The isolation of nucleic acids from fixed, paraffin-embedded tissues-which methods are useful when?

PLoS One. 2007 Jun 20;2(6):e537. doi: 10.1371/journal.pone.0000537.


Museums and pathology collections around the world represent an archive of genetic material to study populations and diseases. For preservation purposes, a large portion of these collections has been fixed in formalin-containing solutions, a treatment that results in cross-linking of biomolecules. Cross-linking not only complicates isolation of nucleic acid but also introduces polymerase "blocks" during PCR. A wide variety of methods exists for the recovery of DNA and RNA from archival tissues, and although a number of previous studies have qualitatively compared the relative merits of the different techniques, very few have undertaken wide scale quantitative comparisons. To help address this issue, we have undertaken a study that investigates the quality of nucleic acids recovered from a test panel of fixed specimens that have been manipulated following a number of the published protocols. These include methods of pre-treating the samples prior to extraction, extraction and nucleic acid purification methods themselves, and a post-extraction enzymatic repair technique. We find that although many of the published methods have distinct positive effects on some characteristics of the nucleic acids, the benefits often come at a cost. In addition, a number of the previously published techniques appear to have no effect at all. Our findings recommend that the extraction methodology adopted should be chosen carefully. Here we provide a quick reference table that can be used to determine appropriate protocols for particular aims.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Adult
  • DNA / chemistry
  • DNA / isolation & purification*
  • Fixatives / chemistry*
  • Hot Temperature
  • Humans
  • Lithium Carbonate / pharmacology
  • Lung / metabolism
  • Lymphoma / genetics
  • Middle Aged
  • Paraffin Embedding*
  • Polymerase Chain Reaction
  • RNA / chemistry
  • RNA / isolation & purification*
  • Sarcoma, Kaposi / genetics
  • Spleen / metabolism
  • Tissue Fixation
  • Young Adult


  • Fixatives
  • Lithium Carbonate
  • RNA
  • DNA