Difference between revisions of "Team:Vilnius-Lithuania/Basic"

 
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<h1 class="text-wall-heading">Basic Parts</h1>
 
<h1 class="text-wall-heading">Basic Parts</h1>
 
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<div class="text-wall-area-box">
 
     <h2 class="text-wall-area-box-heading">Separate Soldiers</h2>
 
     <h2 class="text-wall-area-box-heading">Separate Soldiers</h2>
 
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         <p class="text-content">Cell-free systems are becoming an increasingly popular in vitro tool to study biological processes as it is accompanied by less intrinsic and extrinsic noise. Relying on fundamental concepts of synthetic biology, we apply a bottom-up forward engineering approach to create a novel cell-free system for unorthodox protein-evolution. The core of this system is cell-sized liposomes that serve as excellent artificial membrane models. By encapsulating genetic material and full in vitro protein transcription and translation systems within the liposomes, we create reliable and incredibly efficient nanofactories for the production of target proteins. Even though there are many alternative proteins that can be synthesized, our main focus is directed towards membrane proteins, which occupy approximately one third of living-cells’ genomes. Considering their significance, membrane proteins are spectacularly understudied since synthesis and thus characterization of them remain prevailing obstacles to this day. We aim to utilize liposomes as nanofactories for directed evolution of membrane proteins. Furthermore, by means of directed membrane protein-evolution, a universal exposition system will be designed in order to display any protein of interest on the surface of the liposome. This way, a system is built where a phenotype of a particular protein is expressed on the outside while containing its genotype within the liposome. To prove the concept, small antibody fragments will be displayed to create a single-chain variable fragment (scFv) library for rapid screening of any designated target.</p>
+
         <p class="text-content">Basic parts, that we created fall into three categories: coding, regulatory and RNA. Coding parts consist of proteins, that assemble into lipid bilayer. Regulatory parts ensure that protein synthesis starts at desired temperature. RNA is used as a modification platform to produce membrane associated ribosomes which help with protein integration into membrane.</p>
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        </p>
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        <h1>Description</h1>
+
<h1>Basic Parts</h1>     
−
         <p></p>
+
<table class="c39">
−
        <p></p>
+
         <tbody>
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        <h2>What is SynORI?</h2>
+
          <tr class="c9">
−
        <p>SynORI stands for synthetic origin of replication. It is a framework designed to make working with single
+
              <td class="c27" colspan="1" rowspan="1">
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            and multi-plasmid systems precise, easy and on top of that - more functional.</p>
+
                <p class="c5"><span class="c12 c29">Part Number</span></p>
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        <p>The SynORI framework enables scientists to build a multi-plasmid system in a standardized manner by:</p>
+
              </td>
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        <ol>
+
              <td class="c25" colspan="1" rowspan="1">
−
            <li>Selecting the number of plasmid groups</li>
+
                <p class="c5"><span class="c12 c29">Type</span></p>
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            <li>Choosing the copy number of each group</li>
+
              </td>
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            <li>Picking the type of copy number control (specific to one group or regulating all of them at once).</li>
+
              <td class="c16" colspan="1" rowspan="1">
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+
                <p class="c5"><span class="c12 c29">Name</span></p>
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        </ol>
+
              </td>
−
        </p>
+
              <td class="c13" colspan="1" rowspan="1">
−
 
+
                <p class="c5"><span class="c12 c29">Brief description</span></p>
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        <p></p>
+
              </td>
−
        <p>The framework also includes a possibility of adding a selection system that reduces the usage of antibiotics
+
              <td class="c32" colspan="1" rowspan="1">
−
            (only 1 antibiotic for up to 5 different plasmids!) and an active partitioning system to make sure that low
+
                <p class="c5"><span class="c12 c29">Length, nt</span></p>
−
            copy number plasmid groups are not lost during the division.
+
              </td>
−
        </p>
+
          </tr>
−
        <p></p>
+
          <tr class="c9">
−
        <div class="img-cont">
+
              <td class="c27" colspan="1" rowspan="1">
−
            <img src="https://static.igem.org/mediawiki/parts/8/84/Collect.png" alt="img">
+
                <p class="c5"><span class="c0"><a href="http://parts.igem.org/Part:BBa_K2622001"> BBa_2622001</a> </span></p>
−
            <div class="img-label">
+
              </td>
−
            </div>
+
              <td class="c25" colspan="1" rowspan="1">
−
        </div>
+
                <p class="c5"><span class="c0">Coding</span></p>
−
        <h2>Applications</h2>
+
              </td>
−
        <p>
+
              <td class="c16" colspan="1" rowspan="1">
−
            <h5>Everyday lab work</h5>
+
                <p class="c5"><span class="c43">BamB</span></p>
−
            <p>
+
              </td>
−
                A multi-plasmid system that is easy to assemble and control. With our framework the need to limit your
+
              <td class="c13" colspan="1" rowspan="1">
−
                research to a particular plasmid copy number just because there are not enough right replicons to
+
                <p class="c5"><span class="c0">Beta-barrel assembly protein B (BamB)</span></p>
−
                choose from, is eliminated. With SynORI you can easily create a vector with a desired copy number that
+
              </td>
−
                suits your needs.</li>
+
              <td class="c7" colspan="1" rowspan="1">
−
            </p>
+
                <p class="c24"><span class="c0">1261</span></p>
−
            <h5>Biological computing</h5>
+
              </td>
−
            <p>
+
          </tr>
−
                The ability to choose a wide range of copy number options and their control types will make the
+
          <tr class="c9">
−
                synthetic biology engineering much more flexible and predictable. Introduction of plasmid copy number
+
              <td class="c27" colspan="1" rowspan="1">
−
                regulation is equivalent to adding a global parameter to a computer system. It enables the coordination
+
                <p class="c5"><span class="c0"><a href="http://parts.igem.org/Part:BBa_K2622002"> BBa_2622002</a></span></p>
−
                of multiple gene group expression.
+
              </td>
−
            </p>
+
              <td class="c25" colspan="1" rowspan="1">
−
            <h5>Smart assembly of large protein complexes</h5>
+
                <p class="c5"><span class="c0">Coding</span></p>
−
            <p>
+
              </td>
−
                The co-expression of multi-subunit complexes using different replicons brings incoherency to an already
+
              <td class="c16" colspan="1" rowspan="1">
−
                chaotic cell system. This can be avoided by using SynORI, as in this framework every plasmid group uses
+
                <p class="c5 c37"><span class="c0">BamA</span></p>
−
                the same type of control, and in addition can act in a group-specific manner.</p>
+
              </td>
−
 
+
              <td class="c13" colspan="1" rowspan="1">
−
            <h5>Metabolic engineering</h5>
+
                <p class="c5"><span class="c0">Beta-barrel assembly protein A (BamA)</span></p>
−
            <p>
+
              </td>
−
                A big challenge for heterologous expression of multiple gene pathways is to accurately adjust the
+
              <td class="c7" colspan="1" rowspan="1">
−
                levels of each enzyme to achieve optimal production efficiency. Precise promoter tuning in
+
                <p class="c24"><span class="c0">2520</span></p>
−
                transcriptional control and synthetic ribosome binding sites in translational control are already
+
              </td>
−
                widely used to maintain expression levels. In addition to current approaches, our framework allows a
+
          </tr>
−
                simultaneous multiple gene control. Furthermore, an inducible regulation that we offer, can make the
+
          <tr class="c9">
−
                search for perfect conditions a lot easier.
+
              <td class="c27" colspan="1" rowspan="1">
−
 
+
                <p class="c5"><span class="c0"><a href="http://parts.igem.org/Part:BBa_K2622003"> BBa_2622003</a></span></p>
−
 
+
              </td>
−
 
+
              <td class="c25" colspan="1" rowspan="1">
−
            </p>
+
                <p class="c5"><span class="c0">Coding</span></p>
−
 
+
              </td>
−
 
+
              <td class="c16" colspan="1" rowspan="1">
−
        </p>
+
                <p class="c5"><span class="c0">IgA</span></p>
−
        <p>
+
              </td>
−
        </p>
+
              <td class="c13" colspan="1" rowspan="1">
−
        <table style="width:100%">
+
                <p class="c5"><span>Immunoglobulin protease A (IgA) beta-domain from </span><span class="c22">Neisseria gonorrhoeae</span></p>
−
<thead>
+
              </td>
−
<td align='center'>Species sign in ODE system</td>
+
              <td class="c7" colspan="1" rowspan="1">
−
<td align='center'>Species</td>
+
                <p class="c24"><span class="c0">1398</span></p>
−
<td align='center'>Initial concentration (M)</td>
+
              </td>
−
</thead>
+
          </tr>
−
<tbody>
+
          <tr class="c9">
−
<tr>
+
              <td class="c27" colspan="1" rowspan="1">
−
<td align='center'>A</td>
+
                <p class="c5"><span class="c0"><a href="http://parts.igem.org/Part:BBa_K2622004"> BBa_2622004</a></span></p>
−
<td align='center'>pDNA+RNA I+RNAII early</td>
+
              </td>
−
<td align='center'>0</td>
+
              <td class="c25" colspan="1" rowspan="1">
−
</tr>
+
                <p class="c5"><span class="c0">Coding</span></p>
−
<tr>
+
              </td>
−
<td align='center'>B</td>
+
              <td class="c16" colspan="1" rowspan="1">
−
<td align='center'>pDNA+RNA II short</td>
+
                <p class="c5"><span class="c0">scFv_antiVLY</span></p>
−
<td align='center'>0</td>
+
              </td>
−
</tr>
+
              <td class="c13" colspan="1" rowspan="1">
−
<tr>
+
                <p class="c5"><span class="c0">Single chain variable fragment antibody anti-vaginolysin (scFv_antiVGY)</span></p>
−
<td align='center'>RNAI</td>
+
              </td>
−
<td align='center'>RNA I</td>
+
              <td class="c7" colspan="1" rowspan="1">
−
<td align='center'>1E-6</td>
+
                <p class="c24"><span class="c0">733</span></p>
−
</tr>
+
              </td>
−
<tr>
+
          </tr>
−
<td align='center'>D</td>
+
          <tr class="c9">
−
<td align='center'>pDNA+RNA II long</td>
+
              <td class="c27" colspan="1" rowspan="1">
−
<td align='center'>0</td>
+
                <p class="c5"><span class="c0"><a href="http://parts.igem.org/Part:BBa_K2622005"> BBa_2622005</a></span></p>
−
</tr>
+
              </td>
−
<tr>
+
              <td class="c25" colspan="1" rowspan="1">
−
<td align='center'>E</td>
+
                <p class="c5"><span class="c0">Coding</span></p>
−
<td align='center'>pDNA+RNAII primer</td>
+
              </td>
−
<td align='center'>0</td>
+
              <td class="c16" colspan="1" rowspan="1">
−
</tr>
+
                <p class="c5"><span class="c0">GFP Nanobody</span></p>
−
<tr>
+
              </td>
−
<td align='center'>F</td>
+
              <td class="c13" colspan="1" rowspan="1">
−
<td align='center'>RNA II long</td>
+
                <p class="c5"><span class="c0">Camelid antibody against green fluorescent protein (GFP Nanobody)</span></p>
−
<td align='center'>0</td>
+
              </td>
−
</tr>
+
              <td class="c7" colspan="1" rowspan="1">
−
<tr>
+
                <p class="c24"><span class="c0">352</span></p>
−
<td align='center'>G</td>
+
              </td>
−
<td align='center'>pDNA</td>
+
          </tr>
−
<td align='center'>4E-8*</td>
+
          <tr class="c9">
−
</tr>
+
              <td class="c27" colspan="1" rowspan="1">
−
<tr>
+
                <p class="c5"><span class="c0"><a href="http://parts.igem.org/Part:BBa_K2622006"> BBa_2622006</a></span></p>
−
<td align='center'>H</td>
+
              </td>
−
<td align='center'>pDNA+RNA II+RNA I late</td>
+
              <td class="c25" colspan="1" rowspan="1">
−
<td align='center'>0</td>
+
                <p class="c5"><span class="c0">Coding</span></p>
−
</tr>
+
              </td>
−
<tr>
+
              <td class="c16" colspan="1" rowspan="1">
−
<td align='center'>RNA II</td>
+
                <p class="c5"><span class="c0">Mistic (Mstx)</span></p>
−
<td align='center'>RNA II</td>
+
              </td>
−
<td align='center'>0</td>
+
              <td class="c13" colspan="1" rowspan="1">
−
</tr>
+
                <p class="c5"><span>Membrane-integrating protein Mistic (MstX) from </span><span class="c22">Bacillus subtilis</span></p>
−
<tr>
+
              </td>
−
<td align='center'>J</td>
+
              <td class="c7" colspan="1" rowspan="1">
−
<td align='center'>RNAI+RNAII</td>
+
                <p class="c24"><span class="c0">330</span></p>
−
<td align='center'>0</td>
+
              </td>
−
</tr>
+
          </tr>
−
</tbody>
+
          <tr class="c9">
−
</table>
+
              <td class="c27" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0"><a href="http://parts.igem.org/Part:BBa_K2622007"> BBa_2622007</a></span></p>
 +
              </td>
 +
              <td class="c25" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">RNA</span></p>
 +
              </td>
 +
              <td class="c16" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">gRNA for ribosome protein L12</span></p>
 +
              </td>
 +
              <td class="c13" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Guide RNA for modification of ribosome protein L12 using CRISPR-Cas9 system</span></p>
 +
              </td>
 +
              <td class="c7" colspan="1" rowspan="1">
 +
                <p class="c24"><span class="c0">174</span></p>
 +
              </td>
 +
          </tr>
 +
          <tr class="c9">
 +
              <td class="c27" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0"><a href="http://parts.igem.org/Part:BBa_K2622008"> BBa_2622008</a></span></p>
 +
              </td>
 +
              <td class="c25" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">RNA</span></p>
 +
              </td>
 +
              <td class="c16" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">gRNA for ribosome protein L23</span></p>
 +
              </td>
 +
              <td class="c13" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Guide RNA for modification of ribosome protein L23 using CRISPR-Cas9 system</span></p>
 +
              </td>
 +
              <td class="c7" colspan="1" rowspan="1">
 +
                <p class="c24"><span class="c0">174</span></p>
 +
              </td>
 +
          </tr>
 +
          <tr class="c9">
 +
              <td class="c27" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0"><a href="http://parts.igem.org/Part:BBa_K2622009"> BBa_2622009</a></span></p>
 +
              </td>
 +
              <td class="c25" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">RNA</span></p>
 +
              </td>
 +
              <td class="c16" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">gRNA for ribosome protein L24</span></p>
 +
              </td>
 +
              <td class="c13" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Guide RNA for modification of ribosome protein L24 using CRISPR-Cas9 system</span></p>
 +
              </td>
 +
              <td class="c7" colspan="1" rowspan="1">
 +
                <p class="c24"><span class="c0">174</span></p>
 +
              </td>
 +
          </tr>
 +
          <tr class="c9">
 +
              <td class="c27" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0"><a href="http://parts.igem.org/Part:BBa_K2622010"> BBa_2622010</a></span></p>
 +
              </td>
 +
              <td class="c25" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Regulatory</span></p>
 +
              </td>
 +
              <td class="c16" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">RNA thermoswitch1 (GJ2)</span></p>
 +
              </td>
 +
              <td class="c13" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Temperature-sensitive non-coding RNA 1</span></p>
 +
              </td>
 +
              <td class="c7" colspan="1" rowspan="1">
 +
                <p class="c24"><span class="c0">39</span></p>
 +
              </td>
 +
          </tr>
 +
          <tr class="c9">
 +
              <td class="c27" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0"><a href="http://parts.igem.org/Part:BBa_K2622011"> BBa_2622011</a></span></p>
 +
              </td>
 +
              <td class="c25" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Regulatory</span></p>
 +
              </td>
 +
              <td class="c16" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">RNA thermoswitch2 (GJ3)</span></p>
 +
              </td>
 +
              <td class="c13" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Temperature-sensitive non-coding RNA 2</span></p>
 +
              </td>
 +
              <td class="c7" colspan="1" rowspan="1">
 +
                <p class="c24"><span class="c0">38</span></p>
 +
              </td>
 +
          </tr>
 +
          <tr class="c9">
 +
              <td class="c27" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0"><a href="http://parts.igem.org/Part:BBa_K2622012"> BBa_2622012</a></span></p>
 +
              </td>
 +
              <td class="c25" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Regulatory</span></p>
 +
              </td>
 +
              <td class="c16" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">RNA thermoswitch3 (GJ6)</span></p>
 +
              </td>
 +
              <td class="c13" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Temperature-sensitive non-coding RNA 3</span></p>
 +
              </td>
 +
              <td class="c7" colspan="1" rowspan="1">
 +
                <p class="c24"><span class="c0">53</span></p>
 +
              </td>
 +
          </tr>
 +
          <tr class="c9">
 +
              <td class="c27" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0"><a href="http://parts.igem.org/Part:BBa_K2622013"> BBa_2622013</a></span></p>
 +
              </td>
 +
              <td class="c25" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Regulatory</span></p>
 +
              </td>
 +
              <td class="c16" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">RNA thermoswitch4 (GJ9)</span></p>
 +
              </td>
 +
              <td class="c13" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Temperature-sensitive non-coding RNA 4</span></p>
 +
              </td>
 +
              <td class="c7" colspan="1" rowspan="1">
 +
                <p class="c24"><span class="c0">32</span></p>
 +
              </td>
 +
          </tr>
 +
          <tr class="c9">
 +
              <td class="c27" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0"><a href="http://parts.igem.org/Part:BBa_K2622014"> BBa_2622014</a></span></p>
 +
              </td>
 +
              <td class="c25" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Regulatory</span></p>
 +
              </td>
 +
              <td class="c16" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">RNA thermoswitch5 (GJ10)</span></p>
 +
              </td>
 +
              <td class="c13" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Temperature-sensitive non-coding RNA 5</span></p>
 +
              </td>
 +
              <td class="c7" colspan="1" rowspan="1">
 +
                <p class="c24"><span class="c0">33</span></p>
 +
              </td>
 +
          </tr>
 +
          <tr class="c9">
 +
              <td class="c27" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0"><a href="http://parts.igem.org/Part:BBa_K2622015"> BBa_2622015</a></span></p>
 +
              </td>
 +
              <td class="c25" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Coding</span></p>
 +
              </td>
 +
              <td class="c16" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">BamC</span></p>
 +
              </td>
 +
              <td class="c13" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Beta-barrel assembly protein C (BamC)</span></p>
 +
              </td>
 +
              <td class="c7" colspan="1" rowspan="1">
 +
                <p class="c24"><span class="c0">1057</span></p>
 +
              </td>
 +
          </tr>
 +
          <tr class="c9">
 +
              <td class="c27" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0"><a href="http://parts.igem.org/Part:BBa_K2622016"> BBa_2622016</a></span></p>
 +
              </td>
 +
              <td class="c25" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Regulatory</span></p>
 +
              </td>
 +
              <td class="c16" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">RNA thermoswitch 6 (Sw2)</span></p>
 +
              </td>
 +
              <td class="c13" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Temperature-sensitive non-coding RNA 6</span></p>
 +
              </td>
 +
              <td class="c7" colspan="1" rowspan="1">
 +
                <p class="c24"><span class="c0">33</span></p>
 +
              </td>
 +
          </tr>
 +
          <tr class="c9">
 +
              <td class="c27" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0"><a href="http://parts.igem.org/Part:BBa_K2622017"> BBa_2622017</a></span></p>
 +
              </td>
 +
              <td class="c25" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Regulatory</span></p>
 +
              </td>
 +
              <td class="c16" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">RNA thermoswitch 7 (Sw3)</span></p>
 +
              </td>
 +
              <td class="c13" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Temperature-sensitive non-coding RNA 7</span></p>
 +
              </td>
 +
              <td class="c7" colspan="1" rowspan="1">
 +
                <p class="c24"><span class="c0">33</span></p>
 +
              </td>
 +
          </tr>
 +
          <tr class="c9">
 +
              <td class="c27" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0"><a href="http://parts.igem.org/Part:BBa_K2622018"> BBa_2622018</a></span></p>
 +
              </td>
 +
              <td class="c25" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Regulatory</span></p>
 +
              </td>
 +
              <td class="c16" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">RNA thermoswitch 8 (Sw6)</span></p>
 +
              </td>
 +
              <td class="c13" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Temperature-sensitive non-coding RNA 8</span></p>
 +
              </td>
 +
              <td class="c7" colspan="1" rowspan="1">
 +
                <p class="c24"><span class="c0">33</span></p>
 +
              </td>
 +
          </tr>
 +
          <tr class="c9">
 +
              <td class="c27" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0"><a href="http://parts.igem.org/Part:BBa_K2622019"> BBa_2622019</a></span></p>
 +
              </td>
 +
              <td class="c25" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Regulatory</span></p>
 +
              </td>
 +
              <td class="c16" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">RNA thermoswitch 9 (Sw7)</span></p>
 +
              </td>
 +
              <td class="c13" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Temperature-sensitive non-coding RNA 9</span></p>
 +
              </td>
 +
              <td class="c7" colspan="1" rowspan="1">
 +
                <p class="c24"><span class="c0">33</span></p>
 +
              </td>
 +
          </tr>
 +
          <tr class="c9">
 +
              <td class="c27" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0"><a href="http://parts.igem.org/Part:BBa_K2622020"> BBa_2622020</a></span></p>
 +
              </td>
 +
              <td class="c25" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Regulatory</span></p>
 +
              </td>
 +
              <td class="c16" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">RNA thermoswitch 10 (Sw9)</span></p>
 +
              </td>
 +
              <td class="c13" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Temperature-sensitive non-coding RNA 10</span></p>
 +
              </td>
 +
              <td class="c7" colspan="1" rowspan="1">
 +
                <p class="c24"><span class="c0">33</span></p>
 +
              </td>
 +
          </tr>
 +
          <tr class="c9">
 +
              <td class="c27" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0"><a href="http://parts.igem.org/Part:BBa_K2622021"> BBa_2622021</a></span></p>
 +
              </td>
 +
              <td class="c25" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Regulatory</span></p>
 +
              </td>
 +
              <td class="c16" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">RNA thermoswitch 11 (Sw11)</span></p>
 +
              </td>
 +
              <td class="c13" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Temperature-sensitive non-coding RNA 11</span></p>
 +
              </td>
 +
              <td class="c7" colspan="1" rowspan="1">
 +
                <p class="c24"><span class="c0">33</span></p>
 +
              </td>
 +
          </tr>
 +
          <tr class="c9">
 +
              <td class="c27" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0"><a href="http://parts.igem.org/Part:BBa_K2622022"> BBa_2622022</a></span></p>
 +
              </td>
 +
              <td class="c25" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Coding</span></p>
 +
              </td>
 +
              <td class="c16" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">BamD</span></p>
 +
              </td>
 +
              <td class="c13" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Beta-barrel assembly protein D (BamD)</span></p>
 +
              </td>
 +
              <td class="c7" colspan="1" rowspan="1">
 +
                <p class="c24"><span class="c0">757</span></p>
 +
              </td>
 +
          </tr>
 +
          <tr class="c9">
 +
              <td class="c27" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0"><a href="http://parts.igem.org/Part:BBa_K2622023"> BBa_2622023</a></span></p>
 +
              </td>
 +
              <td class="c25" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Coding</span></p>
 +
              </td>
 +
              <td class="c16" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">BamE</span></p>
 +
              </td>
 +
              <td class="c13" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Beta-barrel assembly protein E (BamE)</span></p>
 +
              </td>
 +
              <td class="c7" colspan="1" rowspan="1">
 +
                <p class="c24"><span class="c0">448</span></p>
 +
              </td>
 +
          </tr>
 +
          <tr class="c9">
 +
              <td class="c27" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0"><a href="http://parts.igem.org/Part:BBa_K2622024"> BBa_2622024</a></span></p>
 +
              </td>
 +
              <td class="c25" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Coding</span></p>
 +
              </td>
 +
              <td class="c16" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">SurA</span></p>
 +
              </td>
 +
              <td class="c13" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Survival protein A (SurA)</span></p>
 +
              </td>
 +
              <td class="c7" colspan="1" rowspan="1">
 +
                <p class="c24"><span class="c0">1374</span></p>
 +
              </td>
 +
          </tr>
 +
          <tr class="c9">
 +
              <td class="c27" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0"><a href="http://parts.igem.org/Part:BBa_K2622048"> BBa_2622048</a></span></p>
 +
              </td>
 +
              <td class="c25" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Coding</span></p>
 +
              </td>
 +
              <td class="c16" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">OmpA full</span></p>
 +
              </td>
 +
              <td class="c13" colspan="1" rowspan="1">
 +
                <p class="c5"><span class="c0">Full length outer transmembrane protein A (OmpA)</span></p>
 +
              </td>
 +
              <td class="c7" colspan="1" rowspan="1">
 +
                <p class="c24"><span class="c0">1041</span></p>
 +
              </td>
 +
          </tr>
 +
        </tbody>
 +
    </table>
 
     </div>
 
     </div>
 
</div>
 
</div>

Latest revision as of 20:35, 4 November 2018

Basic Parts

Separate Soldiers

Basic parts, that we created fall into three categories: coding, regulatory and RNA. Coding parts consist of proteins, that assemble into lipid bilayer. Regulatory parts ensure that protein synthesis starts at desired temperature. RNA is used as a modification platform to produce membrane associated ribosomes which help with protein integration into membrane.

Basic Parts

Part Number

Type

Name

Brief description

Length, nt

BBa_2622001

Coding

BamB

Beta-barrel assembly protein B (BamB)

1261

BBa_2622002

Coding

BamA

Beta-barrel assembly protein A (BamA)

2520

BBa_2622003

Coding

IgA

Immunoglobulin protease A (IgA) beta-domain from Neisseria gonorrhoeae

1398

BBa_2622004

Coding

scFv_antiVLY

Single chain variable fragment antibody anti-vaginolysin (scFv_antiVGY)

733

BBa_2622005

Coding

GFP Nanobody

Camelid antibody against green fluorescent protein (GFP Nanobody)

352

BBa_2622006

Coding

Mistic (Mstx)

Membrane-integrating protein Mistic (MstX) from Bacillus subtilis

330

BBa_2622007

RNA

gRNA for ribosome protein L12

Guide RNA for modification of ribosome protein L12 using CRISPR-Cas9 system

174

BBa_2622008

RNA

gRNA for ribosome protein L23

Guide RNA for modification of ribosome protein L23 using CRISPR-Cas9 system

174

BBa_2622009

RNA

gRNA for ribosome protein L24

Guide RNA for modification of ribosome protein L24 using CRISPR-Cas9 system

174

BBa_2622010

Regulatory

RNA thermoswitch1 (GJ2)

Temperature-sensitive non-coding RNA 1

39

BBa_2622011

Regulatory

RNA thermoswitch2 (GJ3)

Temperature-sensitive non-coding RNA 2

38

BBa_2622012

Regulatory

RNA thermoswitch3 (GJ6)

Temperature-sensitive non-coding RNA 3

53

BBa_2622013

Regulatory

RNA thermoswitch4 (GJ9)

Temperature-sensitive non-coding RNA 4

32

BBa_2622014

Regulatory

RNA thermoswitch5 (GJ10)

Temperature-sensitive non-coding RNA 5

33

BBa_2622015

Coding

BamC

Beta-barrel assembly protein C (BamC)

1057

BBa_2622016

Regulatory

RNA thermoswitch 6 (Sw2)

Temperature-sensitive non-coding RNA 6

33

BBa_2622017

Regulatory

RNA thermoswitch 7 (Sw3)

Temperature-sensitive non-coding RNA 7

33

BBa_2622018

Regulatory

RNA thermoswitch 8 (Sw6)

Temperature-sensitive non-coding RNA 8

33

BBa_2622019

Regulatory

RNA thermoswitch 9 (Sw7)

Temperature-sensitive non-coding RNA 9

33

BBa_2622020

Regulatory

RNA thermoswitch 10 (Sw9)

Temperature-sensitive non-coding RNA 10

33

BBa_2622021

Regulatory

RNA thermoswitch 11 (Sw11)

Temperature-sensitive non-coding RNA 11

33

BBa_2622022

Coding

BamD

Beta-barrel assembly protein D (BamD)

757

BBa_2622023

Coding

BamE

Beta-barrel assembly protein E (BamE)

448

BBa_2622024

Coding

SurA

Survival protein A (SurA)

1374

BBa_2622048

Coding

OmpA full

Full length outer transmembrane protein A (OmpA)

1041
invert