Deciphering the intercalative binding modes of benzoyl peroxide with calf thymus DNA

Abstract

The binding of benzoyl peroxide (BPO), a flour brightener, with calf thymus DNA (ctDNA) was predicted by molecular simulation, and this were confirmed using multi-spectroscopic techniques and a chemometrics algorithm. The molecular docking result showed that BPO could insert into the base pairs of ctDNA, and the adenine bases were the preferential binding sites which were validated by the analysis of Fourier transform infrared spectra. The mode of binding of BPO with ctDNA was an intercalation as supported by the results from ctDNA melting and viscosity measurements, iodide quenching effects and competitive binding investigations. The circular dichroism and DNA cleavage assays indicated that BPO induced a conformational change from B-like DNA structure towards to A-like form, but did not lead to significant damage in the DNA. The complexation was driven mainly by hydrogen bonds and hydrophobic interactions. Moreover, the ultraviolet-visible (UV-vis) spectroscopic data matrix was resolved by a multivariate curve resolution-alternating least-squares algorithm. The equilibrium concentration profiles for the components (BPO, ctDNA and BPO-ctDNA complex) were extracted from the highly overlapping composite response to quantitatively monitor the BPO-ctDNA interaction. This study has provided insights into the mechanism of the interaction of BPO with ctDNA and potential hazards of the food additive.

Novel 3,9-Disubstituted Acridines with Strong Inhibition Activity against Topoisomerase I: Synthesis, Biological Evaluation and Molecular Docking Study

“…The presence of isoelliptic points in the spectra suggests the presence of a single binding mechanism [ 21 ]. The red shift of the positive band (275 nm) may be the result of the conformational transition of ct DNA B-form to A-form through the weakening of the π-π* stacking of base pairs, an effect which may be the result of the insertion of the acridine ring into the DNA [ 22 ]. In comparison with the data obtained in the UV-Vis assays, it is possible to conclude that the results of the circular dichroism study support the hypothesis that binding occurred through intercalation in at least one part of the molecule.…”

Multi-Spectroscopic and Molecular Simulation Approaches to Characterize the Intercalation Binding of 1-Naphthaleneacetic Acid With Calf Thymus DNA

“…The variations of peak intensity in the CD spectra, in particular, indicated the stability of the right-handed B-form of ctDNA (Sharifinia et al, 2020 ), and the binding of NAA to ctDNA increased the base stacking degree of ctDNA and decreased the right-handed helicity of ctDNA (Li et al, 2014 ). Moreover, the red shift of the positive band demonstrated that ctDNA conformation tended to change from B-conformation to the more likely A-conformation as the π-π * stacking of base pairs was weakened when NAA was inserted into ctDNA (Xia et al, 2017 ).…”