In situ Hybridization (ISH), unlike immunohistochemistry that localizes proteins in tissue sections, uses labeled complementary DNA or RNA probes to localize a specific DNA or RNA sequence in a tissue section or whole mount. DNA ISH can be used to determine the structure of chromosomes. Fluorescent DNA ISH (FISH) can be used in diagnostics to assess chromosomal integrity. RNA ISH is used to measure and localize mRNA and other transcripts.
The method first treats cells and tissues to fix the target transcripts in place and to increase access of the probe. The probe hybridizes to the target sequence at elevated temperature, and then the excess probe is washed away. Solution parameters such as temperature, salt and/or detergent concentration can be manipulated to remove any non-specific binding. The probe that was labeled (by radio, fluorescent, or antigen) is localized and quantitated in the tissue using autoradiography, fluorescence microscopy or immunohistochemistry, respectively. FISH (fluorescent in situ hybridization) utilizes fluorescent-labeled probes rather than fluorescent secondary antibodies.