Difference between revisions of "Help:Barcode"
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| + | <DIV style='width:90%;margin:5px auto;padding:10px;border: 1px solid pink'>Barcodes are now discontinued. Parts that were constructed with barcodes will still have that DNA in their samples, | ||
| + | but future versions of the part should not have the barcode. This will be better dealt with when the mutant system is in place.</div> | ||
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| + | [[Image:feature_barcode.png|frame|float|left|An example of a BioBrick barcode, shown under Part Design:Features, ssDNA viewing mode]] | ||
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"]) | 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"]) | ||
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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. |
Latest revision as of 19:31, 12 July 2017
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.