ssGreen® is one of the most sensitive stains for post-electrophoresis staining of RNA and single-stranded DNA (ssDNA) in agarose or polyacrylamide gels. The fluorescence quantum yield of the ssGreen/RNA complex is more than 7× higher than that of the ethidium bromide/RNA complex. Although ssGreen is not selective for RNA staining, the dye exhibits about 1.5× greater quantum yield when bound to RNA than double-stranded DNA, which makes it unique among all nucleic acid dyes.
ssGreen staining is compatible with denaturing gels. On agarose/formaldehyde and polyacrylamide/urea gels, the sensitivity of ssGreen is slightly reduced but still superior to that of ethidium bromide. Staining agarose/formaldehyde gels with ssGreen does not interfere with transfer of RNA to filters or subsequent hybridization in Northern blot analysis as long as 0.1%–0.3% SDS is included in prehybridization and hybridization buffers.
Staining gels with ssGreen has fewer steps than those with ethidium bromide. Because the fluorescence of ssGreen/RNA complexes is not quenched by formaldehyde or urea, there is no need to wash these denaturants out of gels before staining. Also, ssGreen stain has a low intrinsic fluorescence, allowing gel viewing and photographing without preliminary removing unbound dye.