Abstract
Radical cation injection, transport, and reaction in DNA structures containing a triplex region were examined. An anthraquinone-linked polypyrimidine oligonucleotide was designed to form a pyrimidine· purine × pyrimidine (Y·R×Y) triplex. Spectroscopic and DNase I footprinting experiments verified triplex formation and indicated intercalation of the anthraquinone group at the triplex−duplex junction. Irradiation of the triplex at 350 nm (only the anthraquinone absorbs) leads to reactions at remote locations in both the duplex and triplex regions. These reactions are revealed as strand breaks by subsequent treatment of the irradiated samples with piperidine. Radical cations injected at the triplex−duplex junction migrate into and through the triplex region. The effect of cytosine protonation on radical cation migration and reaction was examined. These observations support the charge transport mechanism in DNA that we recently identified as phonon-assisted polaron hopping.
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