why do some regions in the chromosome stain darker than others?

Answer 1

I think the answer to your question lies in the fact that some of the DNA is "wound" tighter than other sections along the chromosome.

The tightly wound DNA is typically not transcribed in somatic cells (it might be a different story for germ line chromosomes, or chromosomes from embryonic tissue, and even stem cells for that matter).

When a gene is constantly being transcribed, say for example genes for hemoglobin, the cell prefers to keep the region open for easy access. It can do so by acetylation of histone molecules.

When histone is not acetylated, then the molecule keep the chromosome wrapped up tight.

When the dye attaches to the chromosome, tightly packaged DNA appears darker because there is a high concentration of dye in that smaller surface area.

So staining helps identify euchromatin (actively transcribed DNA sequence, stains lighter) and heterochromatin ("inactive" DNA sequence, stains darker).

The dye has the propensity to stain both types of chromatin equally. But it's the density of the dye which makes it appear darker or lighter.

It was fun thinking about your question. Pass on the good karma!

Answer 2

Different composition at different places. All chromosomes are composed of polynucleotides as well as histones composed of proteins.

Answer 3

They'll absorb more of the stain than other parts.