PrbbBB:Internal

BioBricks Collection
Our local "Biobricks" are currently stored in freezer boxes in the Serrano and Isalan labs. We generally try to have, for each, a cell stock at -80 and a DNA stock at -20. But bear with us, we are still sorting out some of the details and are very open to suggestions.

The plates with last year's MIT registry collection are available in the Serrano lab. The new (2008) collection has quality issues... use the 2007 collection if possible.

Our samples are tracked in our local "BrickIt" web repository:

(Currently, this web site is only visible from within the CRG network.)
 * BrickIt@CRG

But you are welcome to enter your BioBricks even before you have them -- this can be quite helpful for planning your experiments.

Contact Raik for a brief introduction into the BrickIt web site!

BioBricks Format
The BioBricks standard defines a fixed prefix and suffix sequence for wrapping DNA fragments. Prefix and Suffix each contain 2 different restriction sites which are used for the assembly reaction (of which we use a quicker alternative). In order to construct your own BioBricks, you thus have to introduce these standard flanks and ensure that there are no BioBrick restriction sites within your fragment.

Unfortunately, this standard BioBricks format does not allow for the creation of protein fusions. This has led to the proposal of several competing non-standard alternative formats. A short overview and discussion is given here. The messy situation has spilled over to the PRBB -- Marco has constructed his BioBricks using the older BioFusion (Silver lab) format whereas Raik has chosen the newer Fusion (Freiburg) Format for his collection (we try to establish this format as official standard with the BioBricks foundation). We are working on protocols for the conversion between the two formats.

Advise

 * 1) Regardless which format you choose, try deleting all restriction sites for both: EcoRI, XbaI, SpeI, PstI, and NgoMIV, AgeI. This will allow the straightforward PCR-conversion of your part between all formats.
 * 2) Choose the classic 1.0 BioBrick format if you are not planning any protein fusions -- i.e. if you are only working with non-coding fragments or whole proteins. This gives you full compatibility with the rich MIT collection and you can also freely mix in all of Raik's protein parts (which behave like whole proteins in the classic assembly) and you can mix in all of Marco's non-coding parts. In fact, you can also create occasional protein fusions from Fusion or BioFusion - formatted fragments and then switch to classic assembly for the remaining construction.
 * 3) Look how Marco's and Raik's collection overlap with your own plans, study the  disadvantages of both formats and go for one of them.