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What Happens to the Size of DNA Fragments as You Move from the Cathode to the Anode End of the Gel?

Agarose gel electrophoresis is a method used to visualize DNA as well as separate fragments of DNA by size. Electrophoresis utilizes an electrical field in order to separate electrically charged molecules. Deoxyribonucleic acid, or DNA, carries a net negative charge; this makes it possible to electrophoretically draw the molecules towards a positively charged pole. Agarose gel serves as the medium through which the DNA molecules migrate as they are separated by electrophoresis.

Loading the Gel
- Agarose gel electrophoresis separates DNA molecules based on the size of the fragments contained in the sample. Small holes at the top of the gel, called "wells," are loaded with the liquid containing the DNA to be examined. This end of the gel is placed at the anode, or negatively charged electrical source.
Small Fragments
- DNA fragments are drawn towards the cathode, or positively charged electrical source. As the molecules migrate through the agarose gel, they begin to separate according to size. The smallest fragments of DNA are those of the lowest molecular weight; these fragments are the quickest to migrate toward the cathode end of the gel.
Larger Fragments
- As fragments of DNA get bigger and have higher molecular weights, they are slower to move through the agarose gel towards the cathode; therefore, the largest fragments of DNA are found near the anode end of the gel, while the smallest fragments of DNA are found near the cathode end.
Visualization
- DNA fragments can be visualized under an ultraviolet light source by staining them with a special chemical called ethidium bromide. When exposed to u.v. light, fragmented DNA will appear in a ladder formation, with the heaviest and largest fragments of DNA at the top of the ladder and the lightest, smallest DNA fragments at the bottom of the ladder.

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