In situ hybridization is like all nucleic acid hybridization in being a technique in which single-stranded nucleic acids (DNA or RNA) are permitted to interact so that complexes, or hybrids, are formed by molecules with sufficiently similar, complementary sequences. Through nucleic acid hybridization, the degree of sequence identity can be determined and specific sequences detected and sometimes those sequences can be located on a specific chromosome.
In situ hybridization is done for this purpose. It involves hybridizing a labelled nucleic acid (often labelled with a fluorescent dye) to suitably prepared cells or histological sections. This is used particularly to look for specific transcription or localization of genes to specific chromosomes (via fluorescent in situ hybridization, or FISH analysis).