What are PCR inhibitors?
What are PCR inhibitors?
Impurities that interfere with PCR amplification are known as PCR inhibitors. PCR inhibitors are present in a large variety of sample types and may lead to decreased PCR sensitivity or even false-negative PCR results. PCR inhibitors may have both inorganic and organic origins (Schrader 2012).
1. Inorganic PCR inhibitors include:
-Calcium or other metal ions that compete with magnesium
-EDTA that binds to magnesium, reducing its concentration
2. Some organic PCR inhibitors include:
-Polysaccharides and glycolipids that mimic the structure of nucleic acids, interfering with primers binding to the template
-Melanin and collagen that form a reversible complex with DNA polymerase
-Humic acids that interact with template DNA and polymerase, preventing the enzymatic reaction, even at low concentrations
-Urea that may lead to degradation of the polymerase
3. Other organic compounds that can inhibit PCR include:
-Hemoglobin, lactoferrin, and IgG in blood, serum, or plasma samples
-Anticoagulants such as heparin
-Polyphenols, pectin, and xylane from plants
-Ethanol, isopropyl alcohol, phenol, or detergents such as SDS
If inhibitors are present in the template preparation, a 100-fold dilution of the starting template may sufficiently dilute the inhibitor and allow amplification. Alternatively, ethanol precipitation of the template may be needed to resolve the problem.
References
Schrader, C., et al. PCR inhibitors—occurrence, properties and removal. J Appl Microbiol. 113:1014–1026 (2012).