Counterion-dye staining method for DNA in agarose gels using crystal violet and methyl orange

Sensitive and safe methods for visualization of DNA in agarose gels are des cribed. 0.001 % crystal violet dissolved in distilled water was used for DN A staining on agarose gels and it could detect as little as 16 ng of DNA (3 kb, pGem-7Zf/EcoRI) without destaining procedure. The detection limit is f our times lower than that of ethidium bromide. To improve the sensitivity, we studied a counterion-dye staining method using methyl orange as a counte rion-dye which contributes to reduce excessive background staining by cryst al violet. Dye concentration, pH of staining solution, mixing molar ratio o f two dyes, and staining times were optimized for the counterion-dye staini ng. By the staining with a mixed solution of 0.0025% crystal violet and 0.0 005% methyl orange in distilled water, 8 ng of the 3 kb DNA in an agarose g el was detected within 30 min.