Fluorescence in situ hybridization (FISH), long the method of choice for chromosomal cytogenetics, is becoming recognized as a powerful method for correlative histochemical detection of multiple messenger ribonucleic acid (mRNA) in cells. The technique is based upon the principle of the binding of a labeled strand of DNA (an oligonucleotide probe) or RNA (a riboprobe) to complementary strands of mRNA. In the traditional in situ hybridization method, nucleic acid probes are labeled with radioactive isotopes and the hybrids are localized by autoradiography. More recently, labeling of the probes with digoxigenin, biotin, or fluorescein has allowed nonisotopic detection of probe-mRNA hybrids with immunoenzymatic techniques that are based on peroxidase or alkaline phosphatase histochemistry, in which the results are observed as brightfield stains. FISH is similar to conventional nonisotopic in situ hybridization except that the labeled nucleic acid probes are detected by fluorescence microscopy.

The FISH technique has advantages for performing correlative histochemistry. The results of a FISH protocol can be observed within a few hours of completing the hybridization protocol instead of waiting for days as is the case with isotopic methods. FISH permits cellular resolution and facilitates multiple labeling, where in situ hybridization probes can be resolved at the level of individual cells (Hahn et al. 1998).