FRET-based microscopy techniques detect the result of energy transfer between fluorophores that label proteins inside living cells. The efficient transfer of energy requires that donor and acceptor fluorophores are in close proximity (<80 Å), and that there is a substantial overlap of the donor emission and acceptor absorption spectra. This spectral overlap, however, limits FRET measurements because it contributes a significant spectral bleed-through (SBT) background to the FRET signal. Image processing to remove the SBT background based on reference images acquired from separate control cells is commonly used to determine FRET efficiency, but these approaches vary in their accuracy7. An alternative technique, acceptor photobleaching FRET (apFRET), measures de-quenching of the donor signal after selective bleaching of the acceptor to determine the proportion of donor energy that was lost to FRET8,9. Because each cell serves as its own control, apFRET does not require separate measurements from reference cells. Measurements of dynamic interactions between proteins, however, require an approach that combines both kinetic microscopy and FRET measurements.
The PQ-FRET approach takes advantage of the kinetic measurements made possible by PA-GFP, and uses the activated PA-GFP as a FRET acceptor for CFP. The Förster distance (R0) for this pair, determined from their spectral overlap integral8,9 is approximately 41 Å. Upon photoactivation, PA-GFP provides an absorbing species for energy transfer that can quench the CFP signal, with added benefit that PA-GFP allows the monitoring of protein mobilities. The quenching of CFP by the activated PA-GFP provides a measure of FRET that does not require correction for SBT. Further, each cell serves as its own control, allowing small changes in donor signal to be accurately measured. To illustrate the application of the PQ-FRET technique, we demonstrate measurements of the dynamic interactions between the transcription factor C/EBPα and the heterochromatin binding protein HP1α.
We first determined that mobility measurements made with photoactivation of PA-GFP-HP1α were comparable with those made by monitoring FRAP (Fig. 2). These experiments, which showed the rapid diffusion of HP1α throughout the nuclear compartment, reaching equilibrium in about 25 s, allowed us to define the time lapse conditions necessary to acquire the photoquenching data (steps 7-15 above). The cells that co-expressed PA-GFP-HP1α and CFP-C/EBPα were selected based on CFP fluorescence (Fig. 3a). The PA-GFP-HP1α was then photoactivated in a discrete spot, and the intensity of CFP-C/EBPα was monitored over time in several different ROI in the cell nucleus (Fig. 3a). The results show that after a brief delay following photoactivation (about 1, 2, and 4 s for ROI 1, 2 and 3, respectively, Fig. 3b), the CFP labeling C/EBPα was rapidly quenched by the activated PA-GFP-HP1α. The quenching of CFP measured in the different regions of the nucleus varied between 5% to 12 % depending on the final ratio of PA-GFP to CFP (IA/ID) in each ROI (Fig. 3b) with a mean halftime to steady state of about 1 s. To demonstrate that the quenching of CFP-C/EBPα by PA-GFP-HP1α was specific, we imaged cells under identical conditions that co-expressed PA-GFP-HP1α and CFP-promyelocytic leukemia (PML) protein, which forms distinct PML bodies in the cell nucleus10.
Although there was overlap in the distribution of HP1α and PML, these proteins clearly occupied distinct subnuclear domains, and there was no change in the CFP signal over the full time course of the photoactivation and diffusion of PA-GFP-HP1α (Fig. 3c,d). In addition, control experiments with cells that expressed the CFP-fusion protein alone showed that CFP was not photobleached under the laser power and scanning conditions used1. Importantly, we also verified our PQ-FRET measurements by donor fluorescence lifetime measurements. The measurement of donor fluorescence lifetime, the average time a population of fluorophores spends in the excited state, provides one of the most direct measures of energy transfer8,9. Because energy transfer dissipates the excited-state energy of the donor, its fluorescence lifetime is shortened in the presence of acceptor. We used time-correlated single photon counting fluorescence lifetime imaging microscopy (FLIM) to detect changes in donor lifetime following the photoactivation of PA-GFP1. The time-domain FLIM measurements from cells expressing CFP-C/EBPα alone indicated an average fluorescence lifetime of about 2.14 ns, which was unaffected by the photoactivation protocol. For cells that co-expressed CFP-C/EBPα and PA-GFP-HP1α, upon photoactivation of PA-GFP the mean CFP lifetime distribution was shifted to shorter times (1.82 ns)1. Together, these results show the utility of PQ-FRET method for measuring the dynamic interactions of proteins in living cells.
Three different parameters could be determined from these measurements. First, the diffusion of PA-GFP-HP1α reflects the mobility of the HP1α within the nucleus. Second, the rate of quenching of the CFP-C/EBPα provided a measure of how rapidly the PA-GFP-HP1α exchanged with both the non-activated PA-GFP-HP1α and the endogenous HP1 proteins. Third, the steady-state level of CFP quenching indicated the FRET efficiency at a particular donor/acceptor ratio. This method showed that the association between C/EBPα and HP1α was extremely dynamic. Following a brief delay after photoactivation of PA-GFP-HP1α there was a rapid quenching of the CFP-C/EBPα. The kinetics reflected the mobility of PA-GFP-HP1α within the 3D volume of the nucleus, as well as its rapid exchange within protein complexes. The PQ-FRET assay provides a new approach to directly study the dynamic interactions of proteins in living cells. This method has distinct advantages over sensitized emission and photodestructive approaches typically used to measure FRET. First, unlike FRET measurements of sensitized emission from the acceptor, the detection of donor quenching does not require correction for the SBT background. Second, in contrast to photodestructive methods like apFRET, PQ-FRET uses photoactivation of the acceptor in a single discrete region of the cell, allowing the dynamic process of donor quenching to be monitored in real time in the entire cell compartment.