Team:Freiburg bioware/general

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">    FREiGEM  

   Home   The Team  <ul> Overview</a></li> Portraits</a></li> </ul> </li> <span class="l"> <span class="t">The Project </a> <ul> Summary</a> </li> Highlights</a></li> </ul> </li> <span class="l"> <span class="t">Human Practice </a> <ul> Ethics</a> </li> Safety</a></li> </ul> </li> <li><a href="http://2009.igem.org/Team:Freiburg_bioware/Notebook"><span class="l"> <span class="t">Notebook </a></li> <li><a href="http://2009.igem.org/Team:Freiburg_bioware/cloning1"><span class="l"> <span class="t">Parts </a> <ul> <li><a href="http://2009.igem.org/Team:Freiburg_bioware/cloning1">Basic Parts</a></li> <li><a href="http://2009.igem.org/Team:Freiburg_bioware/cloning">Composite Parts</a></li> </ul> </li> <li><a href="http://2009.igem.org/Team:Freiburg_bioware/Collaboration"><span class="l"> <span class="t">Collaboration </a></li> <li><a href="http://2009.igem.org/Team:Freiburg_bioware/Modeling"><span class="l"> <span class="t">Modeling </a></li> </ul> <h2 class="art-PostHeaderIcon-wrapper"> <img style="width: 28px; height: 25px;" alt="" src="http://2009.igem.org/wiki/images/2/2a/Freiburg09_Post_tanne_2.png" /> General Activities

<b>Characterize or improve an existing BioBrick Part or Device and enter this information back on the Registry.</b>

We corrected the sequences of the existing basic parts: <a href="http://partsregistry.org/Part:BBa_K157004" class="external text" title="http://partsregistry.org/Part:BBa_K157004" rel="nofollow">BBa_K157004</a>,<a href="http://partsregistry.org/Part:BBa_K157009" class="external text" title="http://partsregistry.org/Part:BBa_K157009" rel="nofollow">BBa_K157009</a>,<a href="http://partsregistry.org/Part:BBa_K157011" class="external text" title="http://partsregistry.org/Part:BBa_K157011" rel="nofollow">BBa_K157011</a> and <a href="http://partsregistry.org/Part:BBa_K157012" class="external text" title="http://partsregistry.org/Part:BBa_K157012" rel="nofollow">BBa_K157012</a>.

The team Freiburg08 had entered the sequence information with the pre- and suffix sequences from <a href="http://partsregistry.org/Assembly_standard_25" class="external text" title="http://partsregistry.org/Assembly_standard_25" rel="nofollow">RFC25</a> into the registry, which means they add the nucleotides sequence for the restriction site for and after the part information. This caused an incompatibility in the compatibility check for <a href="http://partsregistry.org/Assembly_standard_25" class="external text" title="http://partsregistry.org/Assembly_standard_25" rel="nofollow">RFC25</a>. Since the <a href="http://partsregistry.org/Assembly_standard_25" class="external text" title="http://partsregistry.org/Assembly_standard_25" rel="nofollow">RFC25</a> is now an officially accepted Registry standard for Biobricks, we deleted the pre and suffix sequences, to use these parts as basic parts for our composite parts. This prevents that the sequence information of the pre and suffix causes a faulty sequence when fused automatically by the registry.

<b>Develop and document a new technical standard that supports the:

</b>design of BioBrick Parts or Devices,

or construction of BioBrick Parts or Devices

In addition to this,we recognized that there was no automated way to fuse basic parts, designed according to the <a href="http://partsregistry.org/Assembly_standard_25" class="external text" title="http://partsregistry.org/Assembly_standard_25" rel="nofollow">RFC25</a>. The automatic fusion program of the registry is only able to fuse basic parts with the normal Biobrick standard, or it gives the option to fuse basic parts blunt end without the Biobrick scar. However, parts according to the RFC25 produce a different scar compared those of the normal Biobrick standard. The difference between the two scars would produce a difference between the theoretical sequence of composite parts and the real sequence when the parts are fused according to <a href="http://partsregistry.org/Assembly_standard_25" class="external text" title="http://partsregistry.org/Assembly_standard_25" rel="nofollow">RFC25</a> in the wet lab. Therefore, we looked for a solution to fuse our basic parts in the right way in silico, so that the sequence in the part registry is correct. We first had the idea to modify the sequence manually by adding the <a href="http://partsregistry.org/Assembly_standard_25" class="external text" title="http://partsregistry.org/Assembly_standard_25" rel="nofollow">RFC25</a> scar to our basic parts, but asked Randy Rettberg also for a better solution. He designed the part <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_B0105" class="external text" title="http://partsregistry.org/wiki/index.php?title=Part:BBa_B0105" rel="nofollow">BBa_B0105</a>, which has the sequence information of the <a href="http://partsregistry.org/Assembly_standard_25" class="external text" title="http://partsregistry.org/Assembly_standard_25" rel="nofollow">RFC25</a> scar. With this, it is possible now to produce composite parts with <a href="http://partsregistry.org/Assembly_standard_25" class="external text" title="http://partsregistry.org/Assembly_standard_25" rel="nofollow">RFC25</a> basic parts by inserting the part <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_B0105" class="external text" title="http://partsregistry.org/wiki/index.php?title=Part:BBa_B0105" rel="nofollow">BBa_B0105</a> between the basic parts. For example, a fusion of the parts BBa_K157011, BBa_K243003, BBa_K157009 according to the RFC25 standard would need to have the above mentioned <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_B0105" class="external text" title="http://partsregistry.org/wiki/index.php?title=Part:BBa_B0105" rel="nofollow">BBa_B0105</a> part inserted between all other parts to generate the following input:

<a href="http://www.molbiotech.uni-freiburg.de/iGEM/wiki2009/index.php/Image:Freiburg09_Registry.jpg" class="image" title="Image:Freiburg09 Registry.jpg"><img alt="Image:Freiburg09 Registry.jpg" src="http://www.molbiotech.uni-freiburg.de/iGEM/wiki2009/images/8/80/Freiburg09_Registry.jpg" border="0" height="117" width="922" /></a>

When you follow these instructions for all parts designed according to <a href="http://partsregistry.org/Assembly_standard_25" class="external text" title="http://partsregistry.org/Assembly_standard_25" rel="nofollow">RFC25</a> the produced sequence is correct.

contact: <a href="mailto:freigem09@googlemail.com">freigem09@googlemail.com</a>