In this study, gel electrophoresis and capture enzyme-linked immunosorbent assay were used to assess the effect of formaldehyde treatment on the structural and immunological properties of bovine pancreatic ribonuclease A (RNase A). Prolonged incubation of RNase A in a 10% formalin solution leads to the formation of extensive intra-and intermolecular cross-links. However, these formaldehyde cross-links do not completely eliminate the recognition of RNase A by a polyclonal antibody. Comparative immunotitration of monomers, dimers, and oligomers greater than pentamers isolated from formalin-treated RNase A demonstrated that reduction of immunoreactivity due to intramolecular modifications prevails over the excluded volume effect of intermolecular cross-links. The latter only becomes important for intermolecular cross-links involving four or more molecules. The restoration of RNase A immunoreactivity during heating correlates with the reversal of formaldehyde cross-links if the incubation temperature does not exceed the denaturation temperature of the formalin-treated RNase A preparation. We conclude that formaldehyde cross-links stabilize antigens against the denaturing effects of high temperature, but the reversal of these cross-links is necessary for the restoration of immunoreactivity. Laboratory Investigation (2004) 84, 300-306, advance online publication, 26 January 2004; doi:10.1038/labinvest.3700041Keywords: antigen retrieval; immunohistochemistry; immunoreactivity; formalin fixation; ribonuclease A; enzymelinked immunosorbent assayIn 1991, Shi et al 1 published their seminal observation that high-temperature incubation of formalinfixed paraffin-embedded tissue sections in buffers for short periods leads to improved immunohistochemical staining. However, more than a decade later, high-temperature antigen retrieval (AR) remains an empirical procedure with several critical parameters that require trial and error optimization. 2,3 Further improvements in AR will require an in-depth understanding of the chemistry of formaldehyde fixation and the molecular mechanism(s) underlying the AR method.It is commonly assumed that decreased immunoreactivity in fixed tissues results from formaldehyde-induced cross-linking. However, cross-linking can affect protein immunoreactivity on many levels. The extremely high concentration of proteins and other solutes within tissues 4,5 leads to the formation of a dense irregular network of cross-links (gelation) that can prevent antibody penetration to the location of its antigen within the tissue. 6 Even if this primary barrier is partially destroyed by enzymatic etching or thermal reversal of cross-linking, additional effects of formaldehyde can impede antigen-antibody interactions. Antibody binding can be inhibited by steric hindrance (excluded volume effect) arising from the shielding of epitopes on the target antigen due to the close proximity of adjacent molecules to which the antigen is cross-linked. Immunoreactivity can be further compromised by formalin-induced chemical mod...