MODIFICATIONS OF HUMAN AND VIRAL DEOXYRIBONUCLEIC-ACID BY FORMALDEHYDE FIXATION

BACKGROUND: Formaldehyde reacts with human and viral DNA through inter action with hydrogen bonds, fixation of DNA-protein, and hydroxymethyl ation of the nucleic acids. Even though most archival tumor tissues ar e fixed with formaldehyde, little has been done to analyze the consequ ences of the reaction of formaldehyde with DNA, Misleading results can be obtained from fixed tissue using polymerase chain reaction (PCR) t yping or restriction fragment length polymorphism analyses. EXPERIMENT AL DESIGN: We have studied variations in fixation time in various tiss ues obtained at autopsy and in prostatic carcinoma biopsies to analyze the effects of the formaldehyde fixation. Different PCR-products were studied after different fixation times. RESULTS: DNA from fixed tissu es appears to be no more fragmented than the native DNA. Changes in th e DNA structure is more important than DNA quantity for performing PCR on fixed tissues. PCR products longer than 2 to 300 bp was difficult to amplify from some tissues. Only 8 hours of fixation can be enough t o inhibit amplification of more than 421 bp. Tissue fixed for longer t han 215 hours cannot be amplified for more than 200 basepair products unless excessive numbers (50-80) of PCR-cycles are used. CONCLUSIONS: The loss of PCR product is related to fixation time and PCR-product-le ngth, probably because of the rate of denaturation followed by modific ation of DNA, Contrary to what has previously been assumed, formaldehy de neither fragments nor reduces the quantity of DNA, but rather chang es the structure of DNA. Different tissues may also react differently with formaldehyde, in part because of different tissue fixation gradie nts. When the PCR product is shorter than 200 bp, DNA isolated from pa raffin-embedded tissues fixed with 4% formaldehyde can be useful to an y kind of PCR product analysis.