Figure 4.1a

Cartoon of a standard DNA extraction procedure from e.g. Qiagen. Formaldehyde does not degrade DNA. This suggests that the PCR inhibition of fixed samples is partially due to limited proteolysis of the formaldehyde aggregated proteins. Since the column matrix in this system binds DNA, it will also bind the associated proteins thus rendering the eluted sample refractory to PCR.

Figure 4.1b

Extraction protocol of choice for formalin fixed samples. In this system the column matrix binds the proteins and so any DNA extensively complexed with protein will not be eluted. DNA less complexed or free from protein aggregation will be eluted. For samples stored for extensive periods in formalin, yield of free DNA will represent a very small percentage of total DNA present in the system.