DNA recovery by phenol/chloroform extraction or GeneClean

Bernard Murray bernard at elsie.nci.nih.gov
Fri Feb 14 16:22:34 EST 1997

In article <330531E5.3699 at well.com>, alsbyte1 at well.com says...
>I have a lot of customers oSteven Goldberg wrote:
>> In article <Pine.GSO.3.95L.970209222612.22253B-100000 at uststf2>, Wilson
>> <netson at uxmail.ust.hk> wrote:
>> > Hello everybody,
>> >         I would like to know which method can recovery DNA from agarose
>> > gel is better: Phenol/chloroform extraction or GeneClean?
>> > Wilson

>> After lots of problems using GeneCleaned DNA in ligations, I switched to
>> the QIAquick gel extraction kit and have had very good luck in terms of
>> yield and purity.
>> Steve

>I have a lot of customers out here who absolutely love Epicentre's 
>Betsy Alberty / ALSBYTE Biotech

No, I've tried GELase and beta-agarase and don't like them at all.
The purified fragments from these methods (so-so yield) are okay
for random primer labelling but give a low efficiency of ligation.
The fragments *can* be cleaned up but the amount of work required
means that it wasn't worth doing the agarose digestion in the first
	My votes for small to medium fragments are as follows;

Quick'n'dirty			Freeze/squeeze
Quick/clean/small amount	QIAquick
Larger amounts			Home made diatomaceous earth (first choice)
				or Qiaex II (slightly higher yield)

The Qiagen methods require careful handling or carryover of reagents
will inhibit ligations.  Overall I like my home made "Merlin" prep
best (I used to love the Promega Magic CleanUp method but the Wizard
equivalent just doesn't work as well).

I have co-workers who swear by electroelution or NA45 paper so
you pays your money and you takes your choice - just have a read
of the reagents FAQ for a bunch of choices.
	And don't forget that borate can inhibit ligases...


Bernard Murray, Ph.D.
bernard at elsie.nci.nih.gov  (National Cancer Institute, NIH, Bethesda MD, USA)

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