Fig. 3.
Efficiency of energy transfer for Cy3, Cy5-labeled DNA duplexes as a function of duplex length. EFRET was measured for each duplex species, from an ensemble of molecules in the steady state (filled circles) or from phospholipid vesicle-encapsulated single molecules (open circles). Estimated errors are shown on the single-molecule data. The data have been simulated by using a model in which the fluorophores undergo a lateral motion within the plane perpendicular to the helical axis, giving a Gaussian distribution of probabilities about the mean relative angle set by the NMR structures. The fluorescent quantum yield for Cy3 was 0.30 (17), and the refractive index 1.33. The half-width giving the best agreement to the experimental data was 55°. Standard B form geometry of the DNA helix was used, with 10.5 bp per turn and a helical rise of 3.6 Å per bp step. The dependence for fully flexible fluorophore (κ2 = 2/3) is also plotted.