Damage to DNA by environmental pollutants mostly result in several chronic diseases. Bisphenol A (BPA), an environmental oestrogen inducing weak estrogenic activity, has raised concerns due to its carcinogenic and DNA damaging potential. On account of developing a feasible and reliable methodology for high performance dsDNA damage indirect monitoring, an electrochemical biosensing device was constructed relying on the unique properties of multi-walled carbon nanotubes (MWCNTs) and using methylene blue (MB) as the electroactive probe. The fabricated electrochemical device was subjected to electrochemical impedance spectroscopy (EIS), cyclic voltammetry (CV) and field emission scanning electron microscope (FESEM) for characterization. Various factors affecting the biosensor performance were optimized. Also, the obtained oxidation signals were applied for indirect detection of BPA and the lowest limit of detection (LOD) was calculated to be 15 nM. Moreover, a molecular dynamic study was further developed to get better insight into the interaction between dsDNA and BPA.