The most widely used histological stains differentiate between the acidic and basic components of cells and tissues.
Basic dyes have a net positive charge and bind to components of cells and tissues that are negatively charged.
Phosphate groups of nucleic acids (DNA and RNA)
Sulfate groups of some polysaccharides (glycosaminoglycans) and some proteins (mucus).
Tissue components that stain with basic dyes are referred to as basophilic.
Acidic dyes have a net negative charge and bind to components of cells and tissues that are positively charged.
Ionized amino groups in proteins (side chains of lysine and arginine).
Tissue components that stain with acid dyes are referred to as acidophilic.
Hematoxylin & Eosin
Hematoxylin and eosin (or H&E) is the most commonly used stain in histology. This stain works well with a variety of fixatives and stains a broad range of cytoplasmic, nuclear, and extracellular matrix features.
Hematoxylin is a positively charged, blue dye complex that stains basophilic structures.
Eosin is a negatively charged, pink dye that stains acidophilic (also known as eosinophilic) structures.
Hydrophobic structures (such as those rich in fats) do not stain well with H&E.