fluorescence resonance energy transfer (alsoknown as F€orster-type resonance energy transfer, FRET) wasdescribed as a physical phenomenon in the middle of the20th century (1), it was an unrecognized tool in biology tillthe 1970s, when Stryer coined the term ‘‘spectroscopic ruler’’to describe the unique capability of FRET to be used as adistance measuring method (2). Despite these initial ad-vances, FRET was regarded as a research method forcomputer and engineering geeks until the 1990s. The intro-duction of fluorescent monoclonal antibodies, green fluores-cent protein derivatives, the development of FRET applica-tions for flow cytometry (3,4), digital imaging microscopy(5,6), and the wide-spread availability of fast computers andflexible evaluation softwares turned FRET into a fashionabletechnique.In FRET, a fluorescent donor interacts with an acceptormolecule which is separated by 2–10 nm from the donor.The interaction results in the transfer of the donor excita-tion energy to the acceptor manifested in, among others,quenching of donor fluorescence and enhancement, or sen-sitization of acceptor fluorescence (7). FRET efficiency issupposed to be dependent only on the donor–acceptor dis-tance, a property one expects from a ‘‘spectroscopic ruler.’’Although in most cases this approximation is acceptable,the validity of the underlying assumption of dynamic aver-aging has to be verified, because if not fulfilled, FRET alsocorrelates with the relative orientation of the donor and theacceptor (8).Early approaches of FRET directly measured the donor-sensitized emission of the acceptor by using special narrowband-pass filter sets to eliminate spectral overspill between thedonor, FRET, and acceptor channels (9). Even today, the litera-ture abounds with methods using FRET intensity (fluores-cence measured in the FRET channel) or uncalibrated FRETparameters. It is highly advisable to use the calibrated FRETef-ficiency instead of enigmatic and dubious parameters to pre-vent drawing false conclusions. As the development in thisarea accelerates, new methods have been described for theaccurate calculation of FRET efficiency between GFP variants(10), to account for the presence of free donors and acceptors(11) and to describe the proximity relationship of more thantwo epitopes (12,13). The fact that FRET reports the distancebetween the donor- and the acceptor-tagged epitopes, i.e., theconformation of the protein, in real-time in living cells madeit possible to solve the three-dimensional structure of mem-brane receptor complexes in intact cells (14). FRET is oftenused as a read-out parameter in assays in which the conforma-tion of a sensor is affected by a protease, ligand, or ion. Thecombination of three fluorophores in a single FRET-basedsensor makes simultaneous measurement of two parameterspossible (15).In the post-genomic era, the protein interactome is gain-ing more importance. Techniques used for the realization ofhigh-throughput mapping of protein interactions (e.g., yeasttwo-hybrid, fluorescence complementation) are now supple-mented by FRET-based sorting of cells in which certain pro-
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