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While ethidium bromide works well for staining larger single-stranded RNA or double-stranded DNA molecules, it doesn't stain smaller nucleic acids very well. I observed that at around 20 bases and below single-stranded nucleic acids are difficult to see with EtBr-staining unless the nucleic acids are highly concentrated.

What are good alternatives for observing small nucleic acids in polyacrylamide gels? The main consideration would be ease-of-use, and it should be possible without any unusual equipment.

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I would think GelRed or GelGreen would be an option too. They claim to be more sensitive than EtBr and certainly less toxic (even moreso than SYBR Green). I haven't personally used them against such a small bp product though. GelRed has basically the same excitation/emission wavelengths as EtBr so no equipment change is needed.

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I have heard several people complaining about GelRed being less sensitive than EtBr. Also, an interesting blog post about the toxicity of EtBr and SYBR Green: rrresearch.fieldofscience.com/2006/10/…. –  nico Jan 7 '12 at 13:29
    
Interesting. I haven't done a comparison so I can't speak one way or the other. But I do remember a similar article sometime back saying a similar thing (EtBr is not as bad as you think, and SYBR Green really isn't a "safer alternative" as advertised). –  bobtheowl2 Jan 11 '12 at 18:41
    
There's no such thing as a "safe" DNA fluorescent stain. The dye works by intercalating between nucleotides in DNA and it stays there. If that segment of DNA later gets copied or read, it will cause errors. Aside from this, one molecule of EtBr intercalates on average, between one of three nucleotides (1 EtBr/3 bases). Signal strength for EtBr or other dyes is directly proportional to mass and length of DNA. –  leonardo Apr 7 '12 at 23:40
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A list of dyes is available here and a list of dyes specific to nucleic acids is available here. I think you have two choices the SYBR Gold nucleic acid gel stain (S11494) which can be detected under UV light (not sure if it can be used with polyacrylamide gels). Your other option which can be used with polyacrylamide gels is the SYBR Green II RNA gel stain (S7564, S7568, S7586), this stain can be detected with UV light post-electrophoresis. It states RNA in the name but it can also be used for ssDNA.

Hope this helps

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