Dimethyl sulfoxide (DMSO) is frequently used as a solvent for many water-insoluble drugs in biological studies at concentrations often up to 1%. However, little is known about its effects on oxidatively generated DNA damage at very low concentrations (0.005-0.5%). This study was undertaken to investigate the effects of DMSO on peroxynitrite-induced DNA strand breaks, a critical event leading to peroxynitrite-elicited cytotoxicity. Incubation of varphiX-174 plasmid DNA, with 3-morpholinosydnonimine (SIN-1), a peroxynitrite generator, led to the formation of DNA strand breaks in a concentration- and time-dependent manner. The presence of DMSO at concentrations of 0.005-0.5% was found to significantly inhibit SIN-1-induced DNA strand breaks in a concentration-dependent manner. However, DMSO at the above concentrations showed no affect on SIN-1-mediated oxygen consumption, indicating that DMSO did not affect the auto-oxidation of SIN-1 to form peroxynitrite. It is observed that incubation of the plasmid DNA with authentic peroxynitrite resulted in significant formation of DNA strand breaks, which could also be dramatically inhibited by the presence of DMSO at 0.005-0.5%. Electron paramagnetic resonance spectroscopy, using 5,5-dimethylpyrroline-N-oxide (DMPO) as a spin trap demonstrated the formation of DMPO-hydroxyl radical adduct from the SIN-1 and authentic peroxynitrite. DMSO at the concentrations ranging from 0.01% to 0.5% significantly inhibited the adduct signal. Taken together, these studies demonstrate, for the first time, that DMSO at extremely low concentrations (0.005-0.5%) can potently inhibit peroxynitrite-mediated DNA strand breakage and hydroxyl radical formation. The results of this study suggest that, where DMSO is applied as a solvent, caution should be observed when evaluating the actions of drugs in experiments involving DNA damage.