Designing PCR primers-How to check them?

brett brett at BORCIM.WUSTL.EDU
Fri Jul 14 17:52:57 EST 1995

>>   Peter ---  bkxo at writes:
>>  I have designed a set of primers for amplification of a 300 bp ds DNA 
>>  fragment from human genomic DNA.     
>>  I am interested to know how other people go about checking primers 
>>  which they have designed before actually ordering them.
>>  You can reach me at   bkxo at     or post a note here.  
>>  Thanx. 
I agree you should yield to your empirical results. However, you can
design your primers intelligently. One thing I've found useful is the
Amplify program available from the Indiana biosci ftp site. Briefly, you
can run the reaction "in silico", and it will point out annoyances such as
potential false priming sites in the template (assuming you know the
genomic sequence in your case), as well as primer-dimers, etc. 

Brett Lindenbach
Lucille P. Markey Student in Human Pathobiology    
Program in Immunology                              
Washington University - St Louis                  
brett at                             

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