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Primer design - (Nov/15/2006 )

I plan to design PCR primers to amply my gene of interest about 660 bps in length. Can I rely on a free software tool like Primer3 and oligo. Could anyone give me an opinion based on past experience, which is the best tool that I can use?

Are commercial software any better then free tools like Primer3?

Plz help.

PCR geek


Earlier I used to take primer sequences from published data but I have started using "primer3" and its working absolutely fine.


I use primer 3. It has yet to fail.


because i always have limitations at where to place the primers i always design the primers by myself and then check for the product as well as their melt temp etc by this program:

PCR check

you have to be careful not to miscopy the primers and stuff like that.


I used primer3 too. But of course I did checked there are other possible dimer formation, blastn (I am doing amplification and need to be specific) =)