FIG. 1.
Model structure of the internally labeled (Cy3)2 dimer in dsDNA. (a) The structural formula of the internally labeled Cy3 chromophore is shown with its insertion linkages to the 3′ and 5′ segments of the sugar-phosphate backbone of ssDNA. A green double-headed arrow indicates the orientation of the electric dipole transition moment (EDTM), which lies parallel to the plane of the trimethine bridge. (b) A dsDNA segment formed from two complementary DNA strands, where each contains an internally labeled Cy3 chromophore, serves as a scaffold to hold the (Cy3)2 dimer in place. Space-filling structural models performed using the Spartan program (Wavefunction, Inc.) suggest that the dimer exhibits the same approximate D2 symmetry as right-handed (B-form) helical dsDNA. The sugar-phosphate backbones of the conjugate strands are shown in black and blue, the bases are shown in gray, and the Cy3 chromophores are shown in green. Additional space-filling renderings of the structure are presented in Fig. S5 of the supplementary material.