FIG. 1.
Labeling chemistry and nomenclature of the internal (iCy3)2 dimer probes positioned within the sugar–phosphate backbones of model ss–dsDNA fork constructs. (a) The Lewis structure of the iCy3 chromophore is shown with its 3′ and 5′ linkages to the sugar–phosphate backbone of a local segment of ssDNA. The double-headed green arrow indicates the orientation of the electric dipole transition moment (EDTM). (b) An (iCy3)2 dimer-labeled DNA fork construct contains the dimer probe near the ss–dsDNA fork junction. The conformation of the (iCy3)2 dimer probe reflects the local secondary structure of the sugar–phosphate backbones at the probe insertion site position. The sugar–phosphate backbones of the conjugate DNA strands are shown in black and blue, the bases are shown in gray, and the iCy3 chromophores are shown in green. (c) The structural parameters that define the local conformation of the (iCy3)2 dimer probe are the inter-chromophore separation vector RAB, the tilt angle θAB, and the twist angle ϕAB. The electrostatic coupling between the iCy3 chromophores gives rise to the anti-symmetric (−) and symmetric (+) excitons, which are indicated by the red and blue arrows, respectively, and whose magnitudes and transition energies depend on the structural parameters. (d) The insertion site position of the iCy3 dimer probe is indicated relative to the pseudo-fork junction using positive integers in the direction toward the double-stranded region and negative integers in the direction toward the single-stranded region.