Construing the Interaction of Antioxidant Coumarin Derivative Daphnetin with Double-Stranded Calf Thymus Deoxyribonucleic Acid: Insights into the Binding Mechanism and Effects on Oxidative DNA Damage

Oxidative damage to DNA has significant consequences for human health and is identified as one of the key contributors to the onset and advancement of several diseases. Therefore, it is crucial to prevent oxidatively driven DNA lesions in both humans and other organisms. This study investigated the potential of daphnetin to protect DNA from oxidative damage and its binding interaction with calf thymus DNA (ct-DNA) employing multispectroscopic techniques, viscosity measurements, gel electrophoresis, docking studies, and molecular dynamics (MD) simulation. The 2-thiobarbituric acid (TBA) colorimetry assay and agarose gel electrophoresis demonstrated that daphnetin acted to protect the deoxyribose sugar and the backbone of the double-stranded DNA structure from damage caused by hydroxyl radicals. Moreover, various <i>in vitro</i> antioxidant assays (DPPH·,·OH, and <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msup><mml:msub><mml:mi>O</mml:mi><mml:mn>2</mml:mn></mml:msub><mml:mrow><mml:mo>·</mml:mo><mml:mo>-</mml:mo></mml:mrow></mml:msup></mml:math>) revealed scavenging activity comparable to that of the antioxidant ascorbic acid, providing insight into the mechanism of DNA protection. UV-vis, fluorescence studies confirmed the complex formation between ct-DNA and daphnetin, with a binding constant on the order of 10³ M^-1, suggesting a weak binding affinity. Competitive displacement assay, thermal denaturation studies, and viscosity measurements indicated groove binding, further supported by molecular docking studies. Furthermore, MD simulation studies confirmed a stable binding of daphnetin with DNA without compromising the structural integrity of DNA.