DNA electrophoresis is an analytical technique used to separate DNA fragments by size. An electric field forces the fragments to migrate through a gel. DNA molecules normally migrate from negative to positive potential due to the net negative charge of the phosphate backbone of the DNA chain. At the scale of the length of DNA molecules, the gel looks much like a random, intricate network. Longer molecules migrate more slowly because they are more easily 'trapped' in the network.
After the separation is completed, the fractions of DNA fragments of different length are often visualizing a fluorescent dye specific for DNA, such as ethidium bromide. The gel shows bands corresponding to different DNA molecules populations with different molecular weight. Fragment size is usually reported in "nucleotides", "base pairs" or "kb" (for 1000's of base pairs) depending upon whether single- or double-stranded DNA has been separated. Fragment size determination is typically done by comparison to commercially available DNA ladders containing linear DNA fragments of known length.
The types of gel most commonly used for DNA electrophoresis are agarose (for relatively long DNA molecules) and polyacrylamide (for high resolution of short DNA molecules, for example in DNA sequencing). Gels have conventionally been run in a "slab" format such as that shown in the figure, but capillary electrophoresis has become important for applications such as high-throughput DNA sequencing. Electrophoresis techniques used in the assessment of DNA damage include alkaline gel electrophoresis and pulsed field gel electrophoresis. The measurement and analysis are mostly done with a specialized gel analysis software Capillary electrophoresis results are typically displayed in a trace view called an electropherogram.
The DNA strand is cut into smaller fragments using a DNA restriction endonuclease, then samples of the DNA solution (DNA sample and buffer) are placed in the wells of the gel and allowed to run for some time (the less the voltage of the electophoresis, the longer time for the DNA sample to run through the gel, and this results in a more accurate separation).