Team:Paris/Notebook/Oligo

From 2008.igem.org

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==Designed Oligonucleotides==
==Designed Oligonucleotides==
{|
{|
Line 107: Line 105:
|- style="background: #dddddd;"
|- style="background: #dddddd;"
| style="background: #D4E2EF;" | O113
| style="background: #D4E2EF;" | O113
-
| FlhDC(nu)-R
+
| FlhDC(rbs)-R
| GTTTCTTCCTGCAGCGGCCGCTACTAGTACAGAATAACCAACTTTATTTTTATG
| GTTTCTTCCTGCAGCGGCCGCTACTAGTACAGAATAACCAACTTTATTTTTATG
| 54
| 54
|
|
-
|Don't amplify the natural rbs of FlhD (only promoter)
+
|Amplify the natural rbs of FlhD
|- style="background: #dddddd;"
|- style="background: #dddddd;"
| style="background: #D4E2EF;" | O114
| style="background: #D4E2EF;" | O114
-
| FliA-PCR1-F
+
| xx FliA-PCR1-F
| GTTTCTTCGAATTCGCGGCCGCTTCTAGAGCCTGATTAACTGAGACTGACGGCAACGC
| GTTTCTTCGAATTCGCGGCCGCTTCTAGAGCCTGATTAACTGAGACTGACGGCAACGC
| 58
| 58
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|- style="background: #dddddd;"
|- style="background: #dddddd;"
| style="background: #D4E2EF;" | O115
| style="background: #D4E2EF;" | O115
-
| FliA-PCR1-R
+
| xx FliA-PCR1-R
| CAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCCGCAGGGTTTTTAATCG
| CAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCCGCAGGGTTTTTAATCG
| 59
| 59
Line 128: Line 126:
|- style="background: #dddddd;"
|- style="background: #dddddd;"
| style="background: #D4E2EF;" | O116
| style="background: #D4E2EF;" | O116
-
| FliA-PCR2-F
+
| xx FliA-PCR2-F
| GAAACGGATAATCATGCCGATAACTCATATAACGCAGGGCTG
| GAAACGGATAATCATGCCGATAACTCATATAACGCAGGGCTG
| 42
| 42
Line 135: Line 133:
|- style="background: #dddddd;"
|- style="background: #dddddd;"
| style="background: #D4E2EF;" | O117
| style="background: #D4E2EF;" | O117
-
| FliA-PCR2-R
+
| xx FliA-PCR2-R
| GTTTCTTCCTGCAGCGGCCGCTACTAGTACCATTACACCTTCA
| GTTTCTTCCTGCAGCGGCCGCTACTAGTACCATTACACCTTCA
GCGGTATAGAGTGAACTCACGATAAA
GCGGTATAGAGTGAACTCACGATAAA
Line 185: Line 183:
|- style="background: #dddddd;"
|- style="background: #dddddd;"
| style="background: #D4E2EF;" | O124
| style="background: #D4E2EF;" | O124
-
| FliL-F
+
| Oligo-pfliL-Forward-TRO
-
| GTTTCTTCGAATTCGCGGCCGCTTCTAGAGCAGCGAGAGGCTGTTGGTATTAATGACT
+
| TCGAATTCGCGGCCGCTTCTAGAGCAAGGGCGTGTAACAGGCAAC
-
| 58
+
| 45
-
|
+
| 60°C
|
|
|- style="background: #dddddd;"
|- style="background: #dddddd;"
| style="background: #D4E2EF;" | O125
| style="background: #D4E2EF;" | O125
-
| FliL-R
+
| Oligo-pfliL-Reverse-TRO
-
| GTTTCTTCCTGCAGCGGCCGCTACTAGTACCAGCGATGAAATACTTGCCATGCGATTT
+
| TCCTGCAGCGGCCGCTACTAGTAGTCATGTGTTGCGGTCTTCCTGTG
-
| 58
+
| 47
-
|
+
| 62°C
|
|
|- style="background: #dddddd;"
|- style="background: #dddddd;"
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|- style="background: #dddddd;"
|- style="background: #dddddd;"
| style="background: #D4E2EF;" | O127
| style="background: #D4E2EF;" | O127
-
| XX Gene-EnvZ-R
+
| Gene-EnvZ-R-TRO
-
| GTTTCTTCGAATTCGCGGCCGCTTCTAGTTATTACCCTTCTTTTGTCGTGCCCTGCGCC
+
| GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTACCCTTCTTTTGTCGTGCCCTGCGCC
-
| 59
+
| 60
-
|
+
| 68°C
|
|
|- style="background: #dddddd;"
|- style="background: #dddddd;"
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|- style="background: #dddddd;"
|- style="background: #dddddd;"
| style="background: #D4E2EF;" | O129
| style="background: #D4E2EF;" | O129
-
| XX Gene-FlgM-R
+
| Gene-FlgM-R-TRO
| GTTTCTTCGAATTCGCGGCCGCTTCTAGTTATTAGTTACTCTGCAAGTCTTGCTGCGCT
| GTTTCTTCGAATTCGCGGCCGCTTCTAGTTATTAGTTACTCTGCAAGTCTTGCTGCGCT
| 59
| 59
-
|
+
| 59°C
|
|
|- style="background: #dddddd;"
|- style="background: #dddddd;"
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|- style="background: #dddddd;"
|- style="background: #dddddd;"
| style="background: #D4E2EF;" | O131
| style="background: #D4E2EF;" | O131
-
| XX Gene-FlhC-R
+
| Gene-FlhC-R-TRO
-
| GTTTCTTCGAATTCGCGGCCGCTTCTAGTTATTAAACAGCCTGTACTCTCTGTTCATCC
+
| GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTAAACAGCCTGTACTCTCTGTTCATCC
-
| 59
+
| 60
-
|
+
| 60°C
|
|
|- style="background: #dddddd;"
|- style="background: #dddddd;"
Line 248: Line 246:
|- style="background: #dddddd;"
|- style="background: #dddddd;"
| style="background: #D4E2EF;" | O133
| style="background: #D4E2EF;" | O133
-
| XX Gene-FlhD-R
+
| Gene-FlhD-R-TRO
-
| GTTTCTTCGAATTCGCGGCCGCTTCTAGTTATTAGGCCCTTTTCTTGCGCAGCGCTTCT
+
| GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTAGGCCCTTTTCTTGCGCAGCGCTTCT
-
| 59
+
| 60
-
|
+
| 68°C
|
|
|- style="background: #dddddd;"
|- style="background: #dddddd;"
Line 262: Line 260:
|- style="background: #dddddd;"
|- style="background: #dddddd;"
| style="background: #D4E2EF;" | O135
| style="background: #D4E2EF;" | O135
-
| xx deux ecoR1 Gene-FliA-F
+
| xx Gene-FliA-F
| GTTTCTTCGAATTCGCGGCCGCTTCTAGATGAATTCACTCTATACCGCTGAAG
| GTTTCTTCGAATTCGCGGCCGCTTCTAGATGAATTCACTCTATACCGCTGAAG
| 53
| 53
Line 277: Line 275:
|- style="background: #dddddd;"
|- style="background: #dddddd;"
| style="background: #D4E2EF;" | O137
| style="background: #D4E2EF;" | O137
-
| Gene-FliArbs-F
+
| xx Gene-FliArbs-F
| GTTTCTTCGAATTCGCGGCCGCTTCTAGTAATCATGCCGATAACTCATATAAC
| GTTTCTTCGAATTCGCGGCCGCTTCTAGTAATCATGCCGATAACTCATATAAC
| 53
| 53
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|- style="background: #dddddd;"
|- style="background: #dddddd;"
| style="background: #D4E2EF;" | O139
| style="background: #D4E2EF;" | O139
-
| xx Gene-OmpR-R
+
| Gene-OmpR-R
-
| GTTTCTTCGAATTCGCGGCCGCTTCTAGTTATTATGCTTTAGAGCCGTCCGGTACAAAG
+
| GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTATGCTTTAGAGCCGTCCGGTACAAAG
-
| 59
+
| 60
-
|
+
| 62°C
|
|
|- style="background: #dddddd;"
|- style="background: #dddddd;"
Line 315: Line 313:
| GCCTGCAGATGCGTAAAGGAGAAGAACTTTTC
| GCCTGCAGATGCGTAAAGGAGAAGAACTTTTC
| 32
| 32
-
|55
+
| 55
-
|Amplify E0240 without the promoter and a PstI restriction site at the beginning
+
| Amplify E0240 without the promoter and a PstI restriction site at the beginning
 +
|- style="background: #dddddd;"
 +
| style="background: #D4E2EF;" | O143
 +
| G-PCRmut-1F
 +
| GGCTGTTTATCGTGAACTCACTCTATACCG
 +
| 30
 +
| 62
 +
| Mutate the EcoRI site of FliA ( without biobrick prefix)
 +
|- style="background: #dddddd;"
 +
| style="background: #D4E2EF;" | O144
 +
| P-FliArbs-R
 +
| CTTCCTGCAGCGGCCGCTACTAGTATTAAACAGCCCTGCGTTATATG
 +
| 47
 +
| 55 - 72
 +
| Amplify the rbs of FliA
 +
|- style="background: #dddddd;"
 +
| style="background: #D4E2EF;" | O145
 +
| P-xb-FliA-F
 +
| GCTTCTAGAGCCTGATTAACTGAGACTGAC
 +
| 30
 +
| 51 - 62
 +
| No EcoRI site on prefix for amplifying promoter
 +
|- style="background: #dddddd;"
 +
| style="background: #D4E2EF;" | O146
 +
| P-FliA-R
 +
| GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATATGAGTTATCGGCATGAT
 +
| 51
 +
| 51 - 71
 +
|
 +
|- style="background: #dddddd;"
 +
| style="background: #D4E2EF;" | O147
 +
| G-xb-FliA-F
 +
| CTTCTAGAACGCAGGGCTGTTTATCGTG
 +
| 28
 +
| 57 - 63
 +
| Amplify the gene with its natural rbs
 +
|- style="background: #dddddd;"
 +
| style="background: #D4E2EF;" | O148
 +
| G-mecoFliA-F
 +
| TCGAATTCGCGGCCGCTTCTAGACAGGGCTGTTTATCGTGAACTCACTCTATA
 +
| 53
 +
| 61 - 74
 +
| Oligo for second run PCR
 +
|- style="background: #dddddd;"
 +
| style="background: #D4E2EF;" | O149
 +
| G-spe-FliA-R
 +
| GCTACTAGTATTATTATAACTTACCCAGTTTAGTGCG
 +
| 37
 +
| 53 - 60
 +
| Oligo FliA for non-mutated sequence
 +
|- style="background: #dddddd;"
 +
| style="background: #D4E2EF;" | O150
 +
| G-FliA-R
 +
| TCCTGCAGCGGCCGCTACTAGTATTATTATAACTTACCCAGTTTAGTGCG
 +
| 50
 +
| 53 - 71
 +
| Oligo for complete mutated sequence - second run of PCR
 +
|- style="background: #dddddd;"
 +
| style="background: #D4E2EF;" | O151
 +
| PG-xb-FliA-R
 +
| GCTTCTAGAATTATTATAACTTACCCAGTTTAGTGCG
 +
| 37
 +
| 53 - 61
 +
| Oligo reverse with xbaI site for non mutated sequence
 +
|- style="background: #dddddd;"
 +
| style="background: #D4E2EF;" | O152
 +
| G-PCRmut-2R
 +
| GGGCAGTCGAACTTGCAGGCGCAATGCTTC
 +
| 30
 +
| 71
 +
| Oligo for first run of PCR, mutate PstI.
 +
|- style="background: #dddddd;"
 +
| style="background: #D4E2EF;" | O153
 +
| G-PCRmut-3F
 +
| GAAGCATTGCGCCTGCAAGTTCGACTGCCC
 +
| 30
 +
| 71
 +
| Oligo for fisrt run of PCR, mutate PstI.
 +
|- style="background: #dddddd;"
 +
| style="background: #D4E2EF;" | O154
 +
| pFlhDC-tto-F
 +
| GTTTCTTCGAATTCGCGGCCGCTTCTAGAGGTCGCTGTCGTTCTCAAAATCGGTG
 +
| 55
 +
| 62 - 75
 +
|
|}
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Latest revision as of 02:50, 27 September 2008

Designed Oligonucleotides

Table of Oligos
Number Name Sequence Length Tm(°C) Comments
O100 FlgA-F GTTTCTTCGAATTCGCGGCCGCTTCTAGAGAGCATATCTCCTCCGCAGGTATCAAAAT 58
O101 FlgA-R GTTTCTTCCTGCAGCGGCCGCTACTAGTAACAGTATCGCGATGATCGCCACGCTACGT 58
O102 FlgB-F GTTTCTTCGAATTCGCGGCCGCTTCTAGAGACAGTATCGCGATGATCGCCACGCTACG 58
O103 FlgB-R GTTTCTTCCTGCAGCGGCCGCTACTAGTAAGCATATCTCCTCCGCAGGTATCAAAATT 58
O104 FlgK-F GTTTCTTCGAATTCGCGGCCGCTTCTAGAGCAGCAGATGAAATCGATAAGCGACAAGG 58
O105 FlgK-R GTTTCTTCCTGCAGCGGCCGCTACTAGTAAACGCCGCCTGGGCCGCGTTCAGTCCGCT 58
O106 FlgM-F GTTTCTTCGAATTCGCGGCCGCTTCTAGAGAGCGGCGTTGTTGATGCAGATGGGAATA 58
O107 FlgM-R GTTTCTTCCTGCAGCGGCCGCTACTAGTACGAAGTGCGATCAATACTCATGGTTTATT 58
O108 FlhB-F GTTTCTTCGAATTCGCGGCCGCTTCTAGAGCCACGTCATATCAGGCGGTCTGATAAGG 58
O109 FlhB-R GTTTCTTCCTGCAGCGGCCGCTACTAGTAGTTTTGTCGTCGCTCTCGTCAGACACGTC 58
O110 FlhDC-Uri-F GTTTCTTCGAATTCGCGGCCGCTTCTAGAGTTGTATGTGCGTGTAGTGACGAGTACAG 58 Don't amplify the both OmpR binding site
O111 FlhDC-Total-F GTTTCTTCGAATTCGCGGCCGCTTCTAGAGTCATTTTTGCTTGCTAGCGTACGGAAAA 58 Amplify the both OmpR binding site
O112 FlhDC(rbs)-R GTTTCTTCCTGCAGCGGCCGCTACTAGTATCCCACCCAGAATAACCAACTTTAT 54 Amplify the natural rbs of FlhD
O113 FlhDC(rbs)-R GTTTCTTCCTGCAGCGGCCGCTACTAGTACAGAATAACCAACTTTATTTTTATG 54 Amplify the natural rbs of FlhD
O114 xx FliA-PCR1-F GTTTCTTCGAATTCGCGGCCGCTTCTAGAGCCTGATTAACTGAGACTGACGGCAACGC 58
O115 xx FliA-PCR1-R CAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCCGCAGGGTTTTTAATCG 59
O116 xx FliA-PCR2-F GAAACGGATAATCATGCCGATAACTCATATAACGCAGGGCTG 42
O117 xx FliA-PCR2-R GTTTCTTCCTGCAGCGGCCGCTACTAGTACCATTACACCTTCA

GCGGTATAGAGTGAACTCACGATAAA

69
O118 FliC-F GTTTCTTCGAATTCGCGGCCGCTTCTAGAGCCAGCGATGAAATACTTGCCATGCGATT 58
O119 FliC-R GTTTCTTCCTGCAGCGGCCGCTACTAGTACAGCGAGAGGCTGTTGGTATTAATGACTT 58
O120 FliE-F GTTTCTTCGAATTCGCGGCCGCTTCTAGAGGTCGCATTCATCGCGCACCTCGTGGCTG 58
O121 FliE-R GTTTCTTCCTGCAGCGGCCGCTACTAGTACTGGCTGATAACCCCTTCAATCCCCTGTA 58
O122 FliF-F GTTTCTTCGAATTCGCGGCCGCTTCTAGAGCTGGCTGATAACCCCTTCAATCCCCTGT 58
O123 FliF-R GTTTCTTCCTGCAGCGGCCGCTACTAGTAGTCGCATTCATCGCGCACCTCGTGGCTGA 58
O124 Oligo-pfliL-Forward-TRO TCGAATTCGCGGCCGCTTCTAGAGCAAGGGCGTGTAACAGGCAAC 45 60°C
O125 Oligo-pfliL-Reverse-TRO TCCTGCAGCGGCCGCTACTAGTAGTCATGTGTTGCGGTCTTCCTGTG 47 62°C
O126 Gene-EnvZ-F GTTTCTTCGAATTCGCGGCCGCTTCTAGATGAGGCGATTGCGCTTCTCGCCAC 53
O127 Gene-EnvZ-R-TRO GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTACCCTTCTTTTGTCGTGCCCTGCGCC 60 68°C
O128 Gene-FlgM-F GTTTCTTCGAATTCGCGGCCGCTTCTAGATGAGTATTGATCGCACTTCGCCTC 53
O129 Gene-FlgM-R-TRO GTTTCTTCGAATTCGCGGCCGCTTCTAGTTATTAGTTACTCTGCAAGTCTTGCTGCGCT 59 59°C
O130 Gene-FlhC-F GTTTCTTCGAATTCGCGGCCGCTTCTAGATGAGTGAAAAAAGCATTGTTCAGG 53
O131 Gene-FlhC-R-TRO GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTAAACAGCCTGTACTCTCTGTTCATCC 60 60°C
O132 Gene-FlhD-F GTTTCTTCGAATTCGCGGCCGCTTCTAGATGCATACCTCCGAGTTGCTGAAAC 53 Don't amplify the natural rbs of FlhD
O133 Gene-FlhD-R-TRO GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTAGGCCCTTTTCTTGCGCAGCGCTTCT 60 68°C
O134 Gene-FlhDCrbs-F GTTTCTTCGAATTCGCGGCCGCTTCTAGACCGCATAAAAATAAAGTTGGTTAT 53 Amplify the natural rbs of FlhD so that we have FlhD and FlhC with both their natural rbs
O135 xx Gene-FliA-F GTTTCTTCGAATTCGCGGCCGCTTCTAGATGAATTCACTCTATACCGCTGAAG 53 Don't Amplify the natural rbs of FliA
O136 xx Gene-FliA-R GTTTCTTCGAATTCGCGGCCGCTTCTAGTTATTATAACTTACCCAGTTTAGTGCGTAAC 59
O137 xx Gene-FliArbs-F GTTTCTTCGAATTCGCGGCCGCTTCTAGTAATCATGCCGATAACTCATATAAC 53 Amplify the natural rbs of FliA
O138 Gene-OmpR-F GTTTCTTCGAATTCGCGGCCGCTTCTAGATGCAAGAGAACTACAAGATTCTGG 53
O139 Gene-OmpR-R GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTATGCTTTAGAGCCGTCCGGTACAAAG 60 62°C
O140 PlasTest_GFP_Rv CCCTGCAGTTAATTAATATAAACGCAGAAAGGCCAC 36 54 Amplify E0240 with a PacI and a PstI restriction site at the end
O141 PTst_GFPrbs+_F GCCTGCAGTCACACAGGAAAGTACTAGATGC 31 56 Amplify E0240 with the promoter and a PstI restriction site at the beginning
O142 PTst_GFPrbs-_F GCCTGCAGATGCGTAAAGGAGAAGAACTTTTC 32 55 Amplify E0240 without the promoter and a PstI restriction site at the beginning
O143 G-PCRmut-1F GGCTGTTTATCGTGAACTCACTCTATACCG 30 62 Mutate the EcoRI site of FliA ( without biobrick prefix)
O144 P-FliArbs-R CTTCCTGCAGCGGCCGCTACTAGTATTAAACAGCCCTGCGTTATATG 47 55 - 72 Amplify the rbs of FliA
O145 P-xb-FliA-F GCTTCTAGAGCCTGATTAACTGAGACTGAC 30 51 - 62 No EcoRI site on prefix for amplifying promoter
O146 P-FliA-R GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATATGAGTTATCGGCATGAT 51 51 - 71
O147 G-xb-FliA-F CTTCTAGAACGCAGGGCTGTTTATCGTG 28 57 - 63 Amplify the gene with its natural rbs
O148 G-mecoFliA-F TCGAATTCGCGGCCGCTTCTAGACAGGGCTGTTTATCGTGAACTCACTCTATA 53 61 - 74 Oligo for second run PCR
O149 G-spe-FliA-R GCTACTAGTATTATTATAACTTACCCAGTTTAGTGCG 37 53 - 60 Oligo FliA for non-mutated sequence
O150 G-FliA-R TCCTGCAGCGGCCGCTACTAGTATTATTATAACTTACCCAGTTTAGTGCG 50 53 - 71 Oligo for complete mutated sequence - second run of PCR
O151 PG-xb-FliA-R GCTTCTAGAATTATTATAACTTACCCAGTTTAGTGCG 37 53 - 61 Oligo reverse with xbaI site for non mutated sequence
O152 G-PCRmut-2R GGGCAGTCGAACTTGCAGGCGCAATGCTTC 30 71 Oligo for first run of PCR, mutate PstI.
O153 G-PCRmut-3F GAAGCATTGCGCCTGCAAGTTCGACTGCCC 30 71 Oligo for fisrt run of PCR, mutate PstI.
O154 pFlhDC-tto-F GTTTCTTCGAATTCGCGGCCGCTTCTAGAGGTCGCTGTCGTTCTCAAAATCGGTG 55 62 - 75



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