There are a few basic tools commonly used in the world of molecular biology. All together and in various combinations, they make up the bulk of our toolbox for studying genes and gene expression. One of these tools is electrophoresis. Electrophoresis is the process of separation in an electric field. It allows molecules to be separated, or sorted, in some kind of matrix based on how they migrate towards a positive or negative charge. A typical matrix to sort DNA is agarose. The agarose forms a "gel" that appears solid, but has small pores through which molecules can travel. DNA is first loaded into slots in the agarose gel. The buffer solution keeps the DNA mobile allowing it to migrate though the pores in the agarose. When the electric current is turned on, the DNA, which is negatively charged because of its molecular structure containing many negatively-charged phosphate groups, will move toward the positively charged pole. The gel acts as a sieve to separate the DNA fragments based on their size. Small pieces move through easily, larger pieces are caught and held in the pores of the gel matrix.

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