A new DNA molecule is like uncharted territory to a scientist. Like any explorer, the first thing a scientist does with new territory is to map its important features, such as size and the relative locations of certain parts. Maps of DNA are called restriction maps, named for the enzymes used as mapping tools.
Restriction enzymes are proteins produced by bacteria.
They act as a very primitive type of bacterial immune system. Working out the locations of the different restriction sites is a problem in logic. Doing a restriction enzyme digest with a single enzyme, for example, only tells you how many sites are present for that enzyme. Doing restriction digests with more than one enzyme at a time can give clues as to where those restriction sites are in relation to each other. First, you examine a mock gel to compare the DNA fragments from restriction digests of the unknown DNA to DNA fragments of known sizes.