Nucleic acids do not absorb light in the range of wavelengths to which the human eye is sensitive and so cannot be visualized directly. A number of indirect methods have been employed to detect nucleic acids following electrophoresis, both within gels and on the surface of membranes after their transfer from gels. The three most common ways of detecting nucleic acids in gels are autoradiography, fluorescent dyes, and silver staining.

Autoradiography

Autoradiography is presently the most sensitive method for detecting nucleic acids following electrophoresis. For many situations the need for sensitivity outweighs the obvious disadvantages associated with handling radioactive materials. The fact that the useful life of the labeled DNA is governed by the half-life of the incorporated isotope is another disadvantage that must be considered. The most common isotopes for labeling nucleic acids are ³²P, ³⁵S, and ³³P.

Traditionally, autoradiography is performed by placing photographic film in contact with the gel surface. Radioactive emission of ß-particles forms a latent image of the bands in the gel by activating silver-halide crystals suspended in the film’s emulsion layer. Chemical reduction of the silver ions within the activated crystals to metallic silver produces a visible image of the bands in the gel. Phosphorescent intensifying screens placed behind the film can be used to amplify the signal several-fold by converting into light energy those particles passing through the film. Disadvantages of film-based autoradiography are the non-linearity and narrow dynamic range of the film’s response and the requirement for a darkroom and film-processing facility.

In the past decade, highly sensitive instruments based on phosphor-storage technology have become widely available. Rather than form a latent image of the gel within silver salts in a film emulsion, energy from radioactive decay is stored within phosphorescent minerals embedded in a reusable plate. Within the instrument this stored energy is released as light energy, which is then measured and converted to digital information. The broad linear dynamic range of phosphor-based imaging allows quantitative analysis in a single exposure of both very weak and very strong signals. These advantages, along with the immediate generation of a digital image format, are seen by many to outweigh the disadvantage of the high initial cost of a phosphor-storage instrument.
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