It is now technically possible to create any desired mutation in a given DNA sequence. So-called site-directed mutagenesis allows the introduction of designed mutations into specific locations. This approach is invaluable for studying gene regulation as well as for functional assessment of proteins and their interactions. Several protocols have been successfully employed to generate such mutants. Here I describe a “linker-scanning” method that I have used to systematically mutate the murine major histocompatibility complex (MHC) class II Eα gene promoter (Fig. 1 , ref. 1 ).