Scientists often need to see whether DNA was successfully prepared from cells or tissues in evidence, how big the molecules are, and how much DNA is in the preparation. Gel methods are commonly used for these purposes. Gel methods provide a way of visualizing DNA.
DNA is a very large molecule that is highly negatively charged. As a result it can be moved by electrophoresis in a gel medium. Electrophoresis is a procedure that uses an electronic field to move big, charged molecules. Agarose gels (similar in consistency to Jell-O) provide a good medium for DNA movement in an electric field. An electrophoresis setup consists of the agarose gel placed in a chamber that separates a positive from a negative compartment and is filled with a solution containing charged particles. The diagram on page 33 shows an electrophoresis setup. A power supply sets up a current in the gel. DNA specimens placed in wells near the negative end will migrate toward the positive end, because DNA is very negatively charged and because unlike charges attract.
Different sized DNA molecules travel different speeds and distances. The larger the DNA molecule, the more slowly it migrates. Thus, the distance a DNA molecule travels gives an indication of how big it is. To help in these estimates scientists typically add standards and calibrators (proteins of known size) to the gel and run them along with the specimens. One factor affecting the size of DNA fragments is degradation. Environmental exposure can cause the DNA in a forensic specimen to degrade, to break into smaller fragments. As a result the specimen will contain an array of different sized DNA molecules. Whereas intact, undegraded DNA appears as a tight band on the agarose gel, degraded DNA is visible as a streak.
DNA is not, however, visible by itself, in a test tube, or on a gel. One must add another material to the DNA to make it visible, and certain dyes that can tuck themselves into the folds of the double helix are used for this purpose. When the DNA-dye complex is illuminated by ultraviolet (UV) light, the DNA fluoresces, so it can be seen. The gels themselves change and degrade over time, so they cannot be kept and stored. Consequently, lab scientists regularly take pictures of these UV illuminated gels to make a permanent record of the outcome of electrophoresis. Furthermore, photography can actually improve visibility of the results. The fluorescent DNA appears white on an otherwise black background in the photo, and it is sometimes easier to see things in the picture than on the gel itself.
