primerdimers

Primer dimers are undesirable artifacts that can occur during polymerase chain reaction (PCR). They are short DNA fragments that are formed when PCR primers anneal to each other and are subsequently extended by the DNA polymerase. This typically happens when the concentration of primers is high and the target DNA concentration is low, or when the primers have complementary sequences that allow them to bind together.

The formation of primer dimers consumes primers and dNTPs, which can reduce the efficiency of amplification of the intended target DNA. In some cases, primer dimers can be amplified to a significant extent and may even be mistaken for the actual PCR product, leading to false-positive results. The size of primer dimers is usually small, generally less than 100 base pairs, and their appearance on an electrophoresis gel can be a single band or a ladder of bands.

Strategies to minimize primer dimer formation include optimizing primer design to avoid complementarity, adjusting primer and dNTP concentrations, and optimizing annealing temperatures and extension times. Using hot-start PCR enzymes, which are inactive until heated to the denaturation temperature, can also help prevent primer dimer formation during the initial setup of the reaction. Careful primer design, including checking for potential self-complementarity and cross-complementarity, is a crucial first step in preventing these artifacts.