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DNA from formalin-fixed tissue: extraction or repair? That is the question
Skage, M.; Schander , C. (2007). DNA from formalin-fixed tissue: extraction or repair? That is the question. Mar. Biol. Res. 3(5): 289-295
In: Marine Biology Research. Taylor & Francis: Oslo; Basingstoke. ISSN 1745-1000, more
Peer reviewed article  

Available in  Authors 

Keywords
    DNA; Fixation; PCR; Marine

Authors  Top 
  • Skage, M.
  • Schander , C.

Abstract
    Establishing effective DNA-based protocols for use on archival material fixed in formaldehyde (formalin) is a particularly challenging task. Formalin fixation induces cross-linking with nucleic acids and proteins, thereby reducing the amount and quality of the extracted DNA. Previous attempts have primarily focused on optimizing DNA extraction protocols. Here we focus on the use of enzymes capable of in vitro repair of DNA extracts prior to amplification of the nucleic acids by the polymerase chain reaction (PCR). The amplification success of mitochondrial DNA was greater using the repair enzyme assay (56%) than with the regular PCR assay (20%), and even more convincing results were obtained with the amplified nuclear ribosomal region (91% versus 21%). These results indicate that in vitro repair of DNA damage (depurinated sites, strand nicks and base modifications) increases the number of samples that amplify, amplify to a greater extent and amplify fewer ancillary bands and that DNA repair has been overlooked as a way of improving the efficiency of molecular methods used on formalin-fixed samples. Fidelity has not been specifically investigated, but preliminary results indicate that misincorporation is not a major problem.

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