I have made a PCR reaction and made a negative control. I found that there is a primer dimerization in most samples. I will decrease the primer concentration but I don't know whether I have to change the annealing temp or not.
There is obvious that in negative ctr you always expect unused primers and primer dimerization. It only the PCR product of interest without any non-specific amplification is the sign of good annealing temperature. To know the best annealing temperature for your gene of interest you can perform gradient of temperatures and look for the temperature which gives you the amplification without any non-specificity.
If you observe formation of primer dimers in your experimental/test reactions along with non-specific amplification, then you need to worry about annealing temperature but it is not surprising that you find it in a negative control. However, that does not mean you can ignore it completely. Its always better to ensure low levels of primer dimer formation. If you are performing a semi-quantitative PCR then it should not be much of an issue as long as you get visibly high intensity and no non-specific bands. But if its a qPCR (real time PCR) then primer dimers are a serious issue as they will drastically affect the reaction efficiency and quantification in which case and you might have to redesign primers with minimal complementarity scores and titrate them.
There are quite a few online tools you can use to look at the tendency of your primers to form dimers and other secondary structures as well.
Obviously in negative control you can see unused primers. Generally I use 20pmol of primer
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