Team:Freiburg bioware/general


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Characterize or improve an existing BioBrick Part or Device and enter this information back on the Registry.
We corrected the sequences of the existing basic parts: BBa_K157004,BBa_K157009,BBa_K157011 and BBa_K157012.

The team Freiburg08 had entered the sequence information with the pre- and suffix sequences from RFC25 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 RFC25. Since the RFC25 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.

Develop and document a new technical standard that supports the:
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 RFC25. 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 RFC25 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 RFC25 scar to our basic parts, but asked Randy Rettberg also for a better solution. He designed the part BBa_B0105, which has the sequence information of the RFC25 scar. With this, it is possible now to produce composite parts with RFC25 basic parts by inserting the part BBa_B0105 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 BBa_B0105 part inserted between all other parts to generate the following input:
Image:Freiburg09 Registry.jpg
When you follow these instructions for all parts designed according to RFC25 the produced sequence is correct.