Help:Standardization

Revision as of 15:12, 16 June 2006 by Smelissali (Talk | contribs)

What you've got: Any non-Biobrick-standardized sequence of DNA that does something interesting
What you want:A Biobrick standardized sequence of interesting DNA

So here's how you do it...

  1. First off, check your DNA sequence for restriction sites. This is easy using available web programs such as
    • [http://tools.neb.com/NEBcutter2/index.php NEB cutter] - by New England Biolabs
    • [http://wishart.biology.ualberta.ca/PlasMapper/ PlasMapper] - developed by the University of Alberta
  2. Next, locate and remove all of the BioBrick standard restriction sites (XbaI, SpeI, EcoRI, PstI) that are on your sequence. To delete sites, there are a few processes you can use:
    • site directed mutagenesis - best for changing or deleting small areas of the genome like the Biobricks standard restriction sites. Openwetware has a nice [http://openwetware.org/wiki/Site-directed_mutagenesis protocol on how to do this].
    • lambda red - best for if you have very large (thousands of kb, entire genes) areas for alteration or deletion. This process is laid out in [http://www.pnas.org/cgi/content/full/97/12/6640 Datsenko and Wanner, 2000]