Detection of DNA in Agarose Gels

Abstract

Nucleic acids that have been subjected to electrophoresis through agarose gels may be detected by staining and visualized by illumination with 300-nm UV light. Methods for staining and visualization of DNA using either ethidium bromide or SYBR Gold are described here. The most convenient and commonly used method to visualize DNA in agarose gels is staining with the fluorescent dye ethidium bromide. Ethidium bromide can be used to detect both singleand doublestranded nucleic acids (both DNA and RNA). However, the affinity of the dye for single-stranded nucleic acid is relatively low and the fluorescent yield is comparatively poor. In fact, most fluorescence associated with staining single-stranded DNA or RNA is attributable to binding of the dye to short intrastrand duplexes in the molecules.