Composite sequence-specific ligands with DNA-damaging groups may dramatically increase the efficacy of radiotherapy. The most promising damage sensitizers are the atoms of heavy elements, in which electrons are emitted from upper orbitals and a multiply charged positive ion forms when an electron is kicked out from lower orbitals. The biophysical mechanisms of DNA damage produced by these sensitizers are far from fully understood. In this work, high-performance polyacrylamide gel electrophoresis (PAGE) in denaturing gel was used to investigate the nature of DNA cleavage on exposure to β radiation for complexes of heavy atom-containing ligands with DNA restriction fragments. It was demonstrated for the first time that DNA in complexes with Pt-bis-netropsin or mercury salts is cleaved in the vicinity of the heavy atom in the presence of radioactive isotopes emitting β particles of different energies. In the presence of 1 M glycerol, the cleavage of the DNA sugar-phosphate backbone was almost entirely due to a neutralization of the multiply charged Auger ion and was not associated with the Auger electron electron-beam radiolysis. Based on the observations, a relatively simple technique was proposed for precise localization of binding sites for various DNA ligands containing a heavy atom. Analysis of the end groups at the cleavage point and the nature of damage to the complementary DNA chain made it possible to speculate about the mechanisms of direct influence of irradiation on a heavy atom.