Radical cation injection, transport, and reaction in DNA structures containing a tripler region were examined. An anthraquinone-linked polypyrimidine oligonucleotide was designed to form a pyrimidine purine x pyrimidine (Y.R x Y) tripler. Spectroscopic and DNase I footprinting experiments verified tripler formation and indicated intercalation of the anthraquinone group at the tripler-duplex junction, irradiation of the tripler at 350 nm (only the anthraquinone absorbs) leads to reactions at remote locations in both the duplex and tripler 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 tripler 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.