Difference between revisions of "Team:Toronto/Composite Part"

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<h2 id="composite-parts">Composite Parts</h2>
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<h2 id="tode-and-todf-plasmid-design">TodE and TodF Plasmid Design</h2>
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<h4 id="note">Note</h4>
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<p>Pseudomonas Putida F1 species degrade toluene with the help of tod operon. Toluene dioxygenase and toluene cis-dihydrodiol dehydroxygenase transcribed from transcribed from todC1C2BA and todD genes respectively facilitate break down of toluene to 3-methylcatechol. Gerben J. Zylstra et al successfully constructed the plasmid pTDG602 containing todC1C2BAD genes. To achieve complete degradation of toluene down to carbon dioxide and water, we focused on designing a plasmid containing todE and todF genes. After cotransformation of DH10B cells with pTDG602 and our plasmid, E.Coli theoretically should contain all the genes required to achieve complete degradation.</p>
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<p>In order to be considered for the <a href="https://2015.igem.org/Judging/Awards#SpecialPrizes">Best New Composite Part
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<p><img src="https://github.com/igemuoftATG/wiki2015/blob/master/images/Pathway.png" alt="alt text"></p>
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award</a>, you must fill out
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<p>In order to achieve the best protein production efficiency, we codon optimized our todE and todF sequences. We used Salis RBS calculator to optimize translation efficiency. We used a tunable promoter to determine optimum transcription for DH10B cells.</p>
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this page. Please give links to the Registry entries for the Composite parts you
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<p><img src="https://github.com/igemuoftATG/wiki2015/blob/master/images/biobrick%20plasmid.png" alt="alt text"></p>
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have made. Please see the Registry&#39;s <a href="http://parts.igem.org/Help:Parts#Basic_and_Composite_Parts">Help:Parts
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<p>We also used BioBricks in the registry to design plasmids with different efficiency by using RDP kit as shown below. In this process, we used promoter BBa_J23102 and RBS BBa_B0030.</p>
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page</a> for more
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<p><img src="file://localhost/Users/joannadowdell/Downloads/TodEplasmid.webp" alt="alt text"></p>
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information on part types.</p>
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<p><img src="https://github.com/igemuoftATG/wiki2015/blob/master/images/TodFplasmid.png" alt="alt text"></p>
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<p>A composite part is a functional unit of DNA consisting of two or more basic
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<p>Note: Links to iGem registry
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parts assembled together.
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BBa_J23102: <a href="http://parts.igem.org/Part:BBa_J23102">http://parts.igem.org/Part:BBa_J23102</a>
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<a href="http://parts.igem.org/wiki/index.php/Part:BBa_I13507">BBa_I13507</a> is an example
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BBa_0030: <a href="http://parts.igem.org/Part:BBa_B0030">http://parts.igem.org/Part:BBa_B0030</a></p>
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of a composite part, consisting of an RBS, a protein coding region for a red
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fluorescent protein, and a terminator.</p>
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<p>New composite BioBrick devices can be made by combining existing BioBrick Parts
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(like Inverters, Amplifiers, Smell Generators, Protein Balloon Generators,
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Senders, Receivers, Actuators, and so on).</p>
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Revision as of 23:03, 18 September 2015

TodE and TodF Plasmid Design

Pseudomonas Putida F1 species degrade toluene with the help of tod operon. Toluene dioxygenase and toluene cis-dihydrodiol dehydroxygenase transcribed from transcribed from todC1C2BA and todD genes respectively facilitate break down of toluene to 3-methylcatechol. Gerben J. Zylstra et al successfully constructed the plasmid pTDG602 containing todC1C2BAD genes. To achieve complete degradation of toluene down to carbon dioxide and water, we focused on designing a plasmid containing todE and todF genes. After cotransformation of DH10B cells with pTDG602 and our plasmid, E.Coli theoretically should contain all the genes required to achieve complete degradation.

alt text

In order to achieve the best protein production efficiency, we codon optimized our todE and todF sequences. We used Salis RBS calculator to optimize translation efficiency. We used a tunable promoter to determine optimum transcription for DH10B cells.

alt text

We also used BioBricks in the registry to design plasmids with different efficiency by using RDP kit as shown below. In this process, we used promoter BBa_J23102 and RBS BBa_B0030.

alt text

alt text

Note: Links to iGem registry BBa_J23102: http://parts.igem.org/Part:BBa_J23102 BBa_0030: http://parts.igem.org/Part:BBa_B0030