I am currently working on ARMS PCR and the result is there is primer dimer in every negative control that i made. I was doing optimatization and there are pirmer dimer in every samples using temperature below 63 degree Celcius, What caused it always show in my negative control? how to prevent the primer dimer.
primer dimer PD occurs when there is homology between parts of the 2 primers so they anneal together at low temperatures . Because primers are in huge excess in pcr reactions once a pd has formed it melts easily and then has perfect homology with the primers and is very short so it amplifies extremely well and often takes over the reaction and you get no product.. Some tries to get rid of pD are 1 use a hot start enzyme works very well
2 use less primer helps
3 adding DMSO up to about 6% can sometimes help
4 redesign the primers but this is probably difficult in your case although the reverse primer could be changed
If the pd only shows in the negative control and your amplification is good in the samples I would use less primer but not worry too much
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