Ext. of DNA from agarose (which agarose)

HARDIES at THORIN.UTHSCSA.EDU HARDIES at THORIN.UTHSCSA.EDU
Tue Oct 4 10:16:28 EST 1994


TJ Murphy asked:

> What is the best agarose to use for these kinds of crush protocols????
> [for getting DNA from gels]

Simon Futers responds

: I have always used "ordinary" agarose.  I do not think there is any best
: agarose for this technique.

I haven't seen a "problem" batch of agarose for about 15 yrs. Before that
it was common to get batches that contaminated your DNA with some poly
anion that copurified with the DNA and bedeviled the R. enzs.  DEAE was
the only thing I ever found to get rid of it.  The suppliers have since
learned to clean up and assay the agarose before selling it.  I agree
with Simon Futers' response except that you could probably still get in
trouble with agarose that wasn't advertised for electrophoresis of 
nucleic acids, or agarose from some new supplier that hasn't learned
their business yet.  <no affiliation with any agarose suppliers>
I don't recommend buying pricey special quality agarose unless you've
actually tested the more ordinary agarose.  You may be paying for someone
to just reassay and repackage the ordinary agarose.  
I do follow the superstition (?) of not pulverizing the agarose any
more than necessary to avoid releasing contaminants.  

Essentially the same story applies to polyacrylamide.

Steve Hardies, Dept. of Biochem., Univ. of Texas HSC at San Antonio
Hardies at thorin.uthscsa.edu




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