The purpose of our studies is to elucidate the kinetics of DNA strand breaks caused by low-energy Auger electron emitters in close proximity to DNA. Previously we have studied the DNA break yields in plasmids after the decay of indium-111 bound to DNA or free in solution. In this work, we compare the DNA break yields in supercoiled DNA of iodine-125 decaying close to DNA following DNA intercalation, minor-groove binding, or surface binding, and at a distance from DNA. Supercoiled DNA, stored at 4 degrees C to accumulate radiation dose from the decay of 125I, was then resolved by gel electrophoresis into supercoiled, nicked circular, and linear forms, representing undamaged DNA, single-strand breaks, and double-strand breaks respectively. DNA-intercalated or groove-bound 125I is more effective than surface-bound radionuclide or 125I free in solution. The hydroxyl radical scavenger DMSO protects against damage by 125I free in solution but has minimal effect on damage by groove-bound 125I.