Understanding of the interactions of ctDNA with an antioxidant flavone analog: Exploring the utility of the small molecule as fluorescent probe for biomacromolecule

Fluorescence Spectroscopy: A Useful Method to Explore the Interactions of Small Molecule Ligands with DNA Structures

Small molecule ligands-DNA interactions have recently received a lot of attention in the fields of life sciences, medicine, and chemical sciences. To decode these interactions, many strategies have been developed. DNA is the primary target for a wide range of drugs that may interact with DNA in particular or non-specific ways and impact its activities. Fluorescence spectroscopy is a highly advanced and non-invasive technology for measuring the concentrations of substrates and products or identifying characteristic processing states. Small molecule ligands-DNA interaction studies are beneficial not only in comprehending the method of interaction, but also in synthesizing DNA-targeted particular drugs. Several small compounds that bind to DNA are clinically established therapeutic medicines, while their specific mechanism of action is unknown. Figuring out their molecular recognizing patterns is the only way to construct innovative compounds that can target specific DNA sequences with strong affinities. This book chapter will mostly explore several fluorescence spectroscopic methodologies used to investigate interactions between small molecule ligands and DNA. In addition, we provide many approaches for determining a drug's binding mode with DNA. These strategies produce data that is both trustworthy and easy to comprehend. All of the knowledge gained by studying these fluorescence spectroscopies are supposed to lead to the development of more efficient new pharmaceuticals that might aid in the treatment of diseases.

Synthesize and multi-spectroscopic studies of zinc-naproxen nanodrug as DNA intercalator agent

The zinc-naproxen complex as a nano-drug (NanoD) was synthesized successfully via fast and effective ultrasound-assisted processes. The chemicophysical properties of the NanoD were determined using FT-IR, XRD, SEM, and EDX mapping analyses. The results confirmed the formation of the 55 nm NanoD laminates. The interaction of the obtained NanoD with calf thymus deoxyribonucleic acid (CT-DNA) was studied as well. Structural and topography changes of DNA in interaction with the NanoD were investigated by atomic force microscopy (AFM). The results of electronic absorption spectroscopy, the DNA-viscosity studies, and competition fluorescence spectroscopy showed that CT-DNA binds to the NanoD through the intercalative binding mode. The data of AFM analysis indicated swollen CT-DNA upon interaction with the NanoD. The in vitro investigation of cytotoxicity of the NanoD on HT-29 and Hep G2 cancer cells demonstrated high cytotoxicity activity of the NanoD than that of cisplatin in HT-29 cell line, especially at lower concentrations.

Phytochemicals toward Green (Bio)sensing

Because of numerous inherent and unique characteristics of phytochemicals as bioactive compounds derived from plants, they have been widely used as one of the most interesting nature-based compounds in a myriad of fields. Moreover, a wide variety of phytochemicals offer a plethora of fascinating optical and electrochemical features that pave the way toward their development as optical and electrochemical (bio)sensors for clinical/health diagnostics, environmental monitoring, food quality control, and bioimaging. In the current review, we highlight how phytochemicals have been tailored and used for a wide variety of optical and electrochemical (bio)sensing and bioimaging applications, after classifying and introducing them according to their chemical structures. Finally, the current challenges and future directions/perspective on the optical and electrochemical (bio)sensing applications of phytochemicals are discussed with the goal of further expanding their potential applications in (bio)sensing technology. Regarding the advantageous features of phytochemicals as highly promising and potential biomaterials, we envisage that many of the existing chemical-based (bio)sensors will be replaced by phytochemical-based ones in the near future.

Insights into the mechanism of groove binding between 4-octylphenol and calf thymus DNA

4-Octylphenol is an endocrine disruptor, belonging to environmental estrogens. It can be enriched in the human body through the food chain and may harm human health. Herein, we used a variety of spectroscopic techniques, molecular docking, and gel electrophoresis to study the interaction of 4-octylphenol and ctDNA. It was found that the mechanism of ctDNA quenching the endogenous fluorescence of 4-octylphenol was static quenching, and formed a complex. The negative enthalpy change (ΔH°), entropy change (ΔS°) and Gibbs free energy (ΔG°) have shown that 4-octylphenol and ctDNA spontaneously bind together under the action of hydrogen bonds and van der Waal's force. Viscosity, melting temperature and iodide quenching experiments showed that 4-octylphenol acted on the groove of ctDNA. Insignificant change in circular dichromism spectra further confirmed this binding mode. The binding sites and groups for 4-octylphenol and ctDNA interaction were identified by molecular docking. Gel electrophoresis found that 4-octylphenol at high concentrations caused DNA cleavage. Above findings may lay a theoretical foundation for understanding the toxicity mechanism of 4-octylphenol.

Groove binding between ferulic acid and calf thymus DNA: spectroscopic methodology combined with chemometrics and molecular docking studies

Ferulic acid (FA), a dietary phenolic acid compound, is proved to possess numerous biological activities. Hence, this study was devoted to explore the interaction between FA and calf thymus DNA (ctDNA) by UV - vis absorption, fluorescence, circular dichroism (CD) spectroscopy combined with multivariate curve resolution-alternating least-squares (MCR - ALS) and molecular docking studies. The concentration curves and the pure spectra of compositions (FA, ctDNA and FA - ctDNA complex) were obtained by MCR - ALS approach to verify and monitor the interaction of FA with ctDNA. The groove binding mode between FA and ctDNA was confirmed by the results of melting analysis, viscosity measurements, single-stranded DNA experiments, and competitive studies. The binding constant of FA - ctDNA complex was 4.87 × 10⁴ L mol^-1 at 298 K. The values of enthalpy (ΔH°) and entropy (ΔS°) changes in the interaction were -16.24 kJ mol^-1 and 35.02 J mol^-1 K^-1, respectively, indicating that the main binding forces were hydrogen bonds and hydrophobic interactions. The result of CD spectra suggested that a decrease in right-handed helicity of ctDNA was induced by FA and the DNA conformational transition from the B-form to the A-form. The results of docking indicated that FA binding with ctDNA in the minor groove. These findings may be conducive to understand the interaction mechanism of FA with ctDNA and the pharmacological effects of FA. Communicated by Ramaswamy H. Sarma[Formula: see text].

Exploring the binding interaction of Maillard reaction by-product 5-hydroxymethyl-2-furaldehyde with calf thymus DNA

BACKGROUND

5-Hydroxymethyl-2-furaldehyde (5-HMF), a by-product of the Maillard reaction, usually present in fried and baked food, may cause potential harm to the human body. Here, the interaction between 5-HMF and calf thymus DNA (ctDNA) under physiological buffer (pH 7.4) was studied using multi-spectroscopic methods combined with multivariate curve resolution-alternating least squares (MCR-ALS) chemometrics and molecular simulation techniques.

RESULTS

The concentration profiles and pure spectra of the three components (5-HMF, ctDNA and 5-HMF-ctDNA complex) were extracted from highly overlapping spectra using MCR-ALS analysis, which verified the formation of 5-HMF-ctDNA complex. The binding constant being of the order of 10³  L mol^-1 at four temperatures (292, 298, 304 and 310 K) indicated a weak affinity in the binding of 5-HMF to ctDNA. The binding interaction was mainly driven by hydrogen bonds and van der Waals forces. Viscosity analysis, melting assay, ionic strength effect and competitive fluorescence studies ascertained that 5-HMF bound to ctDNA through groove binding, and it tended to bind to guanine-cytosine rich region of ctDNA which was characterized using Fourier transform infrared spectra and molecular docking. Circular dichroism spectral analysis and DNA cleavage assays indicated that the ctDNA conformation was altered from B to A form and 5-HMF caused DNA damage at higher concentration.

CONCLUSIONS

The results suggested that 5-HMF bound to ctDNA through groove binding and caused DNA damage. This research may contribute to understand the binding mechanism of 5-HMF to ctDNA and to the assessment of the toxicological effect of 5-HMF in biological processes. © 2018 Society of Chemical Industry.