Mario,

while your question is 10 days old by now, I missed it so far and it 
seems to be still unanswered.

Your suspicion is correct: DAPI (and the Hoechst dyes) are AT 
specific while Chromomycin A3 is GC specific. (Shafer RH et al, Eur. 
J Biochem ,173:377, 1988). Mouse chromosomes have enormous AT-rich 
pericentromeric and paracentromeric repetitive regions (minor and 
major satellite) which cluster in interphase nuclei to chromocenters, 
the "bright intense spots" you observed. The degree of clustering is 
actually dependent on the cell type. If you want to get the oposite 
pattern, you can try Equine cells.

I never did it myself, but I seem to remember that DAPI has been used 
for flowcytometer cell cycle studies.

Steffen


At 13:24 08.10.2009, you wrote:
>Dear List,
>We are testing Chromomycin A3 as nuclear dye in alternative to DAPI 
>in mouse embryo fibroblasts. We noticed that the obtained staining pattern
>looks quite different from the usual one we get.
>Mouse cells usually have bright intense spots corresponding to 
>heterochromatin foci when stained with DAPI,  but I have the 
>impression that the number of spots identified by ChromoA3 is less 
>in number and relative intensity. Do you know if according to the 
>dye specificity we have to expect this result (due to the relative 
>distribution of AT or GC bases)? (Cells were fixed (PAF) and 
>permeabilized to reduce accessibiltiy limitations)
>Any suggestion/experience about nuclear dyes excited in the violet 
>blue range but with greater affinity for heterochromatin 
>(Olivomycin, Quinacrine Mustard, Syto Molecular Probes Dyes..) and 
>feasible for DNA quantitation (like cell cycle evaluation)?
>Thanks
>Mario
>
>--
>Mario Faretta
>Department of Experimental Oncology
>European Institute of Oncology
>c/o IFOM-IEO Campus for Oncogenomics
>via Adamello 16
>20139 Milan
>Italy
>Phone: ++39-02574303054
>email: [log in to unmask]
>http://www.ifom-ieo-campus.it