Team:Paris/Notebook/Oligo
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{{Paris/Menu}} | {{Paris/Menu}} | ||
- | + | ||
- | + | ==Designed Oligonucleotides== | |
- | + | ||
- | ==Designed | + | |
{| | {| | ||
- | |- style="background: # | + | |- style="background: #649CD7;" |
- | ! colspan="5" style="background: # | + | ! colspan="5" style="background: #649CD7;" | Table of Oligos |
- | |- style="background: # | + | |- style="background: #649CD7; text-align: center;" |
|width=5%| Number | |width=5%| Number | ||
|width=10%| Name | |width=10%| Name | ||
- | |width= | + | |width=40%| Sequence |
|width=5%| Length | |width=5%| Length | ||
|width=5%| Tm(°C) | |width=5%| Tm(°C) | ||
- | |width= | + | |width=35%| Comments |
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" |O100 | | style="background: #D4E2EF;" |O100 | ||
| FlgA-F | | FlgA-F | ||
Line 21: | Line 19: | ||
| | | | ||
| | | | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O101 | | style="background: #D4E2EF;" | O101 | ||
| FlgA-R | | FlgA-R | ||
Line 28: | Line 26: | ||
| | | | ||
| | | | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O102 | | style="background: #D4E2EF;" | O102 | ||
| FlgB-F | | FlgB-F | ||
Line 35: | Line 33: | ||
| | | | ||
| | | | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O103 | | style="background: #D4E2EF;" | O103 | ||
| FlgB-R | | FlgB-R | ||
Line 42: | Line 40: | ||
| | | | ||
| | | | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O104 | | style="background: #D4E2EF;" | O104 | ||
| FlgK-F | | FlgK-F | ||
Line 49: | Line 47: | ||
| | | | ||
| | | | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O105 | | style="background: #D4E2EF;" | O105 | ||
| FlgK-R | | FlgK-R | ||
Line 56: | Line 54: | ||
| | | | ||
| | | | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O106 | | style="background: #D4E2EF;" | O106 | ||
| FlgM-F | | FlgM-F | ||
Line 63: | Line 61: | ||
| | | | ||
| | | | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O107 | | style="background: #D4E2EF;" | O107 | ||
| FlgM-R | | FlgM-R | ||
Line 70: | Line 68: | ||
| | | | ||
| | | | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O108 | | style="background: #D4E2EF;" | O108 | ||
| FlhB-F | | FlhB-F | ||
Line 77: | Line 75: | ||
| | | | ||
| | | | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O109 | | style="background: #D4E2EF;" | O109 | ||
| FlhB-R | | FlhB-R | ||
Line 84: | Line 82: | ||
| | | | ||
| | | | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O110 | | style="background: #D4E2EF;" | O110 | ||
| FlhDC-Uri-F | | FlhDC-Uri-F | ||
Line 91: | Line 89: | ||
| | | | ||
|Don't amplify the both OmpR binding site | |Don't amplify the both OmpR binding site | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O111 | | style="background: #D4E2EF;" | O111 | ||
| FlhDC-Total-F | | FlhDC-Total-F | ||
Line 98: | Line 96: | ||
| | | | ||
|Amplify the both OmpR binding site | |Amplify the both OmpR binding site | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O112 | | style="background: #D4E2EF;" | O112 | ||
| FlhDC(rbs)-R | | FlhDC(rbs)-R | ||
Line 105: | Line 103: | ||
| | | | ||
|Amplify the natural rbs of FlhD | |Amplify the natural rbs of FlhD | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O113 | | style="background: #D4E2EF;" | O113 | ||
- | | FlhDC( | + | | FlhDC(rbs)-R |
| GTTTCTTCCTGCAGCGGCCGCTACTAGTACAGAATAACCAACTTTATTTTTATG | | GTTTCTTCCTGCAGCGGCCGCTACTAGTACAGAATAACCAACTTTATTTTTATG | ||
| 54 | | 54 | ||
| | | | ||
- | | | + | |Amplify the natural rbs of FlhD |
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O114 | | style="background: #D4E2EF;" | O114 | ||
- | | FliA-PCR1-F | + | | xx FliA-PCR1-F |
| GTTTCTTCGAATTCGCGGCCGCTTCTAGAGCCTGATTAACTGAGACTGACGGCAACGC | | GTTTCTTCGAATTCGCGGCCGCTTCTAGAGCCTGATTAACTGAGACTGACGGCAACGC | ||
| 58 | | 58 | ||
| | | | ||
| | | | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O115 | | style="background: #D4E2EF;" | O115 | ||
- | | FliA-PCR1-R | + | | xx FliA-PCR1-R |
| CAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCCGCAGGGTTTTTAATCG | | CAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCCGCAGGGTTTTTAATCG | ||
| 59 | | 59 | ||
| | | | ||
| | | | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O116 | | style="background: #D4E2EF;" | O116 | ||
- | | FliA-PCR2-F | + | | xx FliA-PCR2-F |
| GAAACGGATAATCATGCCGATAACTCATATAACGCAGGGCTG | | GAAACGGATAATCATGCCGATAACTCATATAACGCAGGGCTG | ||
| 42 | | 42 | ||
| | | | ||
| | | | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O117 | | style="background: #D4E2EF;" | O117 | ||
- | | FliA-PCR2-R | + | | xx FliA-PCR2-R |
- | | | + | | GTTTCTTCCTGCAGCGGCCGCTACTAGTACCATTACACCTTCA |
+ | GCGGTATAGAGTGAACTCACGATAAA | ||
| 69 | | 69 | ||
| | | | ||
| | | | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O118 | | style="background: #D4E2EF;" | O118 | ||
| FliC-F | | FliC-F | ||
Line 147: | Line 146: | ||
| | | | ||
| | | | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O119 | | style="background: #D4E2EF;" | O119 | ||
| FliC-R | | FliC-R | ||
Line 154: | Line 153: | ||
| | | | ||
| | | | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O120 | | style="background: #D4E2EF;" | O120 | ||
| FliE-F | | FliE-F | ||
Line 161: | Line 160: | ||
| | | | ||
| | | | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O121 | | style="background: #D4E2EF;" | O121 | ||
| FliE-R | | FliE-R | ||
Line 168: | Line 167: | ||
| | | | ||
| | | | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O122 | | style="background: #D4E2EF;" | O122 | ||
| FliF-F | | FliF-F | ||
Line 175: | Line 174: | ||
| | | | ||
| | | | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O123 | | style="background: #D4E2EF;" | O123 | ||
| FliF-R | | FliF-R | ||
- | | | + | | GTTTCTTCCTGCAGCGGCCGCTACTAGTAGTCGCATTCATCGCGCACCTCGTGGCTGA |
| 58 | | 58 | ||
| | | | ||
| | | | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O124 | | style="background: #D4E2EF;" | O124 | ||
- | | | + | | Oligo-pfliL-Forward-TRO |
- | | | + | | TCGAATTCGCGGCCGCTTCTAGAGCAAGGGCGTGTAACAGGCAAC |
- | | | + | | 45 |
+ | | 60°C | ||
| | | | ||
- | + | |- style="background: #dddddd;" | |
- | |- style="background: # | + | |
| style="background: #D4E2EF;" | O125 | | style="background: #D4E2EF;" | O125 | ||
- | | | + | | Oligo-pfliL-Reverse-TRO |
- | | | + | | TCCTGCAGCGGCCGCTACTAGTAGTCATGTGTTGCGGTCTTCCTGTG |
- | | | + | | 47 |
- | | | + | | 62°C |
| | | | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O126 | | style="background: #D4E2EF;" | O126 | ||
| Gene-EnvZ-F | | Gene-EnvZ-F | ||
Line 203: | Line 202: | ||
| | | | ||
| | | | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O127 | | style="background: #D4E2EF;" | O127 | ||
- | | Gene-EnvZ-R | + | | Gene-EnvZ-R-TRO |
- | | | + | | GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTACCCTTCTTTTGTCGTGCCCTGCGCC |
- | | | + | | 60 |
- | | | + | | 68°C |
| | | | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O128 | | style="background: #D4E2EF;" | O128 | ||
| Gene-FlgM-F | | Gene-FlgM-F | ||
Line 217: | Line 216: | ||
| | | | ||
| | | | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O129 | | style="background: #D4E2EF;" | O129 | ||
- | | Gene-FlgM-R | + | | Gene-FlgM-R-TRO |
| GTTTCTTCGAATTCGCGGCCGCTTCTAGTTATTAGTTACTCTGCAAGTCTTGCTGCGCT | | GTTTCTTCGAATTCGCGGCCGCTTCTAGTTATTAGTTACTCTGCAAGTCTTGCTGCGCT | ||
| 59 | | 59 | ||
+ | | 59°C | ||
| | | | ||
- | + | |- style="background: #dddddd;" | |
- | |- style="background: # | + | |
| style="background: #D4E2EF;" | O130 | | style="background: #D4E2EF;" | O130 | ||
| Gene-FlhC-F | | Gene-FlhC-F | ||
Line 231: | Line 230: | ||
| | | | ||
| | | | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O131 | | style="background: #D4E2EF;" | O131 | ||
- | | Gene-FlhC-R | + | | Gene-FlhC-R-TRO |
- | | | + | | GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTAAACAGCCTGTACTCTCTGTTCATCC |
- | | | + | | 60 |
+ | | 60°C | ||
| | | | ||
- | + | |- style="background: #dddddd;" | |
- | |- style="background: # | + | |
| style="background: #D4E2EF;" | O132 | | style="background: #D4E2EF;" | O132 | ||
| Gene-FlhD-F | | Gene-FlhD-F | ||
Line 245: | Line 244: | ||
| | | | ||
|Don't amplify the natural rbs of FlhD | |Don't amplify the natural rbs of FlhD | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O133 | | style="background: #D4E2EF;" | O133 | ||
- | | Gene-FlhD-R | + | | Gene-FlhD-R-TRO |
- | | | + | | GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTAGGCCCTTTTCTTGCGCAGCGCTTCT |
- | | | + | | 60 |
- | | | + | | 68°C |
| | | | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O134 | | style="background: #D4E2EF;" | O134 | ||
| Gene-FlhDCrbs-F | | Gene-FlhDCrbs-F | ||
Line 259: | Line 258: | ||
| | | | ||
|Amplify the natural rbs of FlhD so that we have FlhD and FlhC with both their natural rbs | |Amplify the natural rbs of FlhD so that we have FlhD and FlhC with both their natural rbs | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O135 | | style="background: #D4E2EF;" | O135 | ||
- | | Gene-FliA-F | + | | xx Gene-FliA-F |
| GTTTCTTCGAATTCGCGGCCGCTTCTAGATGAATTCACTCTATACCGCTGAAG | | GTTTCTTCGAATTCGCGGCCGCTTCTAGATGAATTCACTCTATACCGCTGAAG | ||
| 53 | | 53 | ||
| | | | ||
|Don't Amplify the natural rbs of FliA | |Don't Amplify the natural rbs of FliA | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O136 | | style="background: #D4E2EF;" | O136 | ||
- | | Gene-FliA-R | + | | xx Gene-FliA-R |
| GTTTCTTCGAATTCGCGGCCGCTTCTAGTTATTATAACTTACCCAGTTTAGTGCGTAAC | | GTTTCTTCGAATTCGCGGCCGCTTCTAGTTATTATAACTTACCCAGTTTAGTGCGTAAC | ||
| 59 | | 59 | ||
Line 274: | Line 273: | ||
| | | | ||
| | | | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O137 | | style="background: #D4E2EF;" | O137 | ||
- | | Gene-FliArbs-F | + | | xx Gene-FliArbs-F |
| GTTTCTTCGAATTCGCGGCCGCTTCTAGTAATCATGCCGATAACTCATATAAC | | GTTTCTTCGAATTCGCGGCCGCTTCTAGTAATCATGCCGATAACTCATATAAC | ||
| 53 | | 53 | ||
| | | | ||
|Amplify the natural rbs of FliA | |Amplify the natural rbs of FliA | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O138 | | style="background: #D4E2EF;" | O138 | ||
| Gene-OmpR-F | | Gene-OmpR-F | ||
Line 288: | Line 287: | ||
| | | | ||
| | | | ||
- | |- style="background: # | + | |- style="background: #dddddd;" |
| style="background: #D4E2EF;" | O139 | | style="background: #D4E2EF;" | O139 | ||
| Gene-OmpR-R | | Gene-OmpR-R | ||
- | | | + | | GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTATGCTTTAGAGCCGTCCGGTACAAAG |
- | | | + | | 60 |
+ | | 62°C | ||
| | | | ||
+ | |- style="background: #dddddd;" | ||
+ | | style="background: #D4E2EF;" | O140 | ||
+ | | PlasTest_GFP_Rv | ||
+ | | CCCTGCAGTTAATTAATATAAACGCAGAAAGGCCAC | ||
+ | | 36 | ||
+ | |54 | ||
+ | |Amplify E0240 with a PacI and a PstI restriction site at the end | ||
+ | |- style="background: #dddddd;" | ||
+ | | style="background: #D4E2EF;" | O141 | ||
+ | | PTst_GFPrbs+_F | ||
+ | | GCCTGCAGTCACACAGGAAAGTACTAGATGC | ||
+ | | 31 | ||
+ | |56 | ||
+ | |Amplify E0240 with the promoter and a PstI restriction site at the beginning | ||
+ | |- style="background: #dddddd;" | ||
+ | | style="background: #D4E2EF;" | O142 | ||
+ | | PTst_GFPrbs-_F | ||
+ | | GCCTGCAGATGCGTAAAGGAGAAGAACTTTTC | ||
+ | | 32 | ||
+ | | 55 | ||
+ | | 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 | ||
| | | | ||
|} | |} |
Latest revision as of 02:50, 27 September 2008
Designed Oligonucleotides
|