A general method for covalent labeling of fusion proteins in vivo that complements the existing methods for protein labeling in vivo and in vitro is presented. This new method might lead to new ways of studying and manipulating proteins in living cells. Covalent attachment of the small mol. to the fusion protein is achieved by the unusual mechanism of the human DNA repair protein O6-alkylguanine-DNA alkyltransferase, which irreversibly transfers the alkyl group from its substrate, O6-alkylguanine-DNA, to one of its cysteine residues. The applicability of the method in different organisms and its independence of the nature of the label should make this method an important tool for functional studies of proteins in the living cell. [on SciFinder (R)]