The toxicity of Vip3Aa protein on insect pests is known, however, it remains unclear underlying the structure-dependent molecular function of the Vip3Aa protein. To investigate the novel function of the Vip3Aa protein, we isolated recombinant Vip3Aa protein. The recombinant Vip3Aa protein was mostly present as oligomeric form depending on the hydrophobic amino acid residue. We found that the oligomeric Vip3Aa protein specifically binds to nucleic acids, including single-stranded (ssDNA) and double-stranded DNA (dsDNA). The conformational and functional domains of the Vip3Aa protein were confirmed by separating the Vip3Aa full and Vip3Aa active (actVip3Aa) forms using size exclusion chromatography and nucleic acid binding activity. Interestingly, actVip3Aa protein had a conformational change and decreased DNA binding activity compared to that of the Vip3Aa full, suggesting that N -terminal part of the Vip3Aa play an important role in maintaining the conformation and nucleic acid binding activity. These studies highlight novel functional characterization of the insecticidal protein Vip3Aa on DNA binding activity and may be attributed to the protection of DNA from the damage caused by oxidative stress. (C) 2020 Elsevier Inc. All rights reserved.