease, a 3'-5' exonuclease, adds BBa prefix (fwd) || T7gene5-F || CAATGGAATTCGCGGCCGCTTCTAGATGATCGTTTCTGACATCGAA || 46
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|Amplifies T7 gene 5 exonuclease, a 3'-5' exonuclease, adds BBa suffix (rev) || T7gene5-R ||
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CAATTTCTGCAGCGGCCGCTACTAGTATCAGTGGCAAATCGCCCAATTAGG || 51
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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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|T7 gene 5 primer, 3'-5' exonuclease, adds BBa prefix (fwd) || T7gene5-F || CAATGGAATTCGCGGCCGCTTCTAGATGATCGTTTCTGACATCGAA || 46
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|T7 gene 5 primer, 3'-5' exonuclease, adds BBa suffix (rev)  || T7gene5-R || CAATTTCTGCAGCGGCCGCTACTAGTATCAGTGGCAAATCGCCCAATTAGG || 51
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|Gene 6 ORF from T7 phage (fwd; Prefix adapter)  || T7gene6-F || CAATGGAATTCGCGGCCGCTTCTAGATGGCACTTCTTGACCTTAAA || 46
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|Gene 6 ORF from T7 phage (rev; Suffix adapter)  || T7gene6-R || CAATTTCTGCAGCGGCCGCTACTAGTACTACGGTCTCCACAGG || 43
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|PmeIR ORF (fwd)  || PmeIR-F || ATCCGGAATTCGCGGCGCTTTCTAGATGACAACAAACTCCCCCTCAGACG || 50
|PmeIR ORF (fwd)  || PmeIR-F || ATCCGGAATTCGCGGCGCTTTCTAGATGACAACAAACTCCCCCTCAGACG || 50
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Revision as of 21:09, 20 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

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