Difference between revisions of "Team:Lethbridge/Parts"

 
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<div><img src="https://static.igem.org/mediawiki/2017/6/64/Banner_PAoverview.png"  class="center fit"></div>
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<div><img src="https://static.igem.org/mediawiki/2017/6/64/Banner_PAoverview.png"  class="bannerImg"></div>
 
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        <p class="text12j">The N<i>ex</i>t <i>vivo</i> system is made up of >40 unique parts encoding both protein and RNA components. The main focus of our team this year was to submit all 38 TX-TL protein components to the registry as a <a href="https://2017.igem.org/wiki/index.php?title=Team:Lethbridge/Part_Collection" id="pageLink">collection of parts</a> that anyone could use to produce their own N<i>ex</i>t <i>vivo</i> system. Several of these TX-TL components were already in the registry but were under different expression control, lacked purification tags, and/or were not codon optimized for expression in <i>E. coli</i>. As such we sought to <a href="https://2017.igem.org/Team:Lethbridge/Improve" id="pageLink">improve these parts</a> for future use.</p>
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    <input class="tealButton" type="button" value="Part Collection" onclick="window.location.href='#anchor0'" />
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        <p class="text12j">In addition to the TX-TL proteins, we also sought to BioBrick the ribosomal RNA genes and twenty tRNA genes. As a proof of concept for our novel tRNA purification design we only synthesized one representative tRNA gene before ordering them all. Additionally, the N<i>ex</i>t <i>vivo</i> system makes use of a previously submitted MS2BP part (<a href="http://parts.igem.org/Part:BBa_K2109108" id="pageLink">BBa_K2109108</a>).</p>
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<form>
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     <input class="tealButton" type="button" value="Parts Submitted" onclick="window.location.href='#anchor1'" />
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<form>
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    <input class="tealButton" type="button" value="Composite Parts" onclick="window.location.href='#anchor2'" />
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    <input class="tealButton" type="button" value="Basic Parts" onclick="window.location.href='#anchor4'" />
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 +
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    <input class="tealButton" type="button" value="Previously Used Parts" onclick="window.location.href='#anchor5'" />
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</center><br><br>
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 +
<p class="text12j">The N<i>ex</i>t <i>vivo</i> system is made up of >40 unique parts encoding both protein and RNA components. The main focus of our team this year was to submit all 38 TX-TL protein components to the registry as a <a href="https://2017.igem.org/wiki/index.php?title=Team:Lethbridge/Part_Collection" id="pageLink">collection of parts</a> that anyone could use to produce their own N<i>ex</i>t <i>vivo</i> system. Several of these TX-TL components were already in the registry but were under different expression control, lacked purification tags, and/or were not codon optimized for expression in <i>E. coli</i>. As such we sought to <a href="https://2017.igem.org/Team:Lethbridge/Improve" id="pageLink">improve these parts</a> for future use.</p>
 +
 
 +
    <p class="text12j">In addition to the TX-TL proteins, we also sought to BioBrick the ribosomal RNA genes and twenty tRNA genes. As a proof of concept for our novel tRNA purification design we only synthesized one representative tRNA gene before ordering them all. Additionally, the N<i>ex</i>t <i>vivo</i> system makes use of a previously submitted MS2BP part (<a href="http://parts.igem.org/Part:BBa_K2109108" id="pageLink" target="pageLink">BBa_K2109108</a>).</p>
 +
 
 +
<div style="clear: both" id="anchor0"></div><br><br>
 +
 
 +
<h2 class="segmentHeader">Part Collection</h2>
 +
        <p class="text12j">The <a href="https://2017.igem.org/wiki/index.php?title=Team:Lethbridge/Part_Collection" id="pageLink">N<i>ex</i>t <i>vivo</i> part collection</a> consists of the 38 TX-TL proteins required for RNA transcription and protein synthesis. Each part in the collection has a hexahistidine tag for simultaneous purification of all components, the T7 promoter (<a href="http://partsregistry.org/Part:BBa_I719005" id="pageLink" target="pageLink">BBa_I719005</a>), medium RBS (<a href="http://parts.igem.org/Part:BBa_B0034" id="pageLink" target="pageLink">BBa_B0034</a>), and double terminator (<a href="http://parts.igem.org/Part:BBa_B0015" id="pageLink" target="pageLink">BBa_B0015</a>).</p>
 +
    <p class="text12j">To see our collection on the Registry of Standard Biological Parts, click <a href="http://parts.igem.org/Collections/Cell-Free_TX-TL" id="pageLink">here</a>.</p>.
  
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<div class="segmentDiv">
 
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    <div class="centerContainer">
 
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        <h2 class="segmentHeader">Part Collection</h2>
 
−
        <p class="text12j">The <a href="https://2017.igem.org/wiki/index.php?title=Team:Lethbridge/Part_Collection" id="pageLink">N<i>ex</i>t <i>vivo</i> part collection</a> consists of the 38 TX-TL proteins required for RNA transcription and protein synthesis. Each part in the collection has a hexahistidine tag for simultaneous purification of all components, the T7 promoter (<a href="http://partsregistry.org/Part:BBa_I719005" id="pageLink">BBa_I719005</a>), medium RBS (<a href="http://parts.igem.org/Part:BBa_B0034" id="pageLink">BBa_B0034</a>), and double terminator (<a href="http://parts.igem.org/Part:BBa_B0015" id="pageLink">BBa_B0015</a>).</p>
 
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     <img src="https://static.igem.org/mediawiki/2017/f/f4/T--Lethbridge--partcollection.png" width=1000px; height=533px; padding: 30px class="bannerImg" />
 
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<h2 class="segmentHeader">Parts Submitted</h1>
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        <h2 class="segmentHeader">Parts Submitted</h2>
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<div class="segmentContainer">
 +
     <div class="contentDiv" id="text40" style="padding:10px"><p class="text14">This season we were able to submit 9 parts in pSB1C3 to the registry from our part collection. We aim to continually submit parts as we successfully ligate them into pSB1C3. These include:</p>
 +
    </div>
 +
    <div class="contentDiv">
 +
<h1>Parts in pSB1C3 Table</h1>
 +
    <table id="partTable">
 +
        <th id="col1" style="background-color: #377b7e; color: #ffffff;" class="text12">BioBrick</th>
 +
        <th id="col2" style="background-color: #377b7e; color: #ffffff;" class="text12" >Protein</th>
  
−
<p class="text12j">This season we were able to submit 9 parts in pSB1C3 to the registry from our part collection. We aim to continually submit parts as we successfully ligate them into pSB1C3. These include:</p>
+
    <!--data rows-->
 +
        <tr>
 +
          <td class=xl99 class="text10"><a href="http://parts.igem.org/Part:BBa_K2443001" target="_blank">BBa_K2443001</a></td>
 +
          <td class=xl94 class="text10">ArgRS</td>
 +
        </tr>
  
−
<div class="partTable">
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        <tr>
−
<table id="partTable">
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          <td class=xl100 class="text10"><a href="http://parts.igem.org/Part:BBa_K2443003" target="_blank">BBa_K2443003</a></td>
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    <th id="col1" style="background-color: #377b7e; color: #ffffff;">BioBrick</th>
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          <td class=xl95 class="text10">AsnRS</td>
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    <th id="col2" style="background-color: #377b7e; color: #ffffff;">Protein</th>
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        </tr>
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<!--data rows-->
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<tr>
+
−
  <td class=xl99><a href="http://parts.igem.org/Part:BBa_K2443001">BBa_K2443001</a></td>
+
−
  <td class=xl94><span>ArgRS</span></td>
+
−
</tr>
+
−
   
+
−
<tr>
+
−
  <td class=xl100><a href="http://parts.igem.org/Part:BBa_K2443003">BBa_K2443003</a></td>
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−
  <td class=xl95><span>AsnRS</span></td>
+
−
</tr>
+
  
−
<tr>
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        <tr>
−
  <td class=xl99><a href="http://parts.igem.org/Part:BBa_K2443005">BBa_K2443005</a></td>
+
          <td class=xl99 class="text10"><a href="http://parts.igem.org/Part:BBa_K2443005" target="_blank">BBa_K2443005</a></td>
−
  <td class=xl94><span>GlnRS</span></td>
+
          <td class=xl94 class="text10">GlnRS</td>
−
</tr>
+
        </tr>
−
   
+
−
<tr>
+
−
  <td class=xl100><a href="http://parts.igem.org/Part:BBa_K2443008">BBa_K2443008</a></td>
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−
  <td class=xl95><span>GlyRS Beta</span></td>
+
−
</tr>
+
  
−
<tr>
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        <tr>
−
  <td class=xl99><a href="http://parts.igem.org/Part:BBa_K2443013">BBa_K2443013</a></td>
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          <td class=xl100 class="text10"><a href="http://parts.igem.org/Part:BBa_K2443008" target="_blank">BBa_K2443008</a></td>
−
  <td class=xl94><span>MetRS</span></td>
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          <td class=xl95 class="text10">GlyRS Beta</td>
−
</tr>
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        </tr>
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+
−
<tr>
+
−
  <td class=xl100><a href="http://parts.igem.org/Part:BBa_K2443024">BBa_K2443024</a></td>
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−
  <td class=xl95><span>IF2</span></td>
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−
</tr>
+
  
−
<tr>
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        <tr>
−
  <td class=xl99><a href="http://parts.igem.org/Part:BBa_K2443026">BBa_K2443026</a></td>
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          <td class=xl99 class="text10"><a href="http://parts.igem.org/Part:BBa_K2443013" target="_blank">BBa_K2443013</a></td>
−
  <td class=xl94><span>EF-G</span></td>
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          <td class=xl94 class="text10">MetRS</td>
−
</tr>
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        </tr>
−
   
+
−
<tr>
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−
  <td class=xl100><a href="http://parts.igem.org/Part:BBa_K2443031">BBa_K2443031</a></td>
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−
  <td class=xl95><span>RF3</span></td>
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−
</tr>
+
  
−
<tr>
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        <tr>
−
  <td class=xl101><a href="http://parts.igem.org/Part:BBa_K2443034">BBa_K2443034</a></td>
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          <td class=xl100 class="text10"><a href="http://parts.igem.org/Part:BBa_K2443024" target="_blank">BBa_K2443024</a></td>
−
  <td class=xl96><span>CK</span></td>
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          <td class=xl95 class="text10">IF2</td>
−
</tr>
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        </tr>
−
+
−
</table>
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−
</div>
+
−
</div>
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 +
        <tr>
 +
          <td class=xl99 class="text10"><a href="http://parts.igem.org/Part:BBa_K2443026" target="_blank">BBa_K2443026</a></td>
 +
          <td class=xl94 class="text10">EF-G</td>
 +
        </tr>
 +
 +
        <tr>
 +
          <td class=xl100 class="text10"><a href="http://parts.igem.org/Part:BBa_K2443031" target="_blank">BBa_K2443031</a></td>
 +
          <td class=xl95 class="text10">RF3</td>
 +
        </tr>
 +
 +
        <tr>
 +
          <td class=xl101><a href="http://parts.igem.org/Part:BBa_K2443034" target="_blank">BBa_K2443034</a></td>
 +
          <td class=xl96>CK</td>
 +
        </tr>
 +
    </table>
 
     </div>
 
     </div>
 
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</center>
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 +
<div style="clear:both" id="anchor2"></div><br><br>
  
 
<h2 class="segmentHeader">Composite Parts</h2>
 
<h2 class="segmentHeader">Composite Parts</h2>
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<h2 align= "left">General Protein Construct</h2>
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<h2>General Protein Construct</h2>
  
 
<center>
 
<center>
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     <img src="https://static.igem.org/mediawiki/2017/9/97/T--Lethbridge--generalconstruct.png" width=800px; height=153px; padding: 30px class="bannerImg" />
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     <img src="https://static.igem.org/mediawiki/2017/9/97/T--Lethbridge--generalconstruct.png" width=800px height=153px class="bannerImg" />
 
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</center>
 
<br><br><br><br>
 
<br><br><br><br>
 
              
 
              
−
<h2 align= "left">General RNA Construct</h2>
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<h2>General RNA Construct</h2>
 
              
 
              
 
<center>
 
<center>
−
     <img src="https://static.igem.org/mediawiki/2017/a/a8/T--Lethbridge--RNAconstruct.png" width=800px; height=153px; padding: 30px class="bannerImg" />
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     <img src="https://static.igem.org/mediawiki/2017/a/a8/T--Lethbridge--RNAconstruct.png" width=800px height=153px class="bannerImg" />
 
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−
<p class="text12j">This year we designed <a href="https://2017.igem.org/wiki/index.php?title=Team:Lethbridge/Composite_Part" id="pageLink">41 composite parts</a>. Of the 41 parts, it contains 38 proteins essential for prokaryotic transcription and translation (TX-TL) as well 3 additional constructs for tRNA purification and TX-TL validation.</p>
+
<p class="text12">This year we designed <a href="https://2017.igem.org/wiki/index.php?title=Team:Lethbridge/Composite_Part" id="pageLink">40 composite parts</a>. Of the 40 parts, there are 38 proteins essential for prokaryotic transcription and translation (TX-TL) as well 2 additional constructs for tRNA purification and TX-TL validation.</p>
 
   
 
   
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<div style="clear: both"></div>
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<div style="clear:both" id="anchor3"></div><br><br>
  
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<div class="segmentDiv">
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<h2 class="segmentHeader">Improved Parts</h2>
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        <div class="centerContainer">
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    <p class="text12">Of our 38 TX-TL components, five were already in the registry of standard biological parts. We decided to improve these parts for future use in our N<i>ex</i>t <i>vivo</i> system and for general use by others. Our improvements are documented <a href="https://2017.igem.org/wiki/index.php?title=Team:Lethbridge/Improve" id="pageLink">here.</a></p>
−
            <h2 class="segmentHeader">Improved Parts</h2>
+
−
            <p class="text12j">Of our 38 TX-TL components, five were already in the registry of standard biological parts. We decided to improve these parts for future use in our N<i>ex</i>t <i>vivo</i> system and for general use by others. Our improvements are documented <a href="https://2017.igem.org/wiki/index.php?title=Team:Lethbridge/Improve" id="pageLink">here.</a></p>
+
−
        </div>
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−
</div>
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<br><br>
 
<br><br>
 
      
 
      
 
<center>
 
<center>
−
     <img src="https://static.igem.org/mediawiki/2017/6/6f/T--Lethbridge--improve4.png" width=1000px; height=231px; padding: 30px class="bannerImg" />
+
     <img src="https://static.igem.org/mediawiki/2017/6/6f/T--Lethbridge--improve4.png" width=1000px height=231px class="bannerImg" />
 
</center>
 
</center>
 
<br><br><br><br>
 
<br><br><br><br>
  
−
<div style="clear: both"></div>
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<div style="clear: both" id="anchor4"></div><br><br>
  
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<div class="segmentDiv">
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<h2 class="segmentHeader">Basic Parts</h1>
−
        <div class="centerContainer">
+
        <p class="text12">All <a href="https://2017.igem.org/wiki/index.php?title=Team:Lethbridge/Basic_Part" id="pageLink">basic parts</a> pages created on the registry of standard biological parts. Contains all 38 proteins essential for prokaryotic transcription and translation (TX-TL) as well as the parts for our tRNA purification and TX-TL validation construct.</p>
−
            <h2 class="segmentHeader">Basic Parts</h2>
+
−
            <p class="text12j">All <a href="https://2017.igem.org/wiki/index.php?title=Team:Lethbridge/Basic_Part" id="pageLink">basic parts</a> pages created on the registry of standard biological parts. Contains all 38 proteins essential for prokaryotic transcription and translation (TX-TL) as well as the parts for our tRNA purification and TX-TL validation construct.</p>
+
−
    </div>
+
−
</div>
+
 
<br><br>
 
<br><br>
  
 
<center>
 
<center>
−
     <img src="https://static.igem.org/mediawiki/2017/5/56/T--Lethbridge--cds.png" width=320px; height=69px; padding: 30px class="bannerImg" />
+
     <img src="https://static.igem.org/mediawiki/2017/5/56/T--Lethbridge--cds.png" width=320px height=69px class="bannerImg" />
 
</center>
 
</center>
  
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+
<div style="clear:both" id="anchor5"></div><br><br>
  
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<div class="segmentDiv">
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<center>
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        <div class="centerContainer">
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<h2 class="segmentHeader">Previous Parts Used</h1>
−
            <h2 class="segmentHeader">Previous Parts Used</h2>
+
−
<p class="text12j">During the design of our project we utilized several parts already in the registry in our composite parts including:</p>
+
  
 +
<div class="segmentContainer">
 +
    <div class="contentDiv" id="text40" style="padding:10px">
 +
        <p class="text14">During the design of our project we utilized several parts already in the registry in our composite parts including:</p>
 +
        </div>
 +
    <div class="contentDiv">
 +
<h2>Existing Parts Used Table</h1>
 +
    <table id="partTable">
 +
        <th id="col1" style="background-color: #377b7e; color: #ffffff;" class="text12">BioBrick</th>
 +
        <th id="col2" style="background-color: #377b7e; color: #ffffff;" class="text12">Part</th>
 +
 +
        <!--data rows-->
 +
        <tr>
 +
        <td class=xl99 class="text10"><a href="http://partsregistry.org/Part:BBa_I719005" target="_blank">BBa_I719005</a></td>
 +
        <td class=xl94 class="text10">T7 promoter</td>
 +
        </tr>
 +
 +
        <tr>
 +
        <td class=xl100 class="text10"><a href="http://parts.igem.org/Part:BBa_B0034" target="_blank">BBa_B0034</a></td>
 +
        <td class=xl95 class="text10">medium ribosome binding site (mRBS)</td>
 +
        </tr>
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 +
        <tr>
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        <td class=xl99 class="text10"><a href="http://parts.igem.org/Part:BBa_B0015" target="_blank">BBa_B0015</a></td>
 +
        <td class=xl94 class="text10">Double Terminator</td>
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        </tr>
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        <td class=xl100 class="text10"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_J64997" target="_blank">BBa_J64997</a></td>
 +
        <td class=xl95 class="text10">T7 -10 and rest</td>
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        </tr>
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        <td class=xl99 class="text10"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1983010" target="_blank">BBa_K1983010</a></td>
 +
        <td class=xl94 class="text10">tRNA<sup>Phe</sup></td>
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Latest revision as of 02:15, 2 November 2017

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The Next vivo system is made up of >40 unique parts encoding both protein and RNA components. The main focus of our team this year was to submit all 38 TX-TL protein components to the registry as a collection of parts that anyone could use to produce their own Next vivo system. Several of these TX-TL components were already in the registry but were under different expression control, lacked purification tags, and/or were not codon optimized for expression in E. coli. As such we sought to improve these parts for future use.

In addition to the TX-TL proteins, we also sought to BioBrick the ribosomal RNA genes and twenty tRNA genes. As a proof of concept for our novel tRNA purification design we only synthesized one representative tRNA gene before ordering them all. Additionally, the Next vivo system makes use of a previously submitted MS2BP part (BBa_K2109108).



Part Collection

The Next vivo part collection consists of the 38 TX-TL proteins required for RNA transcription and protein synthesis. Each part in the collection has a hexahistidine tag for simultaneous purification of all components, the T7 promoter (BBa_I719005), medium RBS (BBa_B0034), and double terminator (BBa_B0015).

To see our collection on the Registry of Standard Biological Parts, click here.

.






Parts Submitted

This season we were able to submit 9 parts in pSB1C3 to the registry from our part collection. We aim to continually submit parts as we successfully ligate them into pSB1C3. These include:

Parts in pSB1C3 Table

BioBrick Protein
BBa_K2443001 ArgRS
BBa_K2443003 AsnRS
BBa_K2443005 GlnRS
BBa_K2443008 GlyRS Beta
BBa_K2443013 MetRS
BBa_K2443024 IF2
BBa_K2443026 EF-G
BBa_K2443031 RF3
BBa_K2443034 CK


Composite Parts

General Protein Construct





General RNA Construct






This year we designed 40 composite parts. Of the 40 parts, there are 38 proteins essential for prokaryotic transcription and translation (TX-TL) as well 2 additional constructs for tRNA purification and TX-TL validation.



Improved Parts

Of our 38 TX-TL components, five were already in the registry of standard biological parts. We decided to improve these parts for future use in our Next vivo system and for general use by others. Our improvements are documented here.









Basic Parts

All basic parts pages created on the registry of standard biological parts. Contains all 38 proteins essential for prokaryotic transcription and translation (TX-TL) as well as the parts for our tRNA purification and TX-TL validation construct.





Previous Parts Used

During the design of our project we utilized several parts already in the registry in our composite parts including:

Existing Parts Used Table

BioBrick Part
BBa_I719005 T7 promoter
BBa_B0034 medium ribosome binding site (mRBS)
BBa_B0015 Double Terminator
BBa_J64997 T7 -10 and rest
BBa_K1983010 tRNAPhe