Although formalin-fixed and archived tissues are a huge source of DNA for molecular biological studies in cancer research, screening for genetically based diseases and developmental biology studies, attempts to extract DNA from formalin-fixed tissues for molecular biological studies have been variably successful . Formalin fixation at room temperature results in poor preservation of high-molecular weight DNA, the size of the extracted DNA being directly related to the fixation temperature.
Even short-term treatment of sections with formalin have been shown to significantly reduce DNA solubility , with up to 30% of nucleic acids being lost during the fixation process .
With the expansion of PCR and other techniques for nucleic acid analysis for clinical diagnosis, an understanding of the deleterious effects of formalin as the primary method of choice, followed by recovery of preserved DNA and RNA is becoming increasingly important, as the need for molecular pathology to arrive at a conclusive diagnosis will increase in the future.
Multiple studies have indicated that the use of non cross-linking alcoholic reagents yielded superior results as nucleic acid fixatives, rather than aldehydes.

A Novel Fixative Improves Opportunities of Nucleic Acids and Proteomic Analysis in Human Archive’s Tissues

Giorgio Stanta, MD, Stefano Pozzi Mucelli, MS, Francesca Petrera, MS, Serena Bonin, PhD, and Gianni Bussolati, MD. DIAGN MOL PATHOL. 2006 june 15(2): 115-23.

DNA amplification by PCR	RNA amplification by RT-PCR
Ten samples five from formalin-fixed and five from FineFIX-fixed tissues were subjected for DNA extraction. 250 ng of DNA of each sample has been amplified using a primer of 291 bp (data not shown), 339 bp (A), 1000 bp (B), 1939 bp (data not shown), 2396 bp (C) region of human transthyretin gene. Each gel (A, B and C) shows: Lane 1, molecular size marker; Lane 2-6, DNA obtained from formalin-fixed tissues; Lane 7-11, DNA obtained from FineFIX-fixed tissues; Lane 12, negative control; Lane 13, DNA from HepG2 cells, positive control.	Ten samples five from formalin-fixed and five from FineFIX-fixed tissues were subjected for RNA extraction. 500 ng of RNA extracted from all samples were subjected to DNase and RT-PCR amplification using a set of 170 bp (A), 200 bp (B), 600 bp (C) region of beta-actin gene. Each gel (A, B and C) shows: Lane 1, molecular size marker; Lane 2-6, RNA obtained from formalin-fixed tissues; Lane 7-11, RNA obtained from FineFIX-fixed tissues; Lane 12, negative control; Lane 13, mRNA from HepG2 cells, positive control.
DNA Amplification Comparison Between Formalin and FineFIX, Number of Positive Results After PCR Amplification Lenght (Bases) Formalin Fixed FineFIX 291 5/5 5/5 339 5/5 5/5 1000 0/5 5/5 1900 0/5 5/5 2400 0/5 5/5	RNA Amplification Comparison Between Formalin and FineFIX, Number of Positive Results After RT-PCR Amplification Lenght (Bases) Formalin Fixed FineFIX 77 5/5 5/5 170 5/5 5/5 200 0/5 5/5 450 0/5 5/5 600 0/5 3/5

Protein analysis - Western Blot

Seventy mg of whole protein extract both from formalin-fixed and from FineFIX - fixed tissues was loaded and run onto SDS - PAGE electrophoresis before blotting.
No proteins were detected from the formalin-fixed tissues either for alfa-tubulin (a-tubulin) and for tissue transglutamminase (tTG), although the extract from FineFIX-fixed tissues gave similar protein quality of those from fresh tissues.