For the first time, interaction between non-toxic anthraquinone morindone with both natural and synthetic DNA duplexes has been demonstrated in this paper. Detailed analyses of the binding of morindone with DNA via UV-vis, FTIR, and circular dichroism spectroscopies were carried out. In addition, bioinformatics tools have been employed to scrutinize the binding of the dye with DNA in silico. Results represent morindone to be a better binder with a score of -5.79 compared to EtBr (known mutagenic intercalator) recorded at -5.02. Further interaction is accentuated by the microscope-assisted evidence of nuclear specific staining of tissues by morindone. The electrophoretic analysis reveals the efficacy endowed within morindone dye in rendering protection to DNA exposed to H2O2 damage and thereby conferring it safe to the nucleic acid. As DNA is often the target for majority of anticancer and antibiotic drugs, study on the interaction between molecules like morindone and DNA has relevance and implications in several biological applications including cancer therapy. Thus, we propose that morindone can also be harnessed as a diagnostic probe for DNA structure in addition to DNA-directed therapeutics.