Using intercalated, covalently bound daunomycin as a redox probe, ground state charge transport in DNA films with a perturbation in base pair stacking was examined in comparison with breaks in the sugar-phosphate backbone. While the introduction of one or even two nicks in the sugar-phosphate backbone yields no detectable effect on electron transfer, a CA mismatch significantly attenuates the electron transfer yield. These results confirm that the base pair stack is the pathway for DNA-mediated charge transfer, not the sugar-phosphate backbone.