I have work histamine decarboxylase gene (Hdc) from histamine forming bcateria, my primer was amplified the particular regions but i will get primer diamer in agarose gel... how to avoid the primer diamer in agarose gel?
Try these steps (in order):
1.- Increase Tm.
2.- Design a new primer pair, paying attention to primer dimer formation scores, say, avoid primer pairs with high reverse-complementarity
At any case, for conventional pcr, I wouldn't bother much about primer dimers if you get your band of interest. If it was Real-time PCR, specially with intercalating dyes such as sybr green It would be a huge problem, but not for conventional pcr
Thank you for your promote.... i also have one more question? i am geting faint pcr products, guide me further......
If you have weak signals of your amplicon primer-dimers may be the problem. I concur with the suggestions made by Iker. In case your primers have been checked for self-complementarity and you want to continue using them I would add further suggestions that might be of help. First, if you have not done so alrady, use a Hot Start polymerase. Second, check your primer concentration. Primers at too high concentrations are prone to forming primer-dimers. Third, try touchdown PCR starting with annealing temperatures a few degrees above the calculated Tm, -0.5 to -1 C per cycle until temperature is at Tm.
You can use Primers in the primer bank database (https://pga.mgh.harvard.edu/primerbank/) and then check it in (https://www.idtdna.com/calc/analyzer) and You can choose the best primers
Adjust annealing temperature.Check your template. You need to use more DNA or less,If you have any contaminants in your DNA that might inhibit your taq,If none of these solutions improve your amplification try to design another set of primer.
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