precipitation of very small DNA fragments

CCoburn CCoburn at
Wed Jan 21 15:41:26 EST 1998

In article <69o3jc$28v at>, Ransom Hill Bioscience <visla at> wrote:
>They really are not too small to ethanol precipitate, although you will end up
> with some loss. The way you go about it is to precipitate them in the presence
> of a high concentration of ammonium acetate. You can get rid of the ammonium
> acetate with a speed-vac. HOWEVER, there is a much, much better way. Look in
> BIOTECHNIQUES vol 10. number 4, page 420. It is a report by Freie and Larsen
> on how to desalt short DNA fragments using Sep-Pak (or equivalent) cartridges.
> You will probably want to scale down from the sizes they use (Sep-Paks come in
> a range of sizes). We have used this method for years. It works excellently,
> and with very little loss. DO pay close attention to the flow rates they give.
> They are very important to good recovery. You can get Sep Pak cartridges from
> Waters. Altech and several other companies sell competing products. We have
> tried them all. Sep Paks out perform the others by a significant margin.

I always thought ammonium acetate is used to precipitate DNA when you don't 
wish to precipitate small fragments? I read in Current Protocols in Molecular 
Biology that "the use of ammonium acetate in place of sodium acetate allows 
the preferential precipitation of longer DNA molecules. Thus small single- or 
doublestranded oligonucleotides (less than ~30 bp) and unincorporated 
nucleotides can be effectively removed from DNA solutions."

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