Protocol Online logo
Top : New Forum Archives (2009-): : Molecular Biology

Are there any safe nucleic acid binding dyes that you can add to both the runnin - (Apr/30/2015 )

Is there a cheap and safe replacement for EtBr in agarose gels for visualizing nucleic acid - DNA and RNA? Specifically a dye that you can add to both running buffer and the gel which is how I use EtBr. I do not want to do a post stain because I am too impatient to wait and I occasionally like to view my gel before it has fully resolved. I have heard that these dyes are large and can alter the migration of the nucleic if they are added to the gel so I am not sure if they will all require a post stain. However, I am not aware of all the dyes available or what other people are doing in their labs. I want to get rid of EtBr because of the special requirements for disposal. Plus I would like a dye that I can use for both UV and blue light in case I do not want to expose my DNA to UV. So I was hoping someone had some success with the switch form EtBr to a safe dye. 




In short. No.

No dye binding to DNA is safe. 

SYBR based dyes ar considered "safer" in means of disposal at least, but is hardly cheap.

We were trying to use GelRed stain cause some people felt worried about EtBr, but just from the quality of staining I stopped using it. Even when titrating the concentration down it still causes weird effects on bands, bands are "smiled", with dyed tails, marker seem to be "shaded" in more detail and thus instead of making a ladder it's merged together.. the dye seem to light up more details in the bands, and in bigger visible range, but for band visualisation it is actually worse. Instead of normal stright bands you get some ziggzaged head od the band with tails on the sides.. the running conditions are the same of course.

I stopped using it. We have one bottle of EtBr, that we could use diluted like that for another 5 years and with better visualisation then GelRed. I've seen people using SYBR Green (the recommended concentration) just fine, but I don't know if this is just some difference between the fluorescent dyes or what. Anyway SYBR is even more expensive.


Thanks. I think I will stick to EtBr. The marketing of these dyes by some companies are misleading so I thought I would try to get some input from the users out there.