Chromosomes are thread-like structures located inside the nucleus of animal and plant cells. Each chromosome is made of protein and a single molecule of deoxyribonucleic acid (DNA).

There are several ways a stain can bind to a chromosome, it is necessary to understand how stains bind to the chromosomes.

A stain can bind to the chromosomes by DNA through intercalation, minor groove or major groove binding, or external binding and binding to proteins.

Based on the nature of chromogen, there are three types of stain. 1. Acidic stain (Anionic stain) 2. Basic stain (Cationic stain) 3. neutral stain

Acidic stain (Anionic stain)

• Chromogen of acidic stain is negatively charged.
• Acidic stain are used to stain the positively charged components such as background staining.
• Histone protein is positively charged so it can be stained by acidic stain.
• Examples: Eosin, Nigrosin, India ink

Basic stain (Cationic stain)

• Chromogen or coloured part of basic stain is positively charged.
• Basic stain are used to stain negatively charged components.
• Examples: methylene blue, safranin, malachite green,basic fuchsin, crystal violet

Neutral stain:

• In neutral stain, both cation and anion are coloured, such that net charge is neutral.
• Neutral stain are actually is a salt of acidic and basic stain.
• Examples: giemsa stain.

Fatemeh Farsi you can use both type of dye either acidic or basic but it depends on the target site of chromosomes either DNA or proteins.

You can use acidic dye for protein binding not for DNA binding. If your target site is DNA binding then you cannot use acidic dye because both DNA and acidic dye carrying same charge.

Acidic stains can be used to stain the protein exactly.