Designing PCR primers-How to check them?

Tracy Aquilla aquilla at
Sat Jul 22 10:57:47 EST 1995

In Article <morahan-1807951320270001 at>,
morahan at (Grant Morahan) wrote:
>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

The best way to check your primers is to use them in a PCR! If you're using
a computer program you should do that before synthesizing the oligos. Once
you have them you may as well just try them out.

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