Help:Barcode

From Registry

As BioBrick systems are deployed more widely, it may become important to be able to easily determine whether BioBricks are present in an organic sample. For example, in the European Union, concern over genetically modified foods led to a proposal to mark genetically modified foods with an easily identified genetic 'barcode'. ([http://www.newscientist.com/news/news.jsp?id=ns99993377 See the article in "New Scientist"])

Partly from shared goals and partly as an experiment, we have marked all CDS parts with a special sequence we call a barcode. This sequence is added automatically after the two stop codons whenever the user specifies the part should be 'build with barcode' on the part editing page.

Barcode Algorithm

The barcode sequence is: CXC TGA TAG TGC TAG TGT AGA T CXC (25 bp)

To determine the two X's:

 R = (sum of the digits in the part number) mod 4
 
 If R is: 0, then X = A
          1, then X = C
          2, then X = G
          3, then X = T
 
 Example: BBa_C1053  Sum of digits = 1 + 0 + 5 + 3 = 9, 
                   R = 1, X = C.

To see whether a sample contains a BioBrick system, PCR with the two primers below. Because of the variable base 'X', mix together primers that include all 4 possible bases in that position.

 Forward                  TAG TGC TAG TGT AGA T CXC -->
 Barcode          CXC TGA TAG TGC TAG TGT AGA T CXC
 Reverse      <-- CXC TGA TAG TGC TAG TGT A

The design considerations for BioBrick barcodes were: 1) that the sequence not be found in any organism of interest to us, 2) that it not contain any BioBrick restriction sites, and 3) that it be extensible. The variable base is a hash that helps identify the BioBrick parts without increasing the number of primer variations excessively.