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Multiplex PCR primer designing - (Aug/17/2004 )


can any one suggest me that how can i designed primers for multiplex PCR and theoratically how can i check that these primer will work or not ??????
is any software available ???

thank you.


This topic has been discussed in several threads

For design tools, this may help


Hi ,

I would like to suggest you to use Primer Premier software from PREMIER Biosoft International . To check for a number of primers in a reaction i.e., for a multiplex/nested PCR, you can analyze as many primers as you want, using Multiplex/Nested function.

Best wishes


The following site has a primer design tool for multiplex PCR. It is kind of slow, you would need to limit to a few pairs of primers and not too long PCR products:


I agree with synthia's suggestion, Primer Premier is a good software and one can download it from
for free and request for a time limited key, this compnay also has a molecular beacon software, Beacon Designer which is also very interesting,