Hi,
I'm trying to visualize ssRNA 12-mers on UREA-PAGE with EtBr or GelRed stain; however, I cannot see any bands. In contrast, both EtBr and GelRed seem to detect ssRNA 21-mers without any issue. I've seen SYBR Gold as a highly recommended stain but haven't found any details regarding its ability to detect shortmers.
Thanks,
Andrew
You cannot visualize ssRNA in gel with EtBr, SYBR or any other intercalation dyes because of they need double-stranded structure with stacks of base pairs. Only long RNA can be seen due to their ability to make intramolecular double-strand conformations.
So, you need to use sliver staining (with silver nitrate) or fluorescent probes for visualization
Ivan Bakutenko , I seem to detect ssRNA of 21 nt length without difficulty by post-staining with EtBr after UREA-PAGE, albiet with less sensitivity than double stranded. We do use a considerable mass of ssRNA (10 ug).
Another possible technique is UV shadowing where you put the gel on a thin layer chromatography plate or any other fluorescent surface and illuminate with UV light without any staining. The uv is absorbed by the rna and all absorbing bands are indicated by dark bands of reduced fluorescence from the plate
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