Information concerning the mechanism of electrophoretic DNA separation provided by quantitative video-epifluorescence microscopy.

Changes in conformation, length, and mobility of individual DNA molecules during agarose gel electrophoresis were measured using video micrographs obtained by epifluorescence microscopy. Globular, V-shaped, and linear conformations of DNA are found. The mobility, upon transformation from the globular to the V-shaped conformation, decreases, suggesting a collision with a gel fiber. The duration of interaction between DNA and gel fiber is proportional to the length of DNA. Hypothetically, this proportionality underlies the size separation of DNA by agarose gel electrophoresis. DNA release from the gel fiber appears to involve the movement of the arms of the V-shaped molecule around the gel fiber. Concomitant with this movement is a length reduction the degree of which is constant for DNA of various lengths in a particular buffer milieu. The luminant densitometric profiles of DNA molecules in the V conformation show maxima at the ends and apex of the V. The unequal distribution of nucleotides along the DNA chain appears to provide the driving force for the molecular movement around the gel fiber.