IGEM:Cambridge/2008/Turing Pattern Formation/Primers: Difference between revisions
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| Line 21: | Line 21: | ||
| 80.0+3 | | 80.0+3 | ||
| 34.0% | | 34.0% | ||
|- | |||
|colspan="8" align=center|<pre>at gaattcgcggccgcttctagag TTCATGAAAAACTAAAAAAAATATTG</pre> | |||
|- | |- | ||
|pXyl promoter reverse | |pXyl promoter reverse | ||
| Line 30: | Line 32: | ||
| 79.5+3 | | 79.5+3 | ||
| 44.0% | | 44.0% | ||
|- | |||
|colspan="8" align=center|<pre>gat ctgcagcggccgctactagta TATGTCATATTGTAAGTAAGTTGCAC</pre> | |||
|- | |- | ||
|pSpac promoter forward | |pSpac promoter forward | ||
| Line 39: | Line 43: | ||
| 82.6+3 | | 82.6+3 | ||
| 45.6% | | 45.6% | ||
|- | |||
|colspan="8" align=center|<pre>at gaattcgcggccgcttctagag AGAACAACCTCTGCTAAAATTC</pre> | |||
|- | |- | ||
|pSpac promoter reverse | |pSpac promoter reverse | ||
| Line 48: | Line 54: | ||
| 80.4+3 | | 80.4+3 | ||
| 46.6% | | 46.6% | ||
|- | |||
|colspan="8" align=center|<pre>tat ctgcagcggccgctactagta AAGCTTAATTGTTATCCGCTC</pre> | |||
|- | |- | ||
|pPac promoter forward | |pPac promoter forward | ||
| Line 57: | Line 65: | ||
| 84.5+3 | | 84.5+3 | ||
| 46.6% | | 46.6% | ||
|- | |||
|colspan="8" align=center|<pre>at gaattcgcggccgcttctagag AAACGAGGTCATCATTTCCTT</pre> | |||
|- | |- | ||
|pPac promoter reverse | |pPac promoter reverse | ||
| Line 66: | Line 76: | ||
| 82.1+3 | | 82.1+3 | ||
| 46.0% | | 46.0% | ||
|- | |||
|colspan="8" align=center|<pre>cgc ctgcagcggccgctactagta CAAATGTAGTCTTTGAAAGTATTACA</pre> | |||
|- | |- | ||
|pUpp promoter forward | |pUpp promoter forward | ||
| Line 75: | Line 87: | ||
| 82.6+3 | | 82.6+3 | ||
| 41.3% | | 41.3% | ||
|- | |||
|colspan="8" align=center|<pre>at gaattcgcggccgcttctagag GATGAATAAATTTTGGCGATAT</pre> | |||
|- | |- | ||
|pUpp promoter reverse | |pUpp promoter reverse | ||
| Line 84: | Line 98: | ||
| 80.3+3 | | 80.3+3 | ||
| 44.8% | | 44.8% | ||
|- | |||
|colspan="8" align=center|<pre>tat ctgcagcggccgctactagta GAGGATCAAATACATACAGTTTTCC</pre> | |||
|- | |- | ||
|} | |} | ||
Revision as of 09:50, 13 August 2008
Promoter Primers
calculated using https://www.finnzymes.fi/tm_determination.html
| Primer name | Parent vector | init. length | init. Tm | init. GC% | final length | final Tm | final GC |
|---|---|---|---|---|---|---|---|
| pXyl promoter forward | pSG1154 | 26 | 58.7+3 | 15.3% | 50 | 80.0+3 | 34.0% |
at gaattcgcggccgcttctagag TTCATGAAAAACTAAAAAAAATATTG | |||||||
| pXyl promoter reverse | pSG1154 | 26 bp | 63.0+3 | 26.6 % | 50 | 79.5+3 | 44.0% |
gat ctgcagcggccgctactagta TATGTCATATTGTAAGTAAGTTGCAC | |||||||
| pSpac promoter forward | pMUTIN-YFP | 22 | 58.5+3 | 36.3% | 46 | 82.6+3 | 45.6% |
at gaattcgcggccgcttctagag AGAACAACCTCTGCTAAAATTC | |||||||
| pSpac promoter reverse | pMUTIN-YFP | 21 | 59.3+3 | 38.0% | 45 | 80.4+3 | 46.6% |
tat ctgcagcggccgctactagta AAGCTTAATTGTTATCCGCTC | |||||||
| pPac promoter forward | pMUTIN-YFP | 21 | 61.7+3 | 38.0% | 45 | 84.5+3 | 46.6% |
at gaattcgcggccgcttctagag AAACGAGGTCATCATTTCCTT | |||||||
| pPac promoter reverse | pMUTIN-YFP | 26 | 57.7+3 | 26.6% | 50 | 82.1+3 | 46.0% |
cgc ctgcagcggccgctactagta CAAATGTAGTCTTTGAAAGTATTACA | |||||||
| pUpp promoter forward | pAD45-25 | 22 | 58.8+3 | 27.2% | 46 | 82.6+3 | 41.3% |
at gaattcgcggccgcttctagag GATGAATAAATTTTGGCGATAT | |||||||
| pUpp promoter reverse | pAD45-25 | 25 | 60.9+3 | 36.0% | 49 | 80.3+3 | 44.8% |
tat ctgcagcggccgctactagta GAGGATCAAATACATACAGTTTTCC | |||||||
Bacillus RBS Primers
We made primer sets for 2 ribosomal binding sites in Bacillus of differing binding strengths. We expect B._sub_RBSs to bind very strongly because it is the consensus sequence for RBS in B. subtilis.
B. subtilis consensus RBS - http://www.ncbi.nlm.nih.gov/pubmed/10446248 B._sub_RBSs_F *5' GAATTCGCGGCCGCTTCTAGAG AAAGGAGG TGTTA 3' B._sub_RBSs_R *5' CTGCAGCGGCCGCTACTAGTAACA CCTCCTTT CTCT 3'
RBS modified from ECE112 SpoVG RBS - http://www.bgsc.org/Catalogs/Catpart4.pdf B._sub_RBSw_F *5' GAATTCGCGGCCGCTTCTAGAG AGAGGTGG TGTTA 3' B._sub_RBSw_R *5' CTGCAGCGGCCGCTACTAGTAACA CCACCTCT CTCT 3'
Agr Primers
- These primers are to extract each part of the Agr operon so that a Bacillus RBS can replace the E. coli RBS currently attached to the genes.
agr senders
Agr_B_F *5' GTTTCTT C GAATTC GCGGCCGC T TCTAG ATGaactattttgacaacaa 3' Agr_B_R *5' TT C CTGCAG CGGCCGC T ACTAGT A TTATTA tttcagatcctctttgatg 3' Agr_D_F *5' CTT C GAATTC GCGGCCGC T TCTAG atgaatactctgttcaatctgtttt 3' Agr_D_R *5' TT C CTGCAG CGGCCGC T ACTAGT A TTATTA ttcatgcagctgggtcagct 3'
agr receivers
Agr_C_F *5' GTTTCTT C GAATTC GCGGCCGC T TCTAG atgattctgatgttcaccat 3' Agr_C_R *5' TT C CTGCAG CGGCCGC T ACTAGT A TTATTA gttattgatgatttcgactt 3' Agr_A_F *5' GTTTCTT C GAATTC GCGGCCGC T TCTAG atggaaatcgcactggcta 3' Agr_A_R *5' TT C CTGCAG CGGCCGC T ACTAGT A TTATTA gattttcttgacattgcgta 3'
