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DNA Amplification for Forensic Analysts

No Complementarily to other primers

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Primers should contain fewer than 4 complementary bases especially at the 3' end. Complementarity between two primers, especially at the 3' ends, can lead to the formation of product artifacts arising from amplified primer-dimers and primer-oligomers. The concentration of primers is much higher than that of target DNA in PCR. Therefore, if the primers exhibit self-complementarity they may hybridize to each other and form homo-dimers or hetero-dimers.

Avoiding primers with 3' overlaps is extremely important in multiplex reactions.

  • A self-dimer is formed due to intermolecular interactions of the same primer.
  • A cross dimer is formed due to intermolecular interaction between sense and antisense primers.

In order to detect cross dimers, the sense primer in 5' - 3' direction is compared with the antisense primer in 3' - 5' direction for homology.

Schematic of Stutter Product Formation Process
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