Designing PCR primers-How to check them?

Grant Morahan morahan at
Mon Jul 17 22:20:27 EST 1995

In article <3u6flg$lt9 at>, Peter --- 
bkxo at wrote:

> I have designed a set of primers for amplification of a 300 bp ds DNA 
> fragment from human genomic DNA.        
> I would like to check these primers for any complementarity they may 
> have to repetitive sequences found in the human genome.  I am 
> concerned that the presence of such complemantarity would result in 
> non-specific amplification.
> Is there a database I can access to perform this search? If yes, how?

   Try the PRIMER program from the Whitehead - it will screen oligos for a
number of criteria, including checking vs a repeat seq database. Once you
get primers suggested by PRIMER, check them out for additional potential
problems using AMPLIFY, as recommended in an earlier reply to your post.

Good luck!
    Regards, Grant

Grant Morahan, Ph.D.
The Walter and Eliza Hall Institute of Medical Research
Parkville, Victoria

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