Intercalation of herbicide propyzamide into DNA using acridine orange as a fluorescence probe

• The interaction of propyzamide (PRO) to ctDNA was predicted by molecular docking.
• The binding mode between PRO and ctDNA was an intercalation.
• The competitive intercalation of PRO to ctDNA was monitored by PARAFAC approach.
• PRO preferentially bound to A–T base pairs of ctDNA.
• PRO induced the conformational change of ctDNA from B-form to A-form.

The binding action of PRO associated with calf thymus DNA (ctDNA) was determined using multispectroscopic methods combined with parallel factor analysis (PARAFAC) and molecular docking. The fluorescence titration suggested a static fluorescence quenching of PRO was induced by ctDNA. The positive values of enthalpy changes and entropy changes suggested that the binding reaction was predominantly driven by hydrophobic interactions. Increases in melting temperature and viscosity of ctDNA and decrease in iodide-quenching effect indicated that an intercalative binding of PRO to ctDNA occurred. Moreover, the three-way synchronous fluorescence spectra data from the competitive interaction between PRO and fluorescence probe acridine orange (AO) with ctDNA were resolved by PARAFAC modeling to provide the concentration information and spectra of the three components (PRO, AO and ctDNA–AO complex) for the reaction system, which further supported the intercalation of PRO molecule into ctDNA double-helix by replacing bound AO probe. The molecular docking predicted that the A–T base pairs of ctDNA were the main binding sites for PRO, which was confirmed by Fourier transform infrared analysis, and the conformational change of ctDNA from B-form to A-form induced by PRO was inferred from the circular dichroism spectra studies.

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