Pure and Applied Chemistry

Abstract: Short DNA duplexes can be stabilized by the presence of organic chromophores, which serve as hairpin linkers or end-capping groups. Capped hairpins possessing one or more base pairs form stable folded structures in aqueous solution. Increasing the number of base pairs separating the two chromophores increases both the distance between the two chromophores and the dihedral angle between their electronic transition dipoles. Thus, duplex DNA can serve as a helical scaffold for the study of electronic interactions between two chromophores. Three types of electronic interaction have been investigated: (a) exciton coupling (EC) between two identical chromophores, as probed by exciton-coupled circular dichroism (EC-CD); (b) fluorescence resonance energy transfer (FRET) between a fluorescent donor and acceptor; and (c) photoinduced electron transfer (PET) between an electron donor and acceptor. EC and the efficiency of fluorescence energy transfer are dependent upon both the distance and dihedral angle separating the two chromophores. Electron transfer occurs via both single-step superexchange and bridge-mediated hopping mechanisms, neither of which displays angular dependence. The competition between these mechanisms is dependent upon both the energetics of hole injection into the base-pair bridge and the distance between the donor and acceptor chromophores, superexchange dominating at short distance and hole hopping at longer distances.