Gel electrophoresis

Principles of DNA Gel electrophoresis

    Gel electrophoresis separates DNA fragments by size in a solid support medium (an agarose gel). DNA samples are pipetted into the sample wells, seen as dark slots at the top of the picture. Application of an electric current at the top (anodal, negative) end causes the negatively-charged DNA [remember it's an acid] to migrate (electrophorese) towards the bottom (cathodal, positive) end. The rate of migration is proportional to size: smaller fragments move more quickly, and wind up at the bottom of the gel.

is visualized by including in the gel an intercalating dye, ethidium bromide. DNA fragments take up the dye as they migrate through the gel.
Illumination with ultraviolet light causes the intercalated dye to fluoresce with a pale pink colour.

    Note that the larger fragments fluoresce more intensely. Although each of the fragments of a single class of molecule are present in equimolar proportions, the
smaller fragments include less mass of DNA, take up less dye, and therefore fluoresce less intensely. This is most evident in the lane at the extreme right, which shows a "ladder" set of DNA fragments of known size that can be used to estimate the sizes of the other unknown fragments.

All figure & text material © 2012 by Steven M. Carr