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primer:cross-dimer - How to remove the cross dimer? - (Jul/30/2006 )

Hi all

I am an amateur in doing PCR. I have designed the primer pairs by primer premier 5.0, however, the sense primer have cross dimer ? but i can not move the sense primer's place.
Do you have any idea to solve this problem?thanks!


huh.gif [oh help me please


unfortunately there's not much you can do

if you have to use primers in one spot, and you only get dimers, there's no way to alter the interaction...sorry, the DNA hybridizes where the bases match blink.gif that's both the best and worst thing about working with DNA rolleyes.gif

why are you unable to move the primers? often times a short shift in one or the other will get rid of a dimer?

sometimes you can add increasingly smaller amounts of primer and you can obtain more product in proportion to dimer, or at least enough product to work with...are you cloning?


If there is a possibility for a dimer, it isnt too bad. Some times one cannot avoid, it. I usually order the primers (as they r cheap) and try the PCR.

I heat the primers and template before adding the PCR mixture to avoid dimers in the reaction.