End-to-end diffusion coefficients and distance distributions from fluorescence energy transfer measurements: Enhanced...

We describe a method to improve the resolution of donor-to-acceptor distance distributions in molecules which are flexing on the timescale of the fluorescence lifetime. We measured the timedependent donor decays of two donor (D)-acceptor (A) pairs, where the donor lifetimes were substantially different. The donors were an indole residue (5.7 ns) and a naphthalene residue (24.4 ns). The same dansyl acceptor was used for both D-A pairs. The donor decays are complex due to both a distribution of D-A distances and D-A diffusion. Using the donor decay data for each D-A pair alone, it is difficult to resolve both the distance distribution and the D-to-A diffusion coefficient. However, these values are unambiguously recovered from global analysis of the data from both D-A pairs. The increased resolution from the global analysis is apparently the result of the complementary information content of the data for each D-A pair. The shorter-lived indole donor provides more information on the time-zero distance distribution because there is less time for D-A diffusion, and the longer-lived naphthyl donor is quenched to a greater extent than indole due to the longer time for diffusion-enhanced energy transfer. Simulations were also used to demonstrate the increased resolution of global analysis with different lifetime donors to obtain distance distribution parameters in the presence of D-A diffusion.