VISUALIZATION OF DNA IN AGAROSE GELS AS MIGRATING COLORED BANDS - APPLICATIONS FOR PREPARATIVE GELS AND EDUCATIONAL DEMONSTRATIONS

Visualization of DNA in electrophoretic gels typically requires UV rad iation and the fluorescent dye ethidium bromide. Alternatively, we rep ort here that by inclusion of visible dyes in standard agarose gels, D NA bands are observable in ambient light as they are separating. Such bands can be directly recovered from gels (approximately 50% yield) an d used in standard enzymatic reactions (ligation, endonucleolytic clea vage, random labeling, PCR, and cycle-sequencing) without purification . Of 14 common commercially available stains that could visualize frac tionating DNA, Nile blue was chosen for more extensive analysis as it gave the sharpest and most persistent bands and is not known to be tox ic. Bands containing greater than 40 ng DNA could be detected by direc t visual inspection of gels during electrophoresis. Drying the gels in creased sensitivity to 4 ng. We describe relevant molecular features o f these dyes and detail simple assays that may be employed to find oth er useful, and perhaps superior, dyes. This method also lends itself t o situations in which easy visualization and convenience of DNA electr ophoresis are important, such as classroom demonstrations. (C) 1996 Ac ademic Press, Inc.