design primer for PCR.. - (Sep/09/2005 )

hi to all..

i want to know how we could design a good primer for the PCR?if there happens to have dimer and cross dimer,but no hairpin and false priming,can i still proceed to design it?

what is hairpin and dimer anyway?what they got to do with PCR process then?

in need of information...

thanks guys

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the best primers are without dimer,cross dimer,hairpin and without false match.but if you could not find so standard primers, primers with dimer are permitted, the only thing you should do is to increase the annealling temperature to enimilate the primer dimer problem.

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When primers can hybridise to themselves (internally e.g both ends are complementary) they will form loops or hairpins.
When you have a primer set with a complementary region, they will hybridise to each other, resulting in primer dimers.

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You can also check the deltaG to the formation of the hairpins and dimers. If they are small negatives, the chance of the formation will be a lot lesser.

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