Any suggestions on extracting DNA from older (1-5 years) paraffin-embedded brain tissue? I have been using the Puregene Gentra kit, and while the spec tells me I have some DNA, the PCR says differently. All is ok with the PCR.

Lee:

Hopefully one of these references can be of some help...


Alastair Mark, Helen Trowell, Michael L. Dyall-Smith, and Delwyn J. Dyall-Smith. Extraction of DNA from formalin-fixed paraffin-embedded pathology specimens and its use in hybridization (histo-blot) assays. Application to the detection of human papfltomavirus DNA. Nucleic Acids Res., 26 October 1987; 15: 8565.



NJ Coombs, AC Gough, and JN Primrose. Optimization of DNA and RNA Extractin from Archival Formalin Fixed Tissue.. Nucleic Acids Res., Aug 1999; 27: e12.



T Glenn. Getting DNA from Old Dead Stuff. Department of Biological Sciences, University of South Carolina.



Hendrik N. Poinar, and B. Artur Stankiewicz. Protein preservation and DNA retrieval from ancient tissues. 1999. Vol. 96, Issue 15, 8426-8431.




Please let us know how things turn out for you!

Good luck!

Thanks. Will give them a look.

Tried the Quagen QIAAmp kit and while it didn't work on all the samples, it did work on some, however there was no rhyme or reason to the age of the samples that worked. Some were older, some new. Still working on it, but it's better than nothing. Thanks.

Lee

Lee:

Here's another reference that may help you out. Below is the link to the open-source article.

Shan-Rong Shia, Richard J. Cotea, Lin Wub, Cheng Liua, Ram Datara, Yan Shia, Dongxin Liua, Hyoeun Lima, and Clive R. Taylora DNA Extraction from Archival Formalin-fixed, Paraffin-embedded Tissue Sections Based on the Antigen Retrieval Principle: Heating Under the Influence of pH. Journal of Histochemistry and Cytochemistry, Vol. 50, 1005-1011, August 2002

Summary:
During the course of diagnostic surgical pathology, pathologists have established a large collection of formalin-fixed, paraffin-embedded tissues that form invaluable resources for translational studies of cancer and a variety of other diseases. Accessibility of macromolecules in the fixed tissue specimens is a critical issue as exemplified by heat-induced antigen retrieval (AR) immunohistochemical (IHC) staining. On the basis of observations that heating may also enhance in situ hybridization (ISH) and the similarity of formalin-induced chemical modifications that occur in protein and in DNA, we designed a study to examine the efficiency of DNA extraction from archival formalin-fixed, paraffin-embedded tissues using an adaptation of the basic principles of the AR technique, i.e., heating the tissue under the influence of different pH values. Archival paraffin blocks of lymph nodes, tonsil, and colon were randomly selected. Each paraffin block was prepared in 34 microtubes. For each paraffin block, one tube was used as a control sample, using a non-heating DNA extraction protocol. The other 33 tubes were tested using a heating protocol under 11 variable pH values (pH 2 to 12) under three different heating conditions (80, 100, and 120C). Evaluation of the results of DNA extraction was carried out by measuring yields by photometry and PCR amplification, as well as kinetic thermocycling (KTC)-PCR methods. In general, lower pH (acid) solutions gave inferior results to solutions at higher pH (alkaline). Heating tissues at a higher temperature and at pH 69 gave higher yields of DNA. There appeared to be a peak in terms of highest efficiency of extracted DNA at around pH 9. The average ratios 260:280 of extracted DNA also showed better values for samples heated at 120C. PCR products of three primers showed satisfactory results for DNA extracted from archival paraffin-embedded tissues by heating protocols at pH 612, with results that were comparable to the control sample subjected to the standard non-heating, enzymatic DNA extraction method. This study is the first to document the use of heating at an alkaline pH for DNA extraction from archival formalin-fixed, paraffin-embedded tissues, a recommendation based on the principles of AR for protein IHC. These findings may lead to a more effective protocol for DNA extraction from archival paraffin-embedded tissues and may also provide enhanced understanding of changes that occur during formalin-induced modification of nucleic acids.




Good Luck!