Difference between revisions of "Team:Lethbridge/Parts"

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<h1>Parts</h1>
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<p>Each team will make new parts during iGEM and will submit them to the Registry of Standard Biological Parts. The iGEM software provides an easy way to present the parts your team has created. The <code>&lt;groupparts&gt;</code> tag (see below) will generate a table with all of the parts that your team adds to your team sandbox.</p>
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    <p class="f12">In order to explore the modularity and various applications of Protein Nanocompartments (PNCs), we have designed systems that have distinct PNCs, surface modifiers, and cargos. Most PNCs are designed to have a specific surface modifying feature and cargo that look at different encapsulation strategies that are specific to these specific PNCs.</p>
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<p>Remember that the goal of proper part documentation is to describe and define a part, so that it can be used without needing to refer to the primary literature. Registry users in future years should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.</p>
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<h3>Note</h3>
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<blockquote>Each PNC system covers distinct applications for Research use. Each of our PNC systems is described in detail on our design page.</blockquote>
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<p>Note that parts must be documented on the <a href="http://parts.igem.org/Main_Page"> Registry</a>. This page serves to <i>showcase</i> the parts you have made. Future teams and other users and are much more likely to find parts by looking in the Registry than by looking at your team wiki.</p>
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<p class="f12">There are several capsid proteins described in the registry, including the  <a href= "http://parts.igem.org/Part:BBa_K1442040"target="_blank">MS2 protein</a>. Our project diversified the capsid proteins available on the registry and are designed as composite parts under control of a T7 inducible promoter (<a href= "http://parts.igem.org/Part:BBa_I712074"target="_blank">BBa_I712074</a>) a medium strength RBS (<a href= "http://parts.igem.org/Part:BBa_J61100" target="_blank">BBa_J61100</a>) and a double terminator (<a href= "http://parts.igem.org/Part:BBa_B0014" target="_blank">BBa_B0014</a>).</p>
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<h1> Parts Submitted:</h1>
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    <p class="f12">This year, we submitted a pSB1C3 vector containing the "minimal Arc Gag" (derived from HIV-1 homology) construct to the registry. This construct was theorized and modeled by our team this year. The <i>Arc</i> DNA sequence, originally from <a href="https://www.uniprot.org/uniprot/Q63053" target="_blank">Rat</a> was compared to the HIV-1 DNA sequence due to Arc's relationship to retrotransposons. This part is theorized to retain its abilities to form capsid structures and deliver RNA to cells. Our results can be found <a href= "https://2018.igem.org/Team:Lethbridge/Results>here</a> and the full design of this part can be found <a href= "https://2018.igem.org/Team:Lethbridge/Design">here</a>.
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We hope to finish cloning all of our designed parts for future studies and applications.</p>
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<div><p class="f12" style="text-align: center"><a href="http://parts.igem.org/Part:BBa_K2683009"target="_blank">BBa_K2683009</a></p></div>
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<h3>Adding parts to the registry</h3>
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<p>You can add parts to the Registry at our <a href="http://parts.igem.org/Add_a_Part_to_the_Registry">Add a Part to the Registry</a> link.</p>
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<p>We encourage teams to start completing documentation for their parts on the Registry as soon as you have it available. The sooner you put up your parts, the better you will remember all the details about your parts. Remember, you don't need to send us the DNA sample before you create an entry for a part on the Registry. (However, you <b>do</b> need to send us the DNA sample before the Jamboree. If you don't send us a DNA sample of a part, that part will not be eligible for awards and medal criteria.)</p>
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<a href="http://parts.igem.org/Add_a_Part_to_the_Registry">
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ADD PARTS
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<h1>Basic and Composite Parts:</h1>
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<p class="f12">All of our new parts can be found on the <a href= "https://2018.igem.org/Team:Lethbridge/Basic_Part"target="_blank">basic parts</a> page and have been placed on the iGEM registry. These contain the four protein nanocompartments and the various cargo proteins and external surface modifiers.</p>
 
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<p class="f12"> This year we have designed 9 <a href="https://2018.igem.org/Team:Lethbridge/Composite_Part"target="_blank">composite parts</a> consisting of 4 capsid proteins with surface modifiers, cargoes with specific modifications for encapsulation and an external part for the surface modification of the P22 capsid. Each composite part has the same design, consisting of the T7 inducible promoter (<a href="http://parts.igem.org/Part:BBa_I712074"target="_blank" >BBa_I712074</a>), a medium strength RBS (<a href="http://parts.igem.org/Part:BBa_J61100"target="_blank">BBa_J61100</a>) and a double terminator (<a href="http://parts.igem.org/Part:BBa_B0014" target="_blank">BBa_B0014</a>).</p>
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<h3>Inspiration</h3>
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<p>We have a created  a <a href="http://parts.igem.org/Well_Documented_Parts">collection of well documented parts</a> that can help you get started.</p>
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<p> You can also take a look at how other teams have documented their parts in their wiki:</p>
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<ul>
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<li><a href="https://2014.igem.org/Team:MIT/Parts"> 2014 MIT </a></li>
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<li><a href="https://2014.igem.org/Team:Heidelberg/Parts"> 2014 Heidelberg</a></li>
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<li><a href="https://2014.igem.org/Team:Tokyo_Tech/Parts">2014 Tokyo Tech</a></li>
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</ul>
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<h1>Improved Parts:</h1>
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<div class="oneText-Wrapper">
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<div class="oneText-Text">
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    <p class="f12">As our system deals with the encapsulation of specific cagos one of our future applications is the encapsulation of Cell Free systems. Therefore we are pleased to say that our continuing work with last years project, Next Vivo, will allow us to encapsulate our <a href="https://2017.igem.org/Team:Lethbridge"target="_blank" >cell free system</a>. Since last years Jamboree we have been able to clone and characterize 15 more parts and will now submit them to the registry as improved parts. These parts include a his tag on the N or C terminus for purification and follow the general design of a T7 promoter (<a href="http://parts.igem.org/Part:BBa_I719005"target="_blank" >BBa_I719005</a>), RBS (<a href="http://parts.igem.org/Part:BBa_B0034"target="_blank">BBa_B0034</a>) and Double terminator (<a href="http://parts.igem.org/Part:BBa_B0015"target="_blank" >BBa_B0015</a>).</p>
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<h3>What information do I need to start putting my parts on the Registry?</h3>
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<p>The information needed to initially create a part on the Registry is:</p>
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<ul>
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<li>Part Name</li>
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<li>Part type</li>
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<li>Creator</li>
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<li>Sequence</li>
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<li>Short Description (60 characters on what the DNA does)</li>
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<li>Long Description (Longer description of what the DNA does)</li>
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<li>Design considerations</li>
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</ul>
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<p>
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We encourage you to put up <em>much more</em> information as you gather it over the summer. If you have images, plots, characterization data and other information, please also put it up on the part page. </p>
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      <tr class="f12">
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            <th>Biobrick Number</th>
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            <th>Part Name</th>
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    </tr>
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    <tr class="f11">
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        <td><a href="http://parts.igem.org/Part:BBa_K2683016"target="_blank">BBa_K2683016</a></td>
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        <td>Release Factor 1</td>
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    </tr>
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    <tr class="f11">
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        <td><a href="http://parts.igem.org/Part:BBa_K2683017"target="_blank">BBA_K2683017</a></td>
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        <td>Release Factor 2</td>
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    </tr>
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    <tr class="f11">
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        <td><a href="http://parts.igem.org/Part:BBa_K2683018"target="_blank">BBa_K2683018</a></td>
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        <td> Cysteine tRNS Synthetase (CysRS)</td>
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    </tr>
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    <tr class="f11">
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        <td> <a href="http://parts.igem.org/Part:BBa_K2683019" target="_blank">BBa_K2683019</a></td>
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        <td>Lysine tRNA Synthetase (LysRS)</td>
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    </tr>
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    <tr class="f11">
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        <td> <a href="http://parts.igem.org/Part:BBa_K2683020"target="_blank">BBa_K2683020</a></td>
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        <td>Phenylalanine tRNA Synthetase alpha subunit (PheRS alpha)</td>
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    </tr>
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    <tr class="f11">
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        <td> <a href="http://parts.igem.org/Part:BBa_K2683021"target="_blank">BBa_K2683021</a></td>
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        <td>Serine tRNA Synthetase (SerRS)</td>
 +
    </tr>
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    <tr class="f11">
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        <td> <a href="http://parts.igem.org/Part:BBa_K2683022"target="_blank">BBa_K2683022</a></td>
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        <td>Tryptophan tRNA Synthetase (TrpRS)</td>
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    </tr>
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    <tr class="f11">
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        <td><a href="http://parts.igem.org/Part:BBa_K2683023"target="_blank">BBa_K2683023</a></td>
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        <td>Valine tRNA Synthetase (ValRS)</td>
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    </tr>
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    <tr class="f11">
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        <td><a href="http://parts.igem.org/Part:BBa_K2683024"target="_blank">BBa_K2683024</a></td>
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        <td>Inititation Factor 1</td>
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    </tr>
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    <tr class="f11">
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        <td> <a href="http://parts.igem.org/Part:BBa_K2683025"target="_blank">BBa_K2683025</a></td>
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        <td>Initiation Factor 3</td>
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    </tr>
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    <tr class="f11">
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        <td> <a href="http://parts.igem.org/Part:BBa_K2683026"target="_blank">BBa_K2683026</a></td>
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        <td>Elongation Factor-Thermo Unstable (EF-Tu)</td>
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    </tr>
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    <tr class="f11">
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        <td><a href="http://parts.igem.org/Part:BBa_K2683027"target="_blank">BBa_K2683027</a></td>
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        <td>Elongation Factor- Thermo Stable (EF-Ts)</td></tr>
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    <tr class="f11">
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        <td><a href="http://parts.igem.org/Part:BBa_K2683028"target="_blank" >BBa_K2683028</a></td>
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        <td>MyoKinase (MK)</td></tr>
 +
    <tr class="f11">
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        <td> <a href="http://parts.igem.org/Part:BBa_K2683029"target="_blank">BBa_K2683029</a></td>
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        <td>Nucleoside Diphosphate Kinase (NDK)</td>
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    </tr>
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    <tr class="f11">
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        <td> <a href="http://parts.igem.org/Part:BBa_K2683030"target="_blank">BBa_K2683030</a></td>
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        <td>Peptidyl Prolyl Isomerase (PPiase)</td>
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    </tr>
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</table>
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</center>
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<h1>Existing Parts on the Registry</h1>
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<h3>Part Table </h3>
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<p>Please include a table of all the parts your team has made during your project on this page. Remember part characterization and measurement data must go on your team part pages on the Registry. </p>
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    <p class="f12">For the design of our protein nanocompartments, we have utilized previous parts already found in the registry:</p>
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<groupparts>iGEM18 Lethbridge</groupparts>
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    <tr class="f12">
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        <th>Biobrick Number</th>
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        <th>Part</th>
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    </tr>
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    <tr class="f11">
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        <td><a href="http://parts.igem.org/Part:BBa_I712074" target="_blank" >BBa_I712074</a></td>
 +
        <td>T7 Promoter</td>
 +
    </tr class="f11">
 +
    <tr class="f11">
 +
        <td> <a href="http://parts.igem.org/Part:BBa_J61100" target="_blank">BBa_J61100</a></td>
 +
        <td>Medium strength ribosomal binding site</td>
 +
    </tr>
 +
    <tr class="f11">
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        <td><a href="http://parts.igem.org/Part:BBa_B0014" target="_blank" >BBa_B0014</a></td>
 +
        <td>Double Terminator</td>
 +
    </tr>
 +
</table>
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</center>   
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Latest revision as of 04:00, 18 October 2018



Parts Banner Image


In order to explore the modularity and various applications of Protein Nanocompartments (PNCs), we have designed systems that have distinct PNCs, surface modifiers, and cargos. Most PNCs are designed to have a specific surface modifying feature and cargo that look at different encapsulation strategies that are specific to these specific PNCs.

Each PNC system covers distinct applications for Research use. Each of our PNC systems is described in detail on our design page.

There are several capsid proteins described in the registry, including the MS2 protein. Our project diversified the capsid proteins available on the registry and are designed as composite parts under control of a T7 inducible promoter (BBa_I712074) a medium strength RBS (BBa_J61100) and a double terminator (BBa_B0014).

Parts Submitted:

This year, we submitted a pSB1C3 vector containing the "minimal Arc Gag" (derived from HIV-1 homology) construct to the registry. This construct was theorized and modeled by our team this year. The Arc DNA sequence, originally from Rat was compared to the HIV-1 DNA sequence due to Arc's relationship to retrotransposons. This part is theorized to retain its abilities to form capsid structures and deliver RNA to cells. Our results can be found here. We hope to finish cloning all of our designed parts for future studies and applications.



Basic and Composite Parts:

All of our new parts can be found on the basic parts page and have been placed on the iGEM registry. These contain the four protein nanocompartments and the various cargo proteins and external surface modifiers.

This year we have designed 9 composite parts consisting of 4 capsid proteins with surface modifiers, cargoes with specific modifications for encapsulation and an external part for the surface modification of the P22 capsid. Each composite part has the same design, consisting of the T7 inducible promoter (BBa_I712074), a medium strength RBS (BBa_J61100) and a double terminator (BBa_B0014).

Improved Parts:

As our system deals with the encapsulation of specific cagos one of our future applications is the encapsulation of Cell Free systems. Therefore we are pleased to say that our continuing work with last years project, Next Vivo, will allow us to encapsulate our cell free system. Since last years Jamboree we have been able to clone and characterize 15 more parts and will now submit them to the registry as improved parts. These parts include a his tag on the N or C terminus for purification and follow the general design of a T7 promoter (BBa_I719005), RBS (BBa_B0034) and Double terminator (BBa_B0015).

Biobrick Number Part Name
BBa_K2683016 Release Factor 1
BBA_K2683017 Release Factor 2
BBa_K2683018 Cysteine tRNS Synthetase (CysRS)
BBa_K2683019 Lysine tRNA Synthetase (LysRS)
BBa_K2683020 Phenylalanine tRNA Synthetase alpha subunit (PheRS alpha)
BBa_K2683021 Serine tRNA Synthetase (SerRS)
BBa_K2683022 Tryptophan tRNA Synthetase (TrpRS)
BBa_K2683023 Valine tRNA Synthetase (ValRS)
BBa_K2683024 Inititation Factor 1
BBa_K2683025 Initiation Factor 3
BBa_K2683026 Elongation Factor-Thermo Unstable (EF-Tu)
BBa_K2683027 Elongation Factor- Thermo Stable (EF-Ts)
BBa_K2683028 MyoKinase (MK)
BBa_K2683029 Nucleoside Diphosphate Kinase (NDK)
BBa_K2683030 Peptidyl Prolyl Isomerase (PPiase)


Existing Parts on the Registry

For the design of our protein nanocompartments, we have utilized previous parts already found in the registry:

Biobrick Number Part
BBa_I712074 T7 Promoter
BBa_J61100 Medium strength ribosomal binding site
BBa_B0014 Double Terminator