Abstract: The denaturation and damage of deoxyribonucleic acid (DNA) greatly hinders the replication and transcription of DNA, so the study on the mechanism of DNA damage and denaturation in the physiological environment is benefited to the study of its physical and chemical properties, which is of great significance to the gene therapy. Firstly, using the atomic force microscopy (AFM) to compare DNA in gas and liquid environments, it was found that the DNA images obtained in the liquid environment were clearer than those in the gas phase, and the DNA in the liquid phase was more flexible and relaxed. Secondly, the effect of dimethyl sulfoxide (DMSO) and peroxynitrite (PN) on the morphology of DNA was studied in the liquid phase. It was found that with the increase of the concentration of DMSO, the denatured degree of DNA was enhanced, and the circular DNA molecule changed from an unwound structure to an overlapping helix structure. At the same time, with the increase of the concentration of PN, linear DNA changed from a naturally stretched state to a more bent one, and broke into shorter DNA fragments. Finally, the model diagram was used to explain that DMSO and PN changed the structure of DNA, and damage and degeneration occurred after the structure of DNA became unstable.