Team:SDU-Denmark/primers

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== '''Primers''' ==
== '''Primers''' ==
<br>
<br>
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On this page we list all the primers we designed and used during the summer. Numbers in paranthesis is basic temperature (celcius) <br><br>
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On this page we list all the primers we designed and used during the summer.<br><br>
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'''''Primers for FlhDC master operon'''''
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<table style="text-align: left; width: 100%;" border="1"
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<br>
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cellpadding="2" cellspacing="2">
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We needed to design 4 primers for this part. The FlhDC operon contains a PST1 restriction site, therefore we wanted to introduce a silent mutation, C --> T, at position 822 in the operon.<br><br>
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    <tr>
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''Reverse primer w. mutation at position 13 (gene position 822):'' 5’-CATAAGCTGCGGTCAAAGCTGCCAA -3’ (59)<br><br>
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      <td>Primer name</td>
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''Forward primer w. mutation at position 13 (gene position 822):'' 5’-TTGGCAGCTTTGACCGCAGCTTATG-3’        (59)<br><br>
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      <td>coding sequence</td>
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Lastly we added primers with prefix and suffix to the PCR result of the above:<br><br>
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      <td>Tm (celcius)</td>
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[[FlhDC forward:]]<br>
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      <td>sequence with prefix or suffix</td>
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''Prefixprimer:'' 5'-G TTT CTT CGA ATT CGC GGC CGC TTC TAG ATG CAT ACC TCC GAG TTG CTG AAA-3' (Coding sequence (CS): 56) (Primer total (PT): 72)<br><br>
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      <td>Tm (celcius)</td>
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[[FlhDC reverse:]]<br>
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    </tr>
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''Suffixprimer:'' 5'-GT TTC TTC CTG CAG CGG CCG CTA CTA TTA AAC AGC CTG TAC TCT CTG TTC-3' (CS: 56) (PT: 72)<br><br>
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    <tr>
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'''''SopIItrs'''''
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      <td>FlhD/C primer fw</td>
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<br>
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      <td>5'-ATGCATACCTCCGAGTTGCTGAAA-3'</td>
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''Forward primer:''  5’-GTTTCTTCGAATTCGCGGCCGCTTCTAGATGGTGGGACTTACGACC-3’ (CS: 50) (PT: 73)<br><br>
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      <td>55.7</td>
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''Reverse primer:''  5’-GTTTCTTCCTGCAGCGGCCGCTACTAGTATTAAAATGTTTCCCAGTTCT-3’ (CS: 70) (PT: 44) <br><br>
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      <td>5'-GTTTCTTCGAATTCGCGGCCGCTTCTAGATGCATACCTCCGAGTTGCTGAAA-3'</td>
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      <td>88.3</td>
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    </tr>
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    <tr>
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      <td>FlhD/C primer rv</td>
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      <td>5'-AAACAGCCTGTACTCTCTGTTC-3'</td>
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      <td>53</td>
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      <td>5'-GTTTCTTCCTGCAGCGGCCGCTACTATTAAACAGCCTGTACTCTCTGTTC-3'</td>
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      <td>88.3</td>
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    </tr>
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    <tr>
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      <td>FlhD/C mutation primer fw^</td>
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      <td>5'-TTGGCAGCTTTGCCCGCAGCTTATG-3'</td>
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      <td>61</td>
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      <td></td>
 +
      <td></td>
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    </tr>
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    <tr>
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      <td>FlhD/C mutation primer rv^</td>
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      <td>5'-CATAAGCTGCGGGCAAAGCTGCCAA-3'</td>
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      <td>61</td>
 +
      <td></td>
 +
      <td></td>
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    </tr>
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    <tr>
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      <td>Photosensor primer fw</td>
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      <td>5'-ATGGTGGGACTTACGACCTC-3'</td>
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      <td>53.8</td>
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      <td>5'-GTTTCTTCGAATTCGCGGCCGCTTCTAGATGGTGGGACTTACGACCTC-3'</td>
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      <td>73.1</td>
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    </tr>
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    <tr>
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      <td>Photosensor primer rv</td>
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      <td>5'-TCAGAAGGTTTCCCAGTTCGCATC-3'</td>
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      <td>57.4</td>
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      <td>5'-GTTTCTTCCTGCAGCGGCCGCTACTAGTATCAGAAGGTTTCCCAGTTCGCATC-3'</td>
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      <td>73.9</td>
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    </tr>
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    <tr>
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      <td>beta-caroten monooxygenase primer1 fw</td>
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      <td>5'-ATGGCAGCCGGTGTCTTCAAGAG-3'</td>
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      <td>58.8</td>
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      <td>5'-GAATTCGCGGCCGCTTCTAGATGGCAGCCGGTGTCTTCAAGAG-3'</td>
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      <td>73.1</td>
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    </tr>
 +
    <tr>
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      <td>beta-caroten monooxygenase primer1 rv</td>
 +
      <td>5'-CTAAATGGCATTGGGTGCAAACCATC-3'</td>
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      <td>58</td>
 +
      <td>5'-CTGCAGCGGCCGCTACTAGTACTAAATGGCATTGGGTGCAAACCATC-3'</td>
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      <td>72.4</td>
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    </tr>
 +
    <tr>
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      <td>beta-caroten monooxygenase primer2 fw^^</td>
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      <td>5'-ATGGCAGCCGGTGTCTTCAAGAG-3'</td>
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      <td>58.8</td>
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      <td>5'-CCGCTTCTAGATGGCAGCCGGTGTCTTCAAGAG-3'</td>
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      <td>68.1</td>
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    </tr>
 +
    <tr>
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      <td>beta-caroten monooxygenase primer2 rv^^</td>
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      <td>5'-CTAAATGGCATTGGGTGCAAACCATC-3'</td>
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      <td>58</td>
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      <td>5'-CGCTACTAGTACTAAATGGCATTGGGTGCAAACCATC-3'</td>
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      <td>65.6</td>
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    </tr>
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</table><br>
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^ Mutation primers to introduce a silent mutation at position 822 in the operon<br>
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^^ Due to the formation of hairpin structures of beta-caroten monooxygenase primer 1, primers with prefix and suffix only containing the restrictionsites of xbaI and SpeI respectively were designed.<br><br>
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</div>
</div>

Revision as of 15:32, 17 October 2010

Retrieved from "http://2010.igem.org/Team:SDU-Denmark/primers"