Irradiation of the anthraquinone derivative N,N-Bis(3-aminopropyl)-2-anthraquinonesulfonamide dihydrochloride (AQS2) when bound to DNA leads to strand cleavage, primarily at GG steps. The 1.8 Angstrom X-ray structure of AQS2 bound to the DNA duplex [d(CGTACG)](2) shows an intercalated, groove-reversed complex with the out-of-plane "swallow tail" located in the major groove. Two molecules of AQS2 bind with the chromophores intercalated at each CG step. Extensive guanine-AQS2 interactions are observed in the intercalated complex, indicating that the ground-state anthraquinone and DNA are poised for efficient electron transfer after photoexcitation. AQS2 engages in guanine-selective van der Waals contacts and molecular orbital overlap. Molecular orbitals, calculated using coordinates of the X-ray structure, confirm the extensive electronic overlap between the redox partners. The bases adjacent to the intercalation site are well-stacked. The structure supports a model in which electron transfer from base to AQS2 and hole migration within DNA require significant electronic overlap.