DAPI is used as a stain for DNA heterochromatic and euchromatic regions. The Barr body is heterochromatic.

In the slide of a normal human female cheek's somatic cells, there is apparently no other clear dark spot inside the nucleus than the Barr body against the nuclear inner membrane. - - I used an old microscope so my observation may be wrong as pointed in the comment.

How can you deduce from the given slide that the spot really contains inactive satellite cells that are not used genetically?

Why is the active X chromosome not visible by the same staining method? (It probably can be made visible by some other staining method.)

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    $\begingroup$ Just to clarify, do you mean "there is no other dark spot inside the nucleus?" The Barr Body is not inside the nucleolus, and the nucleolus appears as a DAPI-dim (unstained) spot in interphase nuclei. $\endgroup$
    – KAM
    Jan 4, 2012 at 11:13
  • $\begingroup$ @KAM Yes, I mean that I did not see any other clear dark spot inside the nucleus than the Barr body. Other thing was blurr and not that clear. Thank you for pointing out the mistake: the Barr body is inside the nucleus next to nucleolus or more exactly against the nuclear inner membrane in interphase nucleus. $\endgroup$ Jan 4, 2012 at 22:41

1 Answer 1


DAPI (4',6-diamidino-2-phenylindole) preferentially binds AT-rich DNA (although it binds CG-rich DNA, too), which can give chromosomes distinctive banding patterns if they are polytene or in metaphase. In interphase condensed chromosomes, such as the inactive X chromosomes of female mammals (Barr Body), the relatively high concentration of tightly-packed DNA makes the chromosome appear as a brighter spot in the nucleus. When the DNA of a chromosome is decondensed (such as the rest of the chromosomes in interphase), it appears as more-or-less homogeneously stained DNA in the nucleus.

A great picture is here (see below), A is the DAPI staining, B is a protein localized to the Barr Body, C is the RNA (Xist) which binds the Barr Body.

Barr body

Since the active X is not condensed, it appears as do the rest of the chromosomes, so cannot be identified among the mixture of autosomes. The difference in DAPI appearance has nothing to do with activity per se, but rather differences in how tightly packaged the chromosomes are.

I do not understand the first part of your question, though. You cannot tell from a still image that the Barr Body is relatively inactive. If your were doing experiments on live cells, you could measure RNA production (using a labeled nucleotide), immunofluorescence to show localization of e.g. RNA Polymerase, or reporter genes located on the inactive versus active X chromosomes. If you clarify your question, I can answer better.

  • $\begingroup$ Do you mean that you can see Barr body and the active X chromosome as dark spots to the eye in the given slide? - Assume yes. Then my classmate was wrong in claiming that she can differentiate between the two X-chromosomes from the slide. Like you said you need to measure RNA production to verify the thing. $\endgroup$ Jan 17, 2012 at 13:36

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