page_title: Primer dimer
section_title: Mechanism of formation
hierarchical_section_title: Primer dimer / Mechanism of formation
caption_attribution_description: English: Mechanism of primer dimer formation in PCR
context_page_description: A primer dimer is a potential by-product in the polymerase chain reaction, a common biotechnological method. As its name implies, a PD consists of two primer molecules that have attached to each other because of strings of complementary bases in the primers. As a result, the DNA polymerase amplifies the PD, leading to competition for PCR reagents, thus potentially inhibiting amplification of the DNA sequence targeted for PCR amplification. In quantitative PCR, PDs may interfere with accurate quantification.
context_section_description: A primer dimer is formed and amplified in three steps. In the first step, two primers anneal at their respective 3' ends (step I in the figure). 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. The third step occurs in the next cycle, when a single strand of the product of step II is used as a template to which fresh primers anneal leading to synthesis of more PD product.
caption: Primer dimer is formed and amplified in a three-step process
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