The Concept of Primer Dimer

The concepts of primer dimer arise during reverse transcriptase polymerase chain reaction (RT-PCR) often complicating quantitative analysis. It is thought that when PCR primer ends are complementary to each other or the ends of the each individual primers are complementary, they will bind and result in a primer dimer. Since primers in a PCR reaction are present in large concentrations, interactions between them are very likely. This results in primer dimers that are visible as bands in agarose gel electrophoresis.

There are several ways to reduce the formation of primer dimers accumulation. This is easily done by carefully designing primers for PCR; for example, making sure that there is no complementarity at the 3 prime ends of both the primers. Some researchers like to add Dimethyl sulfoxide (DMSO) that increases the specificity of the DNA template to the primers and hence preventing primer-dimer formation. Other possible ways to reduce primer dimer reactions include the use of hot-start PCR, touch-down PCR, high quality Taq DNA polymerase and increasing the annealing temperature of the primers. Using low concentration of primers often works well.