Principle of Gel Electrophoresis
As mentioned previously, gel electrophoresis involves using an electrical field to separate proteins and nucleic acid fragments based on size, charge, or conformation. This field is typically generated in an electrophoretic chamber (e.g., a hard plastic tank), commonly known as a gel box (Figure 1).
Figure 1. An illustration of gel electrophoresis workflow (figure made in BioRender).
Types of Gel Electrophoresis
The two most common gel electrophoretic methods include agarose gel electrophoresis for separating nucleic acids and polyacrylamide gel electrophoresis (PAGE) for separating proteins, and nucleic acid fragments 500 base pairs or less. The following table summarizes key differences between agarose and polyacrylamide gel electrophoresis.
Table 1. Summary of the key differences between agarose and polyacrylamide gel electrophoresis.
Visualizing DNA Samples After Separation
After separation by electrophoresis, nucleic acid fragments can be visualized using several different methods. The most well-known method for visualizing nucleic acid fragments is staining with ethidium bromide (EtBr). However, because EtBr is highly carcinogenic, cytotoxic, and mutagenic. It is environmentally hazardous and must be handled and disposed of carefully. Safer alternatives to EtBr include novel gel stains, such as Gelite™ Safe *10,000X Water Solution*, Gelite™ Safe *10,000X DMSO Solution*, Helixyte™ Green and Helixyte™ Gold, and gel staining kits, such as Gelite™ Green Nucleic Acid Gel Staining Kit and Gelite™ Orange Nucleic Acid Gel Staining Kit. Not only are these gel stains and kits less mutagenic than EtBr, but Gelite™ Safe, Helixyte™ Green, Helixyte™ Gold, and Gelite™ nucleic acid staining kits can detect nucleic acids in both agarose and polyacrylamide gels, with greater sensitivity and less background interference.
Gelite™ Safe – the most sensitive and robust DNA gel stain
Gelite™ Safe is an extremely sensitive and stable fluorescent dye for visualizing DNA in electrophoretic gels. Unlike the highly-toxic EtBr, Gelite™ Safe is explicitly designed to be less hazardous, non-cytotoxic, and non-mutagenic, providing greater sensitivity and lower background fluorescence than EtBr and SYBR® Safe. The strong DNA binding affinity of Gelite™ Safe allows for DNA to be stained before or post electrophoresis without destaining, and because Gelite™ Safe is specific to DNA, applications in which RNA is present in the sample will not obscure results. Gelite™ Safe has fluorescence excitation maxima at 280 nm and 513 nm and a broad emission profile with a maximum at 552 nm. These unique spectral properties broaden the instrument compatibility of Gelite™ Safe to include UV and blue-light transilluminators, gel documentation systems, and laser scanners, and its single formulation design allows for detection in both the green or red channels at your convenience.
Table 1. Nucleic acid stains for agarose and polyacrylamide gel electrophoresis