Groove binding of indole-3-butyric acid to calf thymus DNA: Spectroscopic and in silico approaches

Abstract

Indole-3-butyric acid (IBA) is a broad-spectrum efficient plant growth regulator. It has been widely used in crop production, but may have a potential security risk due to its residual accumulation in agricultural products. Herein, the binding mode between IBA and calf thymus DNA (ctDNA) and influence of IBA on the structure of ctDNA were explored by using spectroscopic methods, viscosity measurement, melting temperature studies coupled with computational approaches. Fluorescence titration results indicated that ctDNA induced IBA fluorescence quenching in a static manner. The measured thermodynamic parameters demonstrated that the structure of IBA-ctDNA complex was primarily stabilized by hydrogen bonds and van der Waals forces. Fluorescence experiments, viscosity analyses and circular dichroism (CD) measurements confirmed that IBA interacted with ctDNA in terms of groove mode with no significant conformational change of ctDNA. Furthermore, molecular docking showed that IBA was preferentially bound to the minor groove of ctDNA rich in A-T bases. Molecular dynamics simulation further revealed IBA and DNA forming a stable complex and IBA could slightly increase the flexibility of ctDNA base pairs. In addition, IBA did not cause significant damage to the structure of DNA. These findings may supply conducive insights into the toxicity mechanisms of IBA at the molecular level.