Do you want to stain tissuesections? Which material do you want to stain?
For tissue it is a usual method to stain nuclei (chromatin) with hematoxylin and proteins (cytoplasm and extracellular proteins) with eosin. Together it is the HE-stain.
I assume that your question refers to a special topic.
Hello Cyral, as Gudrun mentioned when you are working with tissue sections or cell culture you can detect the protein in which you are interested by immunohistochemistry and couterstain the nuclei either with hematoxylin or nuclea fast red (both nuclea stains). if you're using immunfluorescence you counterstain with Dapi. This an interkalant nuclea stain. If you likt to detect ssDNA you can do this with immuno as well because there are exsiting special antibosdies. In resent times one detect DNA with the so called Feulgen-Reaction. But this was before immunohistochmistry with high specific antibodies give better and more specific results.