We and other users have often observed that GelGreen® stains ssDNA and RNA orange/ pink and dsDNA green. We have also seen that smaller dsDNA fragments can appear orange-pink, the color ranging from white-pink-orange. We are not sure about the underlying mechanism, possibly the structure of single-stranded nucleic acids favors an altered stacking interaction of GelGreen® monomers leading to the formation of J-aggregates that have red emission.

Yes, use the post-staining protocol for polyacrylamide gels. For polyacrylamide gels containing 3.5-10% acrylamide, typical staining time is 30 minutes to 1 hour with gels of higher acrylamide content requiring longer staining time.,

Biotium also offers PAGE GelRed® a non-toxic, non-mutagenic dye specifically designed for staining DNA in polyacrylamide gels.

We don’t recommend adding GelRed® or GelGreen® directly to loading buffer, because this can result in inaccurate band migration. Biotium offers 6X GelRed® Prestain Loading Buffers designed for this application, although we do not recommended them for applications where precise DNA band sizing is required. For the most accurate determination of DNA band sizes, we recommend using GelRed® post-staining (see the GelRed® protocol for details).