The structure and electronic spectra of six DNA conjugates possessing two face-to-face perylenediimide (PDI) chromophores have been investigated. Structures of hairpins possessing two adjacent PDI base analogues opposite a tetrahydrofuran abasic site on the same or opposite strands were simulated using molecular dynamics. These structures are compared with those previously reported for a duplex and hairpin dimer possessing PDI linkers. The minimized structures all have face-to-face PDI geometries but differ in the torsional angle between PDI long axes and the offset between PDI centers. These structures provide the basis for analysing differences in the electronic spectra of the PDI dimers both in the ground state (UV-Vis and circular dichroism spectra) and excited state (fluorescence and transient absorption) determined in aqueous buffer and in the denaturing solvent dimethyl sulfoxide. PDI dimers with rigid structures and large PDI-PDI torsional angles display large effects of exciton coupling in their UV-Vis and CD spectra and also display split transient absorption bands; whereas PDI dimers with smaller PDI-PDI torsional angles and flexible structures display weaker UV-Vis and CD exciton coupling and a single transient absorption band. The excimer fluorescence maxima and decay times for all of these DNA-PDI constructs are similar.
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