cDNA precipitation without coprecipitation of primers

[Bas Jansen]

In article <esgqv2$bu8$1 from news.uni-kl.de>,
 "Simone Marker" <marker from rhrk.uni-kl.de> wrote:

> Hi,
> 
> I need to remove a 47bp primer from an RT reaction, i.e. I want to 
> precipitate the synthesised cDNA without the coprecipitation of the primer. 
> The easiest way would be the purification by spin coulmn, but the amount of 
> my cDNA is very low, so that I'm afraid to lose the cDNA on the column. Does 
> anyone know about precipitation conditions (isoprop/ethanol,different salts) 
> that eclude the coprecipitation of smaller nucleic acid fragments? (my cDNA 
> is at least one kb)

I remember trying to get rid of SAGE primers of around 20 nt by 
precipitating DNA and a little ammonium acetate (7.5 M stock, add 1/10 
v/v) and adding 100% ethanol to an end concentration of 40%. Worked like 
a charm.
Just try to precipitate a few hundred nanograms of your 47 nt oligo in a 
concentration range of ethanol, from 20% up to 70%, and run it on a 
polyacrylamide gel to see whether it is still there.

Bas