In gel electrophoresis, DNA fragments move through a porous matrix made of agarose, a gelatin-like substance purified from seaweed. The agarose is melted like Jell-O® and then poured into a plastic tray to harden into a slab called a gel. A plastic comb inserted at one end while the gel is hardening forms wells where DNA samples can be placed. The DNA is mixed with a loading buffer that contains glycerol—this makes it heavier than water, so it will sink to the bottom of the well. The gel is then covered with a buffer solution that can carry electric current, and electrodes are placed at each end of the gel and connected to a power supply. Because DNA is negatively charged (each nucleotide has a negatively charged phosphate attached to it), it will move toward the positive electrode. Larger molecules move through the agarose more slowly, while smaller ones can slip through the pores faster. So, the
fragments wind up arranged in order
according to size, with the smaller ones
having moved farther toward the positive
pole. Figure 47 shows an example.
Because the DNA is invisible, the loading
buffer also contains two dyes:
bromophenol blue (a small dye molecule
that behaves like a DNA fragment about
600 bases long) and xylene cyanol (a
larger dye that acts like a DNA fragment of
about 4000 bases). These dyes form lines
that give you an idea of how far your DNA
has moved. Some loading buffers also
have a third dye, behaving like a very
small DNA molecule (50 bases or so).
As the DNA migrates, the different fragments will form bands; each band is composed of many identical copies of a particular-size piece of DNA (you can’t do gel electrophoresis with one DNA molecule: you need millions or billions of identical molecules). The last step is to make the DNA bands visible, using a fluorescent molecule that inserts between the bases in the DNA helix. We use a commercial loading buffer called EZ-Vision which includes the fluorescent molecule, so the gel is...
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