Hi Sarah, 

The "background" you are observing is probably mitochondrial DNA.  I observed cytoplasmic signal with DAPI as well, in a part of the cell where mitochondria were enriched (as judged by TEM).  Although clearly visible, this signal was much dimmer than the nuclei and didn't pose a problem for what I was doing.  

If you want to see just the nuclear DNA, try transforming a GFP-Histone plasmid.  

Dan Dickinson 
University of North Carolina 


On Mar 7, 2014, at 4:07 PM, Sarah Marie Bruno <[log in to unmask]> wrote:

> I am a student working with Dr. Carl Franck at Cornell University. I have been trying to stain the nuclei of the dicty cells with DAPI, but I have observed a lot of nonspecific binding. Does anyone have any tips or protocol for selectively staining the nuclei using DAPI?
> 
> Thank you!
> 
> Sarah Marie Bruno