<P> Since EtBr stained DNA is not visible in natural light, scientists mix DNA with negatively charged loading buffers before adding the mixture to the gel . Loading buffers are useful because they are visible in natural light (as opposed to UV light for EtBr stained DNA), and they co-sediment with DNA (meaning they move at the same speed as DNA of a certain length). Xylene cyanol and Bromophenol blue are common dyes found in loading buffers; they run about the same speed as DNA fragments that are 5000 bp and 300 bp in length respectively, but the precise position varies with percentage of the gel . Other less frequently used progress markers are Cresol Red and Orange G which run at about 125 bp and 50 bp, respectively . </P> <P> Visualization can also be achieved by transferring DNA after SDS - PAGE to a nitrocellulose membrane followed by exposure to a hybridization probe . This process is termed Southern blotting . </P> <P> For fluorescent dyes, after electrophoresis the gel is illuminated with an ultraviolet lamp (usually by placing it on a light box, while using protective gear to limit exposure to ultraviolet radiation). The illuminator apparatus mostly also contains imaging apparatus that takes an image of the gel, after illumination with UV radiation . The ethidium bromide fluoresces reddish - orange in the presence of DNA, since it has intercalated with the DNA . The DNA band can also be cut out of the gel, and can then be dissolved to retrieve the purified DNA . The gel can then be photographed usually with a digital or polaroid camera . Although the stained nucleic acid fluoresces reddish - orange, images are usually shown in black and white (see figures). UV damage to the sample can reduce the efficiency of subsequent manipulation of the sample, such as ligation and cloning . This can be avoided by using a blue light excitation source with a blue - excitable stain such as SYBR Green or GelGreen . </P> <P> Gel electrophoresis research often takes advantage of software - based image analysis tools, such as ImageJ . </P>

Why do some pieces of dna move faster and therefore further through the agarose gel