Many compounds also contained in the PCR template beside the target DNA can interfere with the polymerisation of nucleotides by the Taq or a related polymerase. This may result in false negative results, i.e. no PCR product even though the template is present.
Inhibitors from the purification process
- alcohols like ethanol and 2-propanol (isopropanol) from DNA template precipitation (Qiagen test of sequencing inhibition by Welters et al. 1997)
- organic solvents like phenol from phenol/chloroform purification (PMID 8136148)
- salts like KCl, NaCl from precipitation
- detergents like SDS,.. from membrane lysis (PMID 2223070)