Methylene blue: An alternative multi-purpose stain for detection, analysis and isolation of nucleic acids

Abstract

A series of experiments was performed utilizing Methylene Blue (MeB) in place of the intercalating dyes ethidium bromide (EtBr) and acridine orange (AO) to stain, visualize, and isolate DNA and RNA. MeB proved to be superior to the other dyes for several purposes: 1) visualization of glyoxalated (chemically denatured) RNA in agarose gels, 2) staining of nucleic acids that are to be used in subsequent hybridization experiments, and 3) isolation and purification of plasmid DNA by CsCl ultracentrifugation. MeB was found to perform at least as well as EtBr or AO for visualization of DNA in agarose of acrylamide gels, and DNA stained with MeB can be purified from agarose gel slices by the Gene Clean protocol. These results indicate that MeB is a very effective nucleic acid stain. Its safety versus conventional intercalating dyes will be discussed.