In situ hybridization allows you to visualize where a particular mRNA is located inside a tissue such as an embryo. In situ means in the location, so this method allows the investigator to see the normal location for the mRNA of interest.

In top panel of the diagram, one of four cells in a tissue is transcribing the gene of interest, as shown by the lines.

A single-stranded DNA probe (middle panel) is linked to an enzyme and allowed to base pair with the mRNA. After a series of washes, only probes that are correctly base paired with the target mRNA remains in the tissue.

A colorless substrate is incubated with the probe and the substrate is enzymatically converted to a colored product that is easily visualized. Cells that contain the colored product indicate where your mRNA of interest was expressed.