ClonTech RACE PCR

[Gary E. Vallad]

Hi!  I'm having some problems with my RACE PCR reactions and hoping that 
someone may have some insight.  I've been performing 5' and 3' RACE PCR using 
cDNA prepared via ClonTech's Marathon cDNA Kit.  I am getting some useful 
products, but I'm also getting some non-specific products derived from the 
linker specific primer binding to complementary regions in my cDNA other than 
the cDNA linker.  Yet, when I run controls using only my linker specific 
primer alone, I get no product.  Also, I know my gene-specific primers are 
working since when I use both 5' and 3' gene-specific primers in conjunction I 
get the appropriate sized fragment.  I've been getting these non-specific 
products when running a variety of different RACE reactions with different 
gene-specific primer sets.  I'm assuming that they are just miscellaneous 
products isolated along with my fragment of interest in the GeneClean process, 
but I've been getting a high percentage of clones that are these non-specific 
type of products.  Has anyone else had problems with this.  Like I mentioned 
before my control with just the linker-specific primer comes up with no 
products that can be visualized on a gel.  Any help would be much appreciated.

Thanks,

Gary E. Vallad