An Eye for a Dye

Nucleic Acid Dyes and Stains

DNA molecular weight markers stained with Molecular Probes' SYBR Green I

Researchers working with DNA often have two fundamental questions: "How much DNA have I got?" and "What size is it?" Large quantities of DNA can be visualized even without staining or special illumination: The schlieren lines--refractive index changes at the boundaries of concentration differences--reveal the positions of the bands. However, this method is impractical for most applications. Fortunately there are numerous chemicals that show an increased fluorescence upon binding to nucleic acids, allowing easy detection using a light source and the appropriate filters.

Ethidium bromide (2,7-diamino-10-ethyl-9-phenylphenanthridinium bromide; EtBr) has traditionally been used for staining DNA and RNA in gels (and here) following procedures first published in the early 1970s.¹ While the procedures for using EtBr are simple, EtBr is fairly toxic. The material safety data sheet (MSDS) on EtBr does not explicitly list...