end of primer - (Jun/18/2005 )

When designing a primer for PCR, is it supposed to end with C or G?

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Either of that, but in my experience, I had got an unavoidable T at the end of a primer and it still worked nicely. Try to avoid run of G or C (GGG, CCCC).

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Hi biochem,

As dbtl says either is fine and PCR primer design rules are actually guidelines not rules, just because it doesn't obey all rules doesn't mean it won't work. However, it is best to avoid strings of G or C in the end (3 or more) and avoid G/C rich areas directly downstream of the primer, but if unavoidable give it a go anyway.

Hope this helps

Scott

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