Cloning and Expression of DNA Binding Domains Using PCR

Many DNA binding proteins are known to consist of a number of domains-discrete compact regions of a protein that often have distinct functional properties. Structural domains within a protein are generally indicated by limited proteolysis (see Chapter 13 ) and the existence of functional domains can often be tested by genetic experiments (e.g., “domain swapping”). In favorable cases, sequence homologies may also provide circumstantial evidence for domains. Once the existence of domains has been established, one may wish to express them in large quantities for structural analysis, for example, using X-ray crystallography or NMR. The domains may be more soluble than the intact protein, or have other physical properties that are advantageous. Because of their smaller size, structure determination is also likely to be more feasible. Limited proteolysis is an excellent analytical technique for the investigation of domain structure. However, it is inefficient for the large scale production of protein fragments. Cleavage is rarely at unique sites; often a number of proteolytic fragments are produced that may require extensive purification. For such studies, it is clearly an advantage to over-express the truncated proteins directly.