The easiest way to see the results of a gel electrophoresis experiment is to stain the gel with a nucleic acid stain. Ethidium bromide (EtBr) is a common stain in agarose and polyacrylamide gels. EtBr binds to DNA molecules by intercalating between adjacent base pairs and emits an intense red-orange fluorescence under UV light. Bands represent the positions of the different size of DNA fragment. However, EtBr is a powerful mutagen with limited sensitivity.
For safety and environmental reasons, non-mutagenic dyes become popular. Most of these dyes can be used as a stain after electrophoresis or as a component in buffer solutions in gel preparation to dissolve agarose or polyacrylamide. Some dyes require UV irradiation to make the bands visible, but others are visualized under other wavelengths of light, for example, blue light, eliminating the danger of possible exposure to UV.
We offer highly sensitive reagents for staining DNA in electrophoresis gels with higher safety than conventional EtBr staining.
The separation matrixes of nucleic acid electrophoresis include agar, agarose, polyacrylamide, and composite agarose-acrylamide gels. Among them, agarose and polyacrylamide are the two most used gels in nucleic acid electrophoresis. Polyacrylamide gels are suitable for separating nucleic acid molecules smaller than 1000 bp.
Nucleic acid fragment size is usually reported in "nucleotides", "base pairs (bp)" or "kb” depending upon whether single- or double-stranded nucleic acid has been separated. Fragment size is usually determined by comparison with nucleic acid standards that contain fragments of known length.