Team:DTU Denmark/USERprinciple

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    <td align="center" ><font face="arial" size="3"><a class="mainLinks" href="https://2009.igem.org/Team:DTU_Denmark" >Home</a></font> </td>
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    <td align="center" ><font face="arial" size="3"><a class="mainLinks" href="https://2009.igem.org/Team:DTU_Denmark/team" >The Team</a> </font></td>
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    <td align="center" ><font face="arial" size="3"><a class="mainLinks" href="https://2009.igem.org/Team:DTU_Denmark/project" >The Project</a> </font></td>
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    <td align="center" ><font face="arial" size="3"><a class="mainLinks" href="https://2009.igem.org/Team:DTU_Denmark/parts" >Parts submitted</a> </font></td>
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    <td align="center" ><font face="arial" size="3"><a class="mainLinks" href="https://2009.igem.org/Team:DTU_Denmark/modelling">Modelling</a></font> </td>
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    <td align="center" ><font face="arial" size="3"><a class="mainLinks" href="https://2009.igem.org/Team:DTU_Denmark/notebook" title="Day to day lab activity">Notebook</a>
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  <br>
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  The redoxilator<br><br>
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    <a href="https://2009.igem.org/Team:DTU_Denmark/theory" CLASS=leftbar>- Introduction</a><br>
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    <a href="https://2009.igem.org/Team:DTU_Denmark/yeast" CLASS=leftbar>- Results</a><br>
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    <a href="https://2009.igem.org/Team:DTU_Denmark/practicalapproach" CLASS=leftbar>- Applications and perspectives</a><br>
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    <a href="https://2009.igem.org/Team:DTU_Denmark/safety" CLASS=leftbar>- Safety considerations</a><br><br>
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    <br>The USER<sup>TM</sup> assembly standard<br><br>
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    <a href="https://2009.igem.org/Team:DTU_Denmark/USERprinciple" CLASS=leftbar>- USER<sup>TM</sup> cloning</a><br>
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    <a href="https://2009.igem.org/Team:DTU_Denmark/USERconcept" CLASS=leftbar>- USER<sup>TM</sup> fusion</a><br><br>
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    <br>USER<sup>TM</sup> fusion primer design software<br><br>
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    <a href="https://2009.igem.org/Team:DTU_Denmark/USERprogram" CLASS=leftbar>- Abstract</a><br>
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    <a href="https://2009.igem.org/Team:DTU_Denmark/USERprograminstructions" CLASS=leftbar>- Instructions</a><br>
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    <a href="https://2009.igem.org/Team:DTU_Denmark/USERprogramoutputformat" CLASS=leftbar>- Output format</a><br>
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  <b>The project</b><br><br><br>
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<font size="4"><b>USER<sup>TM</sup> fusion assembly standard</b></font><br><br>
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<strong>Our USER fusion biobrick</strong><br>
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<strong>USER fusion of biobricks - how it works</strong><br>
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We have successfully constructed a USER-fusion biobrick (<a href="http://partsregistry.org/Part:BBa_K194003" target="_blank">BBa_K194003</a>), and demonstrated that it works as expected. The biobrick includes a DNA-sequence needed for USER-fusion, which consists of a restriction site and two nicking sites. The entire process of fusing two biobricks are illustrated in the figure, and the same can be done for multiple fragments at once.<br>
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We have successfully constructed a USER-fusion biobrick (<a href="http://partsregistry.org/Part:BBa_K194003" target="_blank">BBa_K194003</a>), and demonstrated that it works as expected. The biobrick includes a DNA-sequence needed for USER-fusion, which consists of a restriction site and two nicking sites. The entire process of fusing two biobricks are illustrated in the figure, and the same can be done for multiple fragments at once.<br>
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Comments or questions to the team? Please <a href="mailto:igem@bio.dtu.dk" CLASS=email>Email us</a> -- Comments of questions to webmaster? Please <a href="mailto:lronn@bio.dtu.dk" CLASS=email>Email us</a>
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Revision as of 22:08, 19 October 2009

Wiki banner 967px.png

The project

Home The Team The Project Parts submitted Modelling Notebook

The redoxilator

 - Introduction
- Results
- Applications and perspectives
- Safety considerations
The USERTM assembly standard

 - USERTM cloning
- USERTM fusion
USERTM fusion primer design software

 - Abstract
- Instructions
- Output format
The project


 USERTM fusion assembly standard

The USER fusion assembly standard allows rapid construction of multi-part devices, without some of the drawbacks of the restriction-enzyme based standard biobrick assembly method. The full USERTM assembly standard (BBF RFC 39) can be found here: XX LINK XX. The main advantages of this assembly method is:

1. Standardized method for assembling several BioBricks or components at a time, in contrast to the "one at a time" assembly procedure normally used.
2. Nearly all restriction sites are allowed in the biobricks.
3. 8 basepair-overhangs allows ligase-free cloning. With the enclosed protocol E. coli can be transformed with a multipart-construct less than 2 hours after your PCR-reaction has completed.
4. The biobricks are joined without leaving a scar which is ideal for fusing protein domain biobricks.
5. Insertions of small sequences between biobricks such as a nuclear localization signal or Gly-Ser-Gly flexible linker is possible with the right primer design.
5. High fidelity is ensured by using PfuTurbo® Cx Hotstart DNA polymerase.
6. By the design of the PCR tails, it can be decided whether the USER cassette should be deleted, copied or moved following insertion.
7. Directionality of inserts are supported.


USER fusion of biobricks - how it works
We have successfully constructed a USER-fusion biobrick (BBa_K194003), and demonstrated that it works as expected. The biobrick includes a DNA-sequence needed for USER-fusion, which consists of a restriction site and two nicking sites. The entire process of fusing two biobricks are illustrated in the figure, and the same can be done for multiple fragments at once.

principle of USERTM-fusion


Procedure (please refer to our Biobrick Assembly Standard BBF RFC 39 for a detailed protocol):

1) The USER fusion biobrick plasmid is digested with the restriction enzyme pacI and the nicking enzyme Nt.Bbv.CI (a nicking enzyme cuts only one strand as illustrated on the figure). This process will linearize the plasmid, and make single stranded overhangs (sticky ends).
2) PCR amplification is performed on the biobricks intended for the fusion. The primer design is facilitated by our novel USERTM fusion primer design software made for this iGEM project.
3) USERTM enzyme mix is added. This will remove the uracil always included in the primers, making sticky end overhangs on all biobricks. Because of the matching sticky ends on all biobricks and linearized plamid, the biobricks will self-assemble in the plasmid.
Two or more biobricks have been joined with all the advantages mentioned above.



Biobricks can be fused directly into the standard plasmid containing the USER biobrick. USER fusion relies on the simultaneously fusion and cloning of multiple PCR fragments

USER fusion of biobricks - how it works 


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Comments or questions to the team? Please <a href="mailto:igem@bio.dtu.dk" CLASS=email>Email us</a> -- Comments of questions to webmaster? Please <a href="mailto:lronn@bio.dtu.dk" CLASS=email>Email us</a>


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