Gel Electrophoresis

Gel electrophoresis is a technique used to separate a mixture of digested DNA fragments. An electrical field is used to move the negatively charged DNA molecules through porous agarose gel. Fragments of the same size and shape move at the same speed, and because smaller molecules travel faster then larger molecules, the mixture is separated into bands.

  

Figure: gel electrophoresis

The amount of exposure the DNA receives to restriction enzymes determines the portion of possible sites that were actually separated. Therefore, by applying different exposures to the same DNA sequence, we can measure all possible lengths of DNA fragments, that one can obtain using a particular enzyme. From this information we can attempt to find out where the sites are located in the original molecule. This problem is known as: