We are looking into following the kinetics of short dsRNA melting and about using a dye that will bind differently to dsRNA and ssRNA. Any idea for such a dye? Or to another simple approach to such measurements?
Just about all the nucleic acid-dependent fluorescent dyes bind more tightly and have a greater fluorescence increase when binding to double-stranded nucleic acids than single-stranded. You could use PicoGreen or RiboGreen or SYBR Green II, for example.