Answer: The Nissl stain is an imaging technique performed on fixed tissue that stains genetic material.
One of the oldest methods of neuronal imaging, the Nissl stain uses cresyl violet acetate or toluidine blue to permanently stain genetic material. The genetic material that is often stained is the DNA within the nucleus and RNA in the rough endoplasmic. The stain is most useful for identifying cytoarchitecture across brain structures (Improved method for combination of immunocytochemistry and Nissl staining).
Some regions of the brain, such as the cortex, are organized in an columnar manner. This organization in the cortex is described in terms of layers, one on top of the next. There are 6 layers of the cortex, and each layer has a unique cell composition. For example, layer 6 and the innermost part of layer 4 of the cortex often contains the cell bodies of several pyramidal cells. Because layer 6 contains the nuclei of several cells, it will appear significantly more dense in staining compared to a layer that has several projection processes.
The major disadvantage of using a cresyl violet Nissl stain is that the detailed morphology of the cell is not stained. Axons, dendritic processes, and the majority of the cytoplasm is low in genetic material. Following a Nissl stain, the cell bodies of a densely branched Purkinje cell and a long and thin bipolar cell would appear similar: only the nucleus and rough endoplasmic reticulum would take up the stain. A Golgi stain will be better for visualizing the morphology of a cell.
With a cresyl violet Nissl stain, the nucleic acid appears dark purple-blue while the areas with low nucleic acid density appears light blue-gray.
The center of the nucleus is the nucleolus, the actual site of storage for DNA. Immediately surrounding the nucleus is often several layer of endoplasmic reticulum, which has genetic material in the form of RNA as it is the process of being translated into protein.
The dye itself is a base, which binds to nucleic acids.
The stain was named after the German neuropathologist Franz Nissl. “Nissl substance” is an older term for the endoplasmic reticulum, which is where the name comes from. “Nissl bodies,” on the other hand, refer to the free ribosomes.