[1] PCR inhibition is the most common cause of amplification failure when sufficient copies of DNA are present.
[3] Alternatively, by reducing the availability of cofactors (such as Mg2+) or otherwise interfering with their interaction with the DNA polymerase, PCR is inhibited.
[3] In a multiplex PCR reaction, it is possible for the different sequences to suffer from different inhibition effects to different extents, leading to disparity in their relative amplifications.
[3] Excess salts including KCl and NaCl, ionic detergents such as sodium deocycholate, sarkosyl and SDS, ethanol, isopropanol and phenol among others, all contribute via various inhibitory mechanisms, to the reduction of PCR efficiency.
[3] Techniques exist and kits are commercially available to enable extraction of DNA to the exclusion of some inhibitors.