Difference between revisions of "Part:BBa K2560256:Design"
 
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===Design Notes===
 
===Design Notes===
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The part contains the whole coding region from the <i>birA</i> gene of <i>C. glutamicum</i> (NCgl0679) without the startcodon. This region is flanked by overhangs which are Phytobrick- and MoClo-compatible and by two BsaI recognition sites (Weber et al., 2011).  
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The part contains the whole coding region from the <i>birA</i> gene of <i>C. glutamicum</i> (NCgl0679) without the startcodon. This region is flanked by overhangs which are Phytobrick- and MoClo-compatible and by two BsaI recognition sites (Weber et al., 2011). It was built with the Marburg Toolbox, a golden gate based toolbox for modular cloning. According to the Marburg Toolbox, the part is designed as a 4Y-part (CDS).
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If <i>birA</i> shall be used with a 5' tag use this part, if there is no need for tagging, use [https://parts.igem.org/wiki/index.php?title=Part:BBa_K2560253 BBa_K2560253]. <br>
 
If <i>birA</i> shall be used with a 5' tag use this part, if there is no need for tagging, use [https://parts.igem.org/wiki/index.php?title=Part:BBa_K2560253 BBa_K2560253]. <br>
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Samols D., Thornton CH., Murtif VL., Kumar GK., Haase FC., Wood HG. (1988). Evolutionary conservation among biotin enzymes. J. Biol. Chem. 263. 6461-6464.
 
Samols D., Thornton CH., Murtif VL., Kumar GK., Haase FC., Wood HG. (1988). Evolutionary conservation among biotin enzymes. J. Biol. Chem. 263. 6461-6464.
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<!-- -->
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===Marburg Toolbox===
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<html>
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<p align="justify">We proudly present the Marburg Collection, a novel golden-gate-based toolbox containing various parts that are compatible with the PhytoBrick system and MoClo. Compared to other bacterial toolboxes, the Marburg Collection shines with superior flexibility. We overcame the rigid paradigm of plasmid construction - thinking in fixed backbone and insert categories - by achieving complete <i> de novo </i> assembly of plasmids.
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<br>
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<br>
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36 connectors facilitate flexible cloning of multigene constructs and even allow for the inversion of individual transcription units. Additionally, our connectors function as insulators to avoid undesired crosstalk.
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<br>
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<br>
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The Marburg Collection contains 123 parts in total, including:
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<br>
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inducible promoters, reporters, fluorescence and epitope tags, oris, resistance cassettes and genome engineering tools. To increase the value of the Marburg Collection, we additionally provide detailed experimental characterization for <i> V. natriegens </i> and a supportive software. We aspire availability of our toolbox for future iGEM teams to empower accelerated progression in their ambitious projects.</p>
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</html>
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<div style="width:100%;display:flex;flex-direction:row;flex-wrap: wrap; justify-content:space-evenly; align-items:center;">
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[[File:T--Marburg--Cloning_Overview.png|800px|thumb|left|'''Figure 3''': <b> Hierarchical cloning is facilitated by subsequent Golden Gate reactions. </b> <br> Basic building blocks like promoters or terminators are stored in level 0 plasmids. Parts from each category of our collection can be chosen to built level 1 plasmids harboring a single transcription unit. Up to five transcription units can be assembled into a level 2 plasmid.]]
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[[File:T--Marburg--Overview_Marburg_Toolbox.png|750px|thumb|middle|'''Figure 4''': <b> Additional bases and fusion sites ensure correct spacing and allow tags. </b> <br> Between some parts, additional base pairs were integrated to ensure correct spacing and to maintain the triplet code.  We expanded our toolbox by providing N- and C- terminal tags by creating novel fusions and splitting the CDS and terminator part, respectively.]]
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</div>
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===Parts of the Marburg Toolbox===
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<div class="PCListIcon" style="display:flex;flex-direction:row; flex-wrap: nowrap; justify-content:space-evenly; align-items:flex-start;font-size:82%;">
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[[File:T--Marburg--5'Con.png|90px|thumb|none|
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<html>
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<ul>
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<b>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560011">K2560011 </a> (5'Connector Dummy) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560055">K2560055 </a> <br>(1-6 <br> Connector) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560065">K2560065 </a> (5'Con1) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560066">K2560066 </a> (5'Con2) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560067">K2560067 </a> (5'Con3) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560068">K2560068 </a> (5'Con4) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560069">K2560069 </a> (5'Con5) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560075">K2560075 </a> (5'Con1 <br> Short Res) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560076">K2560076 </a> (5'Con2 <br> Short) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560077">K2560077 </a> (5'Con3 <br> Short) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560078">K2560078 </a> (5'Con4 <br> Short) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560079">K2560079 </a> (5'Con5 <br> Short) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560095">K2560095 </a> (5'Con1 inv) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560096">K2560096 </a> (5'Con2 inv) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560097">K2560097 </a> (5'Con3 inv) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560098">K2560098 </a> (5'Con4 inv) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560099">K2560099 </a> (5'Con5 inv) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560105">K2560105 </a> (5'Con5 inv <br> Ori) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560107">K2560107 </a> (5'Con1 <br> Res) </li>
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</b>
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</ul>
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</html>]]
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[[File:T--Marburg--Promotor.png|90px|thumb|none|
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<html>
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<ul>
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<b>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560007">K2560007 </a> (J23100) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560009">K2560009 </a> (J23104) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560014">K2560014 </a> (J23106) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560015">K2560015 </a> (J23115) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560017">K2560017 </a> (J23101) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560018">K2560018 </a> (J23102) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560019">K2560019 </a> (J23103) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560020">K2560020 </a> (J23105) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560021">K2560021 </a> (J23107) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560022">K2560022 </a> (J23108) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560023">K2560023 </a> (J23109) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560024">K2560024 </a> (J23110) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560025">K2560025 </a> (J23111) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560026">K2560026 </a> (J23113) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560027">K2560027 </a> (J23114) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560028">K2560028 </a> (J23116) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560029">K2560029 </a> (J23117) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560030">K2560030 </a> (J23118) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560031">K2560031 </a> (J23119) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560123">K2560123 </a> <br>(pTet) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560124">K2560124 </a> (pTrc)  </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560131">K2560131 </a> (Promoter Dummy) </li>
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</ul>
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</b>
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</html>]]
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[[File:T--Marburg--RBS.png|90px|thumb|none|
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<html>
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<ul>
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<b>
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    <li> <a href="https://parts.igem.org/Part:BBa_K2560008">K2560008 </a> (B0034) </li>
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    <li> <a href="https://parts.igem.org/Part:BBa_K2560010">K2560010 </a> (B0032) </li>
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    <li> <a href="https://parts.igem.org/Part:BBa_K2560013">K2560013 </a> (B0031) </li>
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    <li> <a href="https://parts.igem.org/Part:BBa_K2560016">K2560016 </a> (B0030) </li>
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    <li> <a href="https://parts.igem.org/Part:BBa_K2560084">K2560084 </a> <br>(RBS Dummy) </li>
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</b>
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</ul>
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</html>]]
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[[File:T--Marburg--CDS.png|90px|thumb|none|
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<html>
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<ul>
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<b>
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    <li> <a href="https://parts.igem.org/Part:BBa_K2560033">K2560033 </a> (E1010) </li>
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    <li> <a href="https://parts.igem.org/Part:BBa_K2560041">K2560041 </a> (E0030) </li>
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    <li> <a href="https://parts.igem.org/Part:BBa_K2560042">K2560042 </a> (sfGFP) </li>
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    <li> <a href="https://parts.igem.org/Part:BBa_K2560043">K2560043 </a> (sfGFP Vn) </li>
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    <li> <a href="https://parts.igem.org/Part:BBa_K2560047">K2560047 </a> (Cas9) </li>
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    <li> <a href="https://parts.igem.org/Part:BBa_K2560051">K2560051 </a> <br>(Lux Operon) </li>
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    <li> <a href="https://parts.igem.org/Part:BBa_K2560054">K2560054 </a> (dCas9) </li>
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    <li> <a href="https://parts.igem.org/Part:BBa_K2560082">K2560082 </a> <br>(CDS Dummy) </li>
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    <li> <a href="https://parts.igem.org/Part:BBa_K2560114">K2560114 </a> (LacZ Alpha) </li>
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    <li> <a href="https://parts.igem.org/Part:BBa_K2560128">K2560128 </a> (K660004) </li>
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    <li> <a href="https://parts.igem.org/Part:BBa_K2560135">K2560135 </a> <br>(SXT Beta) </li>
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    <li> <a href="https://parts.igem.org/Part:BBa_K2560268">K2560268 </a> <br>(tfox Vc) </li>
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    <li> <a href="https://parts.igem.org/Part:BBa_K2560269">K2560269 </a> <br>(tfox Vn) </li>
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    <li> <a href="https://parts.igem.org/Part:BBa_K2560270">K2560270 </a> <br>(SXT) </li>
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    <li> <a href="https://parts.igem.org/Part:BBa_K2560271">K2560272 </a> <br>(flp recombinase) </li>
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</ul>
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</b>
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</html>]]
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[[File:T--Marburg--Terminator.png|90px|thumb|none|
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<html>
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<ul>
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<b>
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    <li> <a href="https://parts.igem.org/Part:BBa_K2560034">K2560034 </a> (B0010) </li>
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    <li> <a href="https://parts.igem.org/Part:BBa_K2560035">K2560035 </a> (B0015) </li>
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    <li> <a href="https://parts.igem.org/Part:BBa_K2560081">K2560081 </a> (Terminator Dummy) </li>
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    <li> <a href="https://parts.igem.org/Part:BBa_K2560089">K2560089 </a> (B1002) </li>
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    <li> <a href="https://parts.igem.org/Part:BBa_K2560091">K2560091 </a> (B1003) </li>
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    <li> <a href="https://parts.igem.org/Part:BBa_K2560093">K2560093 </a> (B1006) </li>
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</b>
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</ul>
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</html>]]
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[[File:T--Marburg--3'Con.png|90px|thumb|none|<html>
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<ul> <b>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560012">K2560012 </a> (3'Connector Dummy) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560070">K2560070 </a> (3'Con1) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560071">K2560071 </a> (3'Con2) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560072">K2560072 </a> (3'Con3) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560073">K2560073 </a> (3'Con4) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560080">K2560080 </a> (3'Con5 Ori) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560100">K2560100 </a> (3'Con1 inv <br>Short) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560101">K2560101 </a> (3'Con2 inv <br>Short) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560102">K2560102 </a> (3'Con3 inv <br>Short) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560103">K2560103 </a> (3'Con4 inv <br>Short) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560104">K2560104 </a> (3'Con5 inv <br>Short) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560106">K2560106 </a> (3'Con1 inv <br>Short Res) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560108">K2560108 </a> (3'Con1 inv) </li>
 +
<li> <a href="https://parts.igem.org/Part:BBa_K2560109">K2560109 </a> (3'Con1 inv <br>Res) </li>
 +
<li> <a href="https://parts.igem.org/Part:BBa_K2560110">K2560110 </a> (3'Con2 inv) </li>
 +
<li> <a href="https://parts.igem.org/Part:BBa_K2560111">K2560111 </a> (3'Con3 inv) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560112">K2560112 </a> (3'Con4 inv) </li>
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<li> <a href="https://parts.igem.org/Part:BBa_K2560113">K2560113 </a> (3'Con5 inv) </li>
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</ul>
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</b>
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</html>]]
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[[File:T--Marburg--ORI.png|90px|thumb|none|<html>
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<ul> <b>
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    <li> <a href="https://parts.igem.org/Part:BBa_K2560036">K2560036 </a> (ColE1) </li>
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    <li> <a href="https://parts.igem.org/Part:BBa_K2560037">K2560037 </a> (pMB1) </li>
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    <li> <a href="https://parts.igem.org/Part:BBa_K2560046">K2560046 </a> (p15A) </li>
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</ul>
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</b>
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</html>]]
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[[File:T--Marburg--Antibiotic_Resistance.png|90px|thumb|none|
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<html>
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<ul>
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<b>
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    <li><a href="https://parts.igem.org/Part:BBa_K2560048">K2560048 </a> (Cam. Res. RFP) </li>
 +
    <li><a href="https://parts.igem.org/Part:BBa_K2560056">K2560056 </a> <br> (Kan. Res. (pSB3K3) RFP) </li>
 +
    <li><a href="https://parts.igem.org/Part:BBa_K2560057">K2560057 </a> <br> (Kan. Res. (pSB3K3) GFP) </li>
 +
    <li><a href="https://parts.igem.org/Part:BBa_K2560058">K2560058 </a> <br> (Tet. Res. (pSB3T5) RFP) </li>
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    <li><a href="https://parts.igem.org/Part:BBa_K2560059">K2560059 </a> <br> (Tet. Res. (pSB3T5) GFP) </li>
 +
    <li><a href="https://parts.igem.org/Part:BBa_K2560125">K2560125 </a> (Carb. Res. RFP) </li>
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    <li><a href="https://parts.igem.org/Part:BBa_K2560126">K2560126 </a> (Carb. Res. GFP) </li>
 +
    <li><a href="https://parts.igem.org/Part:BBa_K2560127">K2560127 </a> (Carb. Res. into BBa_K2560002) </li>
 +
    <li><a href="https://parts.igem.org/Part:BBa_K2560132">K2560132 </a> (Cam. Res. into BBa_K2560002) </li>
 +
    <li><a href="https://parts.igem.org/Part:BBa_K2560133">K2560133 </a> <br> (Kan. Res. into BBa_K2560002) </li>
 +
    <li><a href="https://parts.igem.org/Part:BBa_K2560134">K2560134 </a> <br> (Tet. Res. into BBa_K2560002) </li>
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 +
</ul>
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</b>
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</html>]]
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</div>
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 +
===Tags and Entry Vectors===
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<div class="PCListIcon" style="display:flex;flex-direction:row; flex-wrap: nowrap; align-items:flex-start; font-size:82%;">
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[[File:T--Marburg--N-Tag.png|90px|thumb|middle|
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<html>
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<ul>
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<b>
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  <li><a href="https://parts.igem.org/Part:BBa_K2560060">K2560060 </a> (E1010 4x) </li>
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  <li><a href="https://parts.igem.org/Part:BBa_K2560063">K2560063 </a> (sfGFP 4x) </li>
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  <li><a href="https://parts.igem.org/Part:BBa_K2560085">K2560085 </a> <br> (His-Tag 4x) </li>
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  <li><a href="https://parts.igem.org/Part:BBa_K2560087">K2560087 </a> (FLAG-Tag 4x) </li>
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  <li><a href="https://parts.igem.org/Part:BBa_K2560129">K2560129 </a> (K660004 4x) </li>
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  <li><a href="https://parts.igem.org/Part:BBa_K2560257">K2560257 </a> (Streptag 4x) </li>
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</ul>
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</b>
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</html>]]
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 +
[[File:T--Marburg--C-Tag.png|90px|thumb|middle|
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<html>
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<ul>
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<b>
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 +
  <li><a href="https://parts.igem.org/Part:BBa_K2560061">K2560061 </a> (E1010 5a) </li>
 +
  <li><a href="https://parts.igem.org/Part:BBa_K2560062">K2560062 </a> (B0015 5b) </li>
 +
  <li><a href="https://parts.igem.org/Part:BBa_K2560064">K2560064 </a> (sfGFP 5a) </li>
 +
  <li><a href="https://parts.igem.org/Part:BBa_K2560086">K2560086 </a> <br> (His-Tag 5a) </li>
 +
  <li><a href="https://parts.igem.org/Part:BBa_K2560088">K2560088 </a> (FLAG-Tag 5a) </li>
 +
  <li><a href="https://parts.igem.org/Part:BBa_K2560090">K2560090 </a> (B1002 5b) </li>
 +
  <li><a href="https://parts.igem.org/Part:BBa_K2560092">K2560092 </a> (B1003 5b) </li>
 +
  <li><a href="https://parts.igem.org/Part:BBa_K2560094">K2560094 </a> (B1006 5b) </li>
 +
  <li><a href="https://parts.igem.org/Part:BBa_K2560117">K2560117 </a> (I11012 5a) </li>
 +
  <li><a href="https://parts.igem.org/Part:BBa_K2560118">K2560118 </a> (M0050 5a) </li>
 +
  <li><a href="https://parts.igem.org/Part:BBa_K2560119">K2560119 </a> (M0051 5a) </li>
 +
  <li><a href="https://parts.igem.org/Part:BBa_K2560130">K2560130 </a> (K660004 5a) </li>
 +
  <li><a href="https://parts.igem.org/Part:BBa_K2560258">K2560258 </a> (Streptag 5a) </li>
 +
 +
 +
</ul>
 +
</b>
 +
</html>]]
 +
 +
 +
[[File:T--Marburg--Entry_Vector.png|90px|thumb|middle|
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<html>
 +
<ul>
 +
<b>
 +
 +
<li><a href="https://parts.igem.org/Part:BBa_K2560001">K2560001 </a> (Entry Vector with RFP dropout) </li>
 +
<li><a href="https://parts.igem.org/Part:BBa_K2560002">K2560002 </a> (Entry Vector with GFP dropout) </li>
 +
<li><a href="https://parts.igem.org/Part:BBa_K2560005">K2560005 </a> (Resistance Entry Vector with RFP Dropout) </li>
 +
<li><a href="https://parts.igem.org/Part:BBa_K2560006">K2560006 </a> (Resistance Entry Vector with GFP Dropout) </li>
 +
<li><a href="https://parts.igem.org/Part:BBa_K2560305">K2560305 </a> (gRNA Entry Vector with GFP Dropout) </li>
 +
 +
 +
</ul>
 +
</b>
 +
</html>]]

Latest revision as of 22:08, 12 October 2018


birA from C. glutamicum, codonoptimized for V. natriegens


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 132
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

The part contains the whole coding region from the birA gene of C. glutamicum (NCgl0679) without the startcodon. This region is flanked by overhangs which are Phytobrick- and MoClo-compatible and by two BsaI recognition sites (Weber et al., 2011). It was built with the Marburg Toolbox, a golden gate based toolbox for modular cloning. According to the Marburg Toolbox, the part is designed as a 4Y-part (CDS).


If birA shall be used with a 5' tag use this part, if there is no need for tagging, use BBa_K2560253.

GGTCTCGGATG-coding_region-GCTTTGAGACC


The sequence was codonoptimized for V. natriegens ATCC 14048.


Source

Source of the part:

Genome: Corynebacterium glutamicum ATCC 13032

Accession number of gene: NCgl0679

Accession number of encoded protein: NP_599941.1

birA was codonoptimized for V. natriegens and then synthetisized and integrated into the vector BBa_K2560002via BsmBI


References

Weber E., Engler C., Gruetzner R., Werner S., Marillonnet S. (2011). A modular cloning system for standardized assembly of multigene constructs. PLoS One 6:e16765. 10.1371/journal.pone.0016765

Samols D., Thornton CH., Murtif VL., Kumar GK., Haase FC., Wood HG. (1988). Evolutionary conservation among biotin enzymes. J. Biol. Chem. 263. 6461-6464.

Marburg Toolbox

We proudly present the Marburg Collection, a novel golden-gate-based toolbox containing various parts that are compatible with the PhytoBrick system and MoClo. Compared to other bacterial toolboxes, the Marburg Collection shines with superior flexibility. We overcame the rigid paradigm of plasmid construction - thinking in fixed backbone and insert categories - by achieving complete de novo assembly of plasmids.

36 connectors facilitate flexible cloning of multigene constructs and even allow for the inversion of individual transcription units. Additionally, our connectors function as insulators to avoid undesired crosstalk.

The Marburg Collection contains 123 parts in total, including:
inducible promoters, reporters, fluorescence and epitope tags, oris, resistance cassettes and genome engineering tools. To increase the value of the Marburg Collection, we additionally provide detailed experimental characterization for V. natriegens and a supportive software. We aspire availability of our toolbox for future iGEM teams to empower accelerated progression in their ambitious projects.


Figure 3: Hierarchical cloning is facilitated by subsequent Golden Gate reactions.
Basic building blocks like promoters or terminators are stored in level 0 plasmids. Parts from each category of our collection can be chosen to built level 1 plasmids harboring a single transcription unit. Up to five transcription units can be assembled into a level 2 plasmid.
Figure 4: Additional bases and fusion sites ensure correct spacing and allow tags.
Between some parts, additional base pairs were integrated to ensure correct spacing and to maintain the triplet code. We expanded our toolbox by providing N- and C- terminal tags by creating novel fusions and splitting the CDS and terminator part, respectively.


Parts of the Marburg Toolbox




Tags and Entry Vectors




  • K2560001 (Entry Vector with RFP dropout)
  • K2560002 (Entry Vector with GFP dropout)
  • K2560005 (Resistance Entry Vector with RFP Dropout)
  • K2560006 (Resistance Entry Vector with GFP Dropout)
  • K2560305 (gRNA Entry Vector with GFP Dropout)