desalting DNA

Hiranya S. Roychowdhury hroychow at NMSU.EDU
Tue Jun 1 11:16:42 EST 1999


At 10:54 AM 6/1/99 +0100, C.S. Wilding wrote:
>Hi,
>I know there has been a bit about this already but...
>I don't think 2X 70% etoh washes are satisfactoraly washing my DNA 
>extractions and am looking for alternatives. Are there any kits that allow 
>either dialysis in a convenient format (easy to get the small vols back 
>from whatever dialysis is performed in), or some kind of column. Cost is 
>an issue due to the high number of samples.
>As for the washes, if you precipitate your DNA with 2 vols etoh you have 
>67% etoh. Why then would washing with 70% remove any salt that had 
>precipitated. I would have thought that something less concentrated is 
>necessary, although I can see that this is not possible unless you want to 
>redissolve the DNA.
>Craig
>
>

You are right.
66-67% EtOH will also work. Indeed, 50% EtOH will work even better in
washing away the salts. However, the solubility of nucleic acids in
ethanol-water depends  also on the size of the NA. While a 50% EtOH will be
safe for large NA's, it will dissolve smaller sizes almost as easlily as it
will the salts. Hence, a compromise concentration of 70% EtOH was chosen to
ensure that as most of the salt is washed away w/o having to sacrifice any DNA. 
So, if somebody wants DNA with absolutely no salt , s/he may soak the DNA
pellet in 70% EtOH for extended periods and do more than just one wash. This
is what I do when I want to get rid of salts or pigments: After the DNA is
pelleted/spooled out from the precipitaion, I let the pellet/spooled DNA sit
in 70%EtOH for 15 min before spinning/spooling out the DNA. I repeat this
two/three times. 
The alternative to this would be dialysis, gel filtration (desalting column)
etc.


Dr. Hiranya Sankar Roychowdhury
GENE LAB/ EPPWS
New Mexico State University
Las Cruces, NM 88003
Ph. (505) 646-5785
hroychow at nmsu.edu




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