Oxygen and nitroaromatic compounds are known to enhance the sensitivity of cells to ionizing radiation. Employing calf thymus DNA and oligo(dA)12/poly(dT), we have examined the differences to DNA damage, in particular thymine glycols and the 3'-DNA termini at strand breaks, arising from irradiation under anoxic and oxic conditions and the presence and absence of misonidazole [1-(2-nitro-1-imidazoyl)-3-methoxy-2-propanol]. We show that (i) irradiation under nitrogen generates strand breaks almost exclusively with 3'-phosphate termini; (ii) irradiation under oxic conditions increases the yield of strand breaks 3-fold, and the 3' termini consist of 3'-phosphoglycolate and 3'-phosphate end groups in a ratio of approximately 1.6; (iii) the patterns of base and sugar damage detectable by a postlabeling assay [Weinfield, M., & Soderlind, K.-J. (1991) Biochemistry 30, 1091-1097] differ completely between DNA irradiated under oxic vs anoxic conditions; (iv) the presence of misonidazole under anoxic conditions does not increase the level of strand breakage but, like oxygen, significantly enhances the formation of 3'-phosphoglycolate end groups; (v) the presence of misonidazole during anoxic irradiation does not increase the yield of any other type of 'oxic' damage detectable by the postlabeling assay, such as thymine glycols; and (vi) misonidazole at concentrations greater than 50 microM affords significant protection to naked DNA, probably by OH radical scavenging, and both the nitroaromatic ring and methoxyisopropanol side chain contribute to this protective action.