Nucleic acids (DNA) and neurotransmitters integrate together in the brain of organisms to make powerful information processing systems. Dopamine is an important neurotransmitter whose complexation with DNA in its protonated form has been implemented in several applications such as sensors, antitumor drugs, and bioengineering. However, the molecular level understanding about the binding of protonated dopamine with the different regions of DNA and its effect on the structure as well as stability of DNA is very limited. The nature of binding of protonated dopamine with DNA and its effect on the stability and structural integrity of DNA have been extensively investigated using different spectroscopic and molecular dynamics (MD) simulation techniques. Spectroscopic studies suggest that the multimodal interaction of protonated dopamine with DNA bases in its groove region enhances its stabilization without causing any perturbation in the canonical form of DNA. MD simulation study depicts that protonated dopamine intrudes into the groove region of DNA by replacing the surrounding water and interacts with the bases in the major and minor grooves of DNA in a multimodal manner. Electrostatic and dispersion interactions contribute to the stabilization of the interaction of dopamine with the minor groove bases of DNA, whereas the role of electrostatic interaction is prominent in the case of the major groove. The binding of dopamine with the groove region of DNA enhances the hydrogen bond between its Watson-Crick base pairs, which results in higher stabilization of DNA as compared to that in buffer condition. This study provides a molecular level insight about the binding of dopamine with DNA, which can be useful in diverse areas ranging from medicine to bioengineering.