Primer dimer

A primer dimer (PD) is a potential by-product in the polymerase chain reaction (PCR), a common biotechnological method.

If this construct is stable enough, the DNA polymerase will bind and extend the primers according to the complementary sequence (step II in the figure).

An important factor contributing to the stability of the construct in step I is a high GC-content at the 3' ends and length of the overlap.

One approach to prevent PDs consists of physical-chemical optimization of the PCR system, i.e. changing the concentrations of primers, magnesium chloride, nucleotides, ionic strength and temperature of the reaction.

This method is somewhat limited by the physical-chemical characteristics that also determine the efficiency of amplification of the target sequence in the PCR.

To overcome this limitation, other methods aim to reduce the formation of PDs only, including primer design, and use of different PCR enzyme systems or reagents.

[9] Chemical modification: in this method a small molecule is covalently bound to the side chain of an amino acid in the active site of the DNA polymerase.

The enzyme also possess inherent primer:template mismatch discrimination, resulting in additional selection against primer-dimers.

Thus, through careful design,[15] primers build from SAMRS could avoid primer-primer interactions and allowing sensitive SNP detection as well as multiplex PCR.

While the methods above are designed to reduce PD formation, another approach aims to minimize signal generated from PDs in quantitative PCR.