A general approach for the sequential labeling of fusion proteins of O 6 -alkylguanine-DNA alkyltransferase (AGT) with different fluorophores in mammalian cells is presented. AGT fusion proteins with different localizations in the cell can be labeled specifically with different fluorophores, and the fluorescence labeling can be used for applications such as multicolor analysis of dynamic processes and fluorescence resonance energy transfer measurements. The facile access to a variety of different AGT substrates as well as the specificity of the labeling reaction should make the approach an important tool to study protein function in live cells.A dvances in fluorescence microscopy and the isolation and engineering of different autofluorescent proteins have revolutionized the way protein function is studied in the living cell (1-3). Beyond localization studies, fusion proteins of autofluorescent proteins can be used to study dynamic processes, follow conformational changes, and detect protein-protein interactions (1, 2, 4). Despite this enormous range of applications for autofluorescent fusion proteins, there are two reoccurring limitations of the approach. The first limitation is the restriction to the fluorophores of the existing autofluorescent proteins. Properties such as emission and excitation wavelength, extinction coefficient, and photostability are characteristic properties of each autofluorescent protein that do not necessarily match the requirements of the envisioned application. The second limitation is caused by the fusion of the autofluorescent protein to the protein of interest. In general, autofluorescent proteins possess a molecular mass of Ͼ25 kDa, and certain autofluorescent proteins furthermore form oligomers, raising the question of to what extent the creation of a fusion protein affects the function of the protein of interest (1, 3).Alternative approaches to make proteins amenable to fluorescence studies in live cells include introduction of chemically labeled proteins through invasive techniques such as microinjection, site-specific incorporation of unnatural fluorescent amino acids, and the selective labeling of fusion proteins (5-10). An example of the latter approach is the so-called tetracysteine tag, which reacts with biarsenical fluorophores to form stable and highly fluorescent complexes (7,8). We recently developed an approach that allows for the labeling of fusion proteins of human O 6 -alkylguanine-DNA alkyltransferase (AGT) with synthetic molecules (9). The labeling is based on the irreversible and specific reaction of AGT with O 6 -benzylguanine (BG) derivatives, leading to the transfer of the synthetic probe to a reactive cysteine residue (Fig. 1). Wild-type human AGT is a monomeric protein of 207 aa, the 30 C-terminal residues of which can be deleted without affecting the activity against BG, making it slightly smaller than autofluorescent proteins (11). Importantly, the rate of the reaction of AGT fusion proteins with BG derivatives is independent of the nature of the label, o...