Difference between revisions of "Help:Barcode"
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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. | 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. | ||
| − | You can find more about [http://www.openwetware.org/wiki/Barcodes barcodes and their development] at the OpenWetWare discussion page | + | You can find more about [http://www.openwetware.org/wiki/Barcodes barcodes and their development] at the OpenWetWare discussion page. |
Revision as of 20:45, 4 May 2007
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 many CDS parts after the standard TAATAA stop codons with a special sequence we call a barcode.
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.
You can find more about [http://www.openwetware.org/wiki/Barcodes barcodes and their development] at the OpenWetWare discussion page.