Difference between revisions of "Team:Warwick/Design"

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         $("#Content1").html("<h2>Synthetic Gene Pathway</h2><img style='width: 100%; background-color: white !important; border-radius: 50px;' src='https://static.igem.org/mediawiki/2018/3/31/T--Warwick--ribodesign1.png'><br><br><p>ATC induces the circuit.<br><br>TetR is disabled by ATC.<br><br>The disabled TetR can no longer inhibit the transcription of the pathogen imitating <a href='http://parts.igem.org/wiki/index.php/Part:BBa_K2841531'>sRNA </a>.<br><br>The <a href='http://parts.igem.org/wiki/index.php/Part:BBa_K2841531'>sRNA</a> can bind to the constitutively expressed riboregulated <a href='http://parts.igem.org/Part:BBa_K2841541'>gRNA</a>, exposing the targeting domain.<br><br>The exposed <a href='http://parts.igem.org/wiki/index.php/Part:BBa_K2841510'>dCAS9</a> recognising cis-acting factor within the <a href='http://parts.igem.org/Part:BBa_K2841541'>gRNA</a> binds to the constitutively expressed <a href='http://parts.igem.org/wiki/index.php/Part:BBa_K2841510'>dCAS9</a> protein. <br><br>Once enabled the dCAS9 protein will bind to the <a href='http://parts.igem.org/wiki/index.php/Part:BBa_K2841517'>LacIq</a> promoter, inhibiting the expression of the LacI repressor protein.<br><br>Once the <a href='http://parts.igem.org/wiki/index.php/Part:BBa_K2841517'>LacI</a> repressor is inhibited, every pLAC will be upregulated due to lack of inhibition<br><br>The sfGFP will be synthesised from the pLAC, resulting in a green fluorescence.<br><br><br>The sRNA and dCAS9 are found on a Kanamycin resistant plasmid.<br><br><br>The gRNA and GFP are found on a Chloramphenicol plasmid.<br><br>The LacI is found on the Z1 cassette found in MG1655 Z1 cells. The Z1 cassette contains a set of repressors for the cell to utilise.<br><br></p>");
 
         $("#Content1").html("<h2>Synthetic Gene Pathway</h2><img style='width: 100%; background-color: white !important; border-radius: 50px;' src='https://static.igem.org/mediawiki/2018/3/31/T--Warwick--ribodesign1.png'><br><br><p>ATC induces the circuit.<br><br>TetR is disabled by ATC.<br><br>The disabled TetR can no longer inhibit the transcription of the pathogen imitating <a href='http://parts.igem.org/wiki/index.php/Part:BBa_K2841531'>sRNA </a>.<br><br>The <a href='http://parts.igem.org/wiki/index.php/Part:BBa_K2841531'>sRNA</a> can bind to the constitutively expressed riboregulated <a href='http://parts.igem.org/Part:BBa_K2841541'>gRNA</a>, exposing the targeting domain.<br><br>The exposed <a href='http://parts.igem.org/wiki/index.php/Part:BBa_K2841510'>dCAS9</a> recognising cis-acting factor within the <a href='http://parts.igem.org/Part:BBa_K2841541'>gRNA</a> binds to the constitutively expressed <a href='http://parts.igem.org/wiki/index.php/Part:BBa_K2841510'>dCAS9</a> protein. <br><br>Once enabled the dCAS9 protein will bind to the <a href='http://parts.igem.org/wiki/index.php/Part:BBa_K2841517'>LacIq</a> promoter, inhibiting the expression of the LacI repressor protein.<br><br>Once the <a href='http://parts.igem.org/wiki/index.php/Part:BBa_K2841517'>LacI</a> repressor is inhibited, every pLAC will be upregulated due to lack of inhibition<br><br>The sfGFP will be synthesised from the pLAC, resulting in a green fluorescence.<br><br><br>The sRNA and dCAS9 are found on a Kanamycin resistant plasmid.<br><br><br>The gRNA and GFP are found on a Chloramphenicol plasmid.<br><br>The LacI is found on the Z1 cassette found in MG1655 Z1 cells. The Z1 cassette contains a set of repressors for the cell to utilise.<br><br></p>");
  
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         $("#Content2").html("<h2>Plasmids and Sequences</h2><img src='https://static.igem.org/mediawiki/2018/5/5d/T--Warwick--ribodesign2.png'><img style='width: 100%' src='https://static.igem.org/mediawiki/2018/5/59/T--Warwick--ribodesign3.png'><img style='width: 100%' src='https://static.igem.org/mediawiki/2018/f/f5/T--Warwick--ribodesign4.png'><img style='width: 100%' src='https://static.igem.org/mediawiki/2018/d/d2/T--Warwick--ribodesign5.png'><img style='width: 100%' src='https://static.igem.org/mediawiki/2018/d/d2/T--Warwick--ribodesign5.png'>");
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         $("#Content2").html("<h2>Plasmids and Sequences</h2><img src='https://static.igem.org/mediawiki/2018/5/5d/T--Warwick--ribodesign2.png'><img style='width: 80%' src='https://static.igem.org/mediawiki/2018/5/59/T--Warwick--ribodesign3.png'><img style='width: 80%' src='https://static.igem.org/mediawiki/2018/f/f5/T--Warwick--ribodesign4.png'><img style='width: 80%' src='https://static.igem.org/mediawiki/2018/d/d2/T--Warwick--ribodesign5.png'><p>Every plasmid in genbank format: <a href='http://parts.igem.org/File:T--Warwick--2018-Entire-Project.zip'>here</a><br><br>We have the full plasmid<br><br>gRNA secondary structure prediction<br><br>Text - how to assume<br><br>ATGTTTAAACACGGATGTTTTATACTAATAGTCTTTTTTTTAGCCAGCTGCTTGTCAGGCTGTCTGGGGGTTTTATGGACTGGGGCAACTCTAGCCTATGACCGGCACAATGTATATAAAAAATTAGATGATTATAATTTAATAAAAGCTCTTAATGATGTTTTAGCTGTCAACCGGACATTTAAAAACTCAGAGACAGTACTGGATATTGCTGTGTTCAACAGAGATATTTTAATAGCAGGGCATGTTCCAACCCAGGAGTTGTACGATGAATTACAACTACGTCTAAGCAAAGTTAAAGGATACAGGCGGTTATTCAATCGTGTAATTATCAATAAAATGCCATCCAACTCGATCCAGGACAGCTGGATTACCACGAAAATCCGTAGCCAAATTTTTGCAGACTCTTCAATCGATCCTAACGCTTTCAAGGTGGTTACTTCTGATCGTGTTGTCTATTTGATGGGAGATGTTCAGACAGAACAAGCTGAAAAAGTGATTAAAATTGCAAGATACACAGGTGGTGTACAGAAAGTAATAAAACTTATGCGGTATTATACTTATCAAACCAGTACGAATATGGCCTGA<br><br>NuPack - accurate prediction (why 1999 paper)<br><br>2d molecular prediction (all constructs)</p>");
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        $("#Content3").html("<img style='width: 80%; background-color: white;' src='https://static.igem.org/mediawiki/2018/7/77/T--Warwick--ribodesign6.png'><br><br><br><img style='width: 80%; background-color: white;' src='https://static.igem.org/mediawiki/2018/3/33/T--Warwick--ribodesign7.png'><br><br><br><img style='width: 80%; background-color: white;' src='https://static.igem.org/mediawiki/2018/9/94/T--Warwick--ribodesign8.png'><br><br><br><img style='width: 80%; background-color: white;' src=''><br><p>We used centrifold method of folding with RNA composer to get some <a href='https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703931/'>results</a></p>");
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        $("#Content4").html("<h2>Alpha RNA Construct:</h2><br><p>CCCAGACAGCCTGAC AAAGGTTTTGCAC GCTAAAAAAAAGACT GTGCAAAACCTTTCGCGGTAGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCG</p><br><br><br><h2>Alpha RNA Pathogen-Imitating Region</h2><br><p>AGTCTTTTTTTTAGC CAGCTGCTT GTCAGGCTGTCTGGGatccttagcgaaagctaaggatttttttt</p><br><br><br><h2>Beta RNA Construct:</h2><br>p>GTACACCACCTGTGTA AAAGGTTTTGCAC TTTTAATCACTTTTT GTGCAAAACCTTTCGCGGTAGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCG</p><br><br><br><h2>Beta RNA Pathogen-Imitating Region</h2><br><p>AAAAAGTGATTAAAA TTGCAAGAT<br>ACACAGGTGGTGTACatccttagcgaaagctaaggatttttttt</p><br><br><br><h2>Gamma RNA Construct:</h2><br><p>GGTTGACAGCTAAAA AAAGGTTTTGCAC GAGCTTTTATTAAATTATAATC GTGCAAAACCTTTCGCGGTAGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCG<br><br><br><h2>Gamma RNA Pathogen-Imitating Region</h2><br><p>GATTATAATTTAATAAAAGCTC TTAATGATG TTTTAGCTGTCAACCatccttagcgaaagctaaggatttttttt</p><br><br><br><h2>Delta RNA Construct:</h2><br><p>TAGGCTAGAGTTGCCAAAGGTTTTGCAC  AAAACCCCCAGACAG GTGCAAAACCTTTCGCGGTAGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCG</p><br><br><br><h2>Delta RNA Pathogen-Imitating Region</h2><br><p>CTGTCTGGGGGTTTTATGGACTGGGGCAACTCTAGCCTAatccttagcgaaagctaaggatttttttt</p>
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Epsilon RNA Construct:
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TCGAGTTGGATGGCAAAAGGTTTTGCAC  TAATTACACGATTGAATAACCGCC GTGCAAAACCTTTCGCGGTAGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCG
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Epsilon RNA Pathogen-Imitating Region
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GGCGGTTATTCAATCGTGTAATTATCAATAAAATGCCATCCAACTCGAatccttagcgaaagctaaggatttttttt");
 
}
 
}
  

Revision as of 23:32, 17 October 2018

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Design