Hi Fanny,

I don't remember any way of staining all RNAs in the cell (nowadays, people can track single RNAs using Cas9, but I guess that wouldn't work for you. Also, staining all RNAs would be messy and noisy). Since you mentioned that you want to look at structures within the nucleus, I assume you want to check the nucleoli. If you want to stain them, you can use silver staining or nucleolus-specific proteins. The third option is a FISH for rRNA.

If you just want to check that you are degrading RNAs in the nucleus, you could also try to purify your nuclei and then run a RNA gel. I'm not sure how it would look like, but my guess is that you should see shorter fragments.

Hope this helps! Best,

J.

Hi Fanny, I use the Click-iT® RNA Alexa Fluor® 594 Imaging Kit, you can find it here: https://www.thermofisher.com/order/catalog/product/C10330

The Click-iT® RNA Alexa Fluor® 594 Imaging Kit enables detection of global RNA transcription temporally and spatially in cells and tissues. Utilizing an alkyne-modified nucleoside, 5-ethynyl uridine (EU), (you need to incubate previously your cells with EU for 24 h) and powerful click chemistry, newly synthesized RNA can be detected without the use of radioactivity or antibodies with a simple, two-step procedure.  Detection utilizes the chemoselective ligation reaction between an azide and an alkyne where the modified RNA (with EU) is detected with a corresponding azide-containing dye.

Hope this helps,

Daniela.