Fig. 2.
Simulation of the dependence of calculated efficiency of energy transfer between Cy3 and Cy5 terminally attached to duplex DNA as a function of the length of the helix. The calculations are based on the extremes of complete fluorophore mobility (κ2 = 2/3) and total rigidity of the fluorophore stacked on B form DNA. The latter calculations were performed for fluorophores lying in planes that are perpendicular to the helical axis (0°), or with the planes inclined to the axis by 10 or 20°. These calculations were based on a measured value of the spectral overlap integral J(λ) = 7.2 × 10−13 M−1 cm3, giving R0 = 60.1 Å when κ2 = 2/3. For the case of rigid and parallel fluorophores, the points plotted are the values for integral numbers of base pairs