Figure 8. Ideal yield, efficiencies and dipole orientation.

(a) Yield of target structures as assessed by gel electrophoresis or fast protein liquid chromatography (FPLC) for multi-dye photonic wire structures and dendrimers with 0.5 × R₀ dye spacing (squares with solid lines) versus the number of arms or branching ratio, as compared with the corresponding yields derived from fitting the emission spectra when the structures are functionalized with either three or four dyes (circles with dashed lines). (b) Actual and ideal anywhere-to-end efficiency computed for the four-dye linear structures as a function of the number of arms with the dye spacing as a parameter. (c) Actual and ideal end-to-end efficiency computed for dendrimers as a function of branching ratio. Highlighting the importance of parallel FRET pathways, three ideal curves are shown, one assuming only nearest-neighbour FRET (schematically depicted inset, left), one including only intra-arm FRET (schematically depicted inset, right) and one including all FRET processes (ideal). (d) Actual and ideal antenna gains as computed for the four-dye linear structures and dendrimers with 0.5 × R₀ dye spacing. Note, the 0.5 × R₀ linear photonic wire structure corresponds to the one-arm dendrimer. (e) Effect of dipole orientation on FRET efficiency assuming ideal formation for the four-dye eight-arm star. Dipole orientation is either random (κ²=2/3) or for the parallel case dipoles on the same arm are coupled with κ²=4. Inset plot shows the same effect on efficiency assuming actual yield. (f) Anywhere-to-end efficiency as the inclination angle of the dyes with respect to the DNA axis varies for the four-dye eight-arm star at 1.0 × R₀ dye spacing, assuming ideal yield. Inset plot shows the difference between dynamic (assuming κ²=2/3) and static averaging, assuming ideal formation for a 0.75 × R₀ photonic wire assuming ideal yield as the number of dyes is increased from an initial Cy3–Cy3.5 configuration of two dyes with the addition of Cy5 (two dyes) and Cy5.5 (four dyes).