A stain (or dye) usually consists of a chromogen and an auxochrome.  Reaction of a benzene derivative with a coloring agent (or chromophore) forms a chromogen.  The auxochrome imparts a positive or negative charge to the chromogen, thus ionizing it.  The ionized stain is capable of binding to cell structures with opposite charges.

Basic stains are cationic; when ionized, the chromogen exhibits a positive charge.  Basic stains bind to negatively charged cell structures like nucleic acids.  Methylene blue, crystal violet and carbolfuchsin are common basic stains.  Acidic stains are anionic; when ionized, the chromogen exhibits a negative charge.  Acidic stains bind to positively charged cell structures like proteins.  Picric acid, eosin and nigrosin are common acidic stains.