In most molecular experiments, nucleic acids are subjected to agarose gel electrophoresis to determine the size of the molecule. The addition of a nucleic acid dye allows the nucleic acid to be detected under the UV image system after running the gel, so the nucleic acid dye is an integral part of the electrophoresis experiment. But when considering the mutagenicity and toxicity of nucleic acid dyes, one must be careful to insure the proper disposal of experimental waste. In this article, a new usage of nucleic acid dye in agarose gel electrophoresis is described where the nucleic acid dyes were added to the loading buffer and nucleic acid marker buffer. The results show that this method has advantages as: a smaller amount of dye can be used, there is less time in contact with the dye, and its operation is easier and reduces toxicity damage. Also the bands showed a much clearer image, having a lower background value. The improved method shows better results with lower toxicity and is superior to the traditional method.