A new insight into the interaction of ZnO with calf thymus DNA through surface defects

Mechanistic investigation into the binding property of Yohimbe towards natural polymeric DNAs

DNA interactions with multivalent ligand(s) have increasingly become the subject of substantial research. For several small molecules with therapeutic potential, nucleic acids serve as their primary molecular target. Such interaction has been shown to affect transcription or replication, ultimately leading to apoptotic cell death. As a result, researchers are becoming increasingly interested in understanding how small molecules interact with DNA making it possible to develop new, DNA-specific drugs. The bioactive indole alkaloid, Yohimbe (Yohimbine; Yh) has been broadly studied in pharmacological properties while its binding mode to DNA has not been explicated so far. This study adopted molecular modelling and multi-spectroscopic methods to investigate the interaction between Yohimbine and herring testes (HT DNA) in physiological conditions. Minor hypochromic and bathochromic shifts of fluorescence intensity were observed, suggesting the binding of Yh to HT DNA. The Scatchard plot analyses using the McGhee-von Hipple method revealed non-cooperative binding and affinities in the range of 105 M-1. The thermodynamic parameters suggested exothermic binding, which was favoured by negative enthalpy and positive entropy changes from temperature-dependent fluorescence experiments. Salt-dependent fluorescence suggested that the interaction between the ligand and DNA was governed by non-polyelectrolytic forces. The results of iodide quenching, urea denaturation assay, dye displacement, and in silico molecular docking, suggested groove binding of Yh to HT DNA. Thus, the groove binding mechanism of interaction was validated by both biophysical and computational techniques. The structural elucidation and energetic profiling of Yh's interaction with naturally occurring polymeric DNA can be useful to the development of DNA-targeted therapeutics.

In vitro cytotoxicity, antibacterial activity and HSA and ct-DNA interaction studies of chlorogenic acid loaded on γ-Fe2O3@SiO2 as new nanoparticles

In this study, nanoparticles with both anticancer and antibacterial features were synthesized through loading chlorogenic acid (CGA) of essential oils on magnetic nanoparticles (MNPs). Characterization of γ-Fe₂O₃@SiO₂-CGA MNPs was performed using Fourier transform infrared (FT-IR) spectroscopy and transmission electron microscopy (TEM) that show effective coating of the MNPs with SiO₂ and CGA ligand and spherical shape of the nanoparticles with a mean diameter of 16 nm, respectively. The cytotoxicity study demonstrated that γ-Fe₂O₃@SiO₂-CGA MNPs had fewer toxic effects on normal cells (Huvec) than on cancerous cells (U-87 MG, A-2780 and A-549), and could be a new potential candidate for use in biological and pharmaceutical applications. The interaction of calf thymus deoxyribonucleic acid (ct-DNA) with γ-Fe₂O₃@SiO₂-CGA MNPs indicated that the anticancer activity might be associated with the DNA binding properties of γ-Fe₂O₃@SiO₂-CGA MNPs. Moreover, the interaction of γ-Fe₂O₃@SiO₂-CGA MNPs with human serum albumin (HSA) suggests that the native conformation of HSA was preserved at the level of secondary structure, indicating that the γ-Fe₂O₃@SiO₂-CGA MNPs do not show any cytotoxicity effect when they are injected into the blood. Antibacterial tests were performed and represented γ-Fe₂O₃@SiO₂-CGA MNPs attained better antibacterial function than CGA as free.

Oxygen vacancy assisted condensation of DNA molecule observed on ZnO thin film

An exotic condensation of DNA molecules is observed on the nanostructured ZnO surface. The ZnO nanostructures (NS) fabricated by thermal vapor deposition technique were associated with a large number of oxygen vacancies on the surface. These oxygen vacancies induced changes in the DNA conformation which further reflected through changes in the persistence length of the DNA molecules. This indicates a reinforcement of the bonds and binding in both the phosphate and the base regions of the DNA molecules with the positively charged core vacancy sites on the ZnO nanostructured surface through strong interaction mediated via long-range electrostatic forces which effectively reduced the end-to-end distance of the λ-DNA molecule. This strongly suggests a transition of the λ-DNA molecule through structural modification into a more compact higher-order fractal dimension from its native state.

Differential Antimycotic and Antioxidant Potentials of Chemically Synthesized Zinc-Based Nanoparticles Derived from Different Reducing/Complexing Agents against Pathogenic Fungi of Maize Crop

The present study aimed for the synthesis, characterization, and comparative evaluation of anti-oxidant and anti-fungal potentials of zinc-based nanoparticles (ZnNPs) by using different reducing or organic complexing-capping agents. The synthesized ZnNPs exhibited quasi-spherical to hexagonal shapes with average particle sizes ranging from 8 to 210 nm. The UV-Vis spectroscopy of the prepared ZnNPs showed variation in the appearance of characteristic absorption peak(s) for the various reducing/complexing agents i.e., 210 (NaOH and NaBH4), 220 (albumin, and thiourea), 260 and 330 (starch), and 351 nm (cellulose) for wavelengths spanning over 190-800 nm. The FT-IR spectroscopy of the synthesized ZnNPs depicted the functional chemical group diversity. On comparing the antioxidant potential of these ZnNPs, NaOH as reducing agent, (NaOH (RA)) derived ZnNPs presented significantly higher DPPH radical scavenging potential compared to other ZnNPs. The anti-mycotic potential of the ZnNPs as performed through an agar well diffusion assay exhibited variability in the extent of inhibition of the fungal mycelia with maximum inhibition at the highest concentration (40 mg L-1). The NaOH (RA)-derived ZnNPs showcased maximum mycelial inhibition compared to other ZnNPs. Further, incubation of the total genomic DNA with the most effective NaOH (RA)-derived ZnNPs led to intercalation or disintegration of the DNA of all the three fungal pathogens of maize with maximum DNA degrading effect on Macrophomina phaseolina genomic DNA. This study thus identified that differences in size and surface functionalization with the protein (albumin)/polysaccharides (starch, cellulose) diminishes the anti-oxidant and anti-mycotic potential of the generated ZnNPs. However, the NaOH emerged as the best reducing agent for the generation of uniform nano-scale ZnNPs which possessed comparably greater anti-oxidant and antimycotic activities against the three test maize pathogenic fungal cultures.

Evaluation of phytotoxicity, cytotoxicity, and genotoxicity of ZnO nanoparticles in Vicia faba

Due to the accelerating use of manufactured nanomaterials, more research is needed to define their impact on plants. The present investigation aimed at evaluating the effect of different levels (0.0, 10, 25, 50, and 100 mg/L) of ZnO nanoparticles (NPs) on Vicia faba during seed germination and seedling establishment. Additionally, V. faba root meristems were used as a model to monitor the cytotoxic and genotoxic effects resulting from exposure to ZnO NPs. The influence of ZnO NPs on three isoenzyme systems, peroxidase, α, and β esterase, was also evaluated using native-PAGE. Our results showed that lower concentrations of ZnO NPs (especially 10 and 25 mg/L) enhanced seed germination and improved seedling growth, while higher concentrations (100 and 200 mg/L) resulted in phytotoxicity. Cytological investigations of ZnO NPs-treated V. faba root cells denoted the clastogenic and aneugenic nature of ZnO NPs. Differential increase in mitotic index and significant alterations in cell cycle were observed upon exposure to ZnO NPs. High concentrations of ZnO NPs markedly induced chromosomal aberration, micronuclei, and vacuolated nuclei formation. Chromosomal breakage, chromosomal bridges, ring chromosomes, laggard chromosomes, and stickiness were also observed at a higher rate. The PAGE analysis showed that ZnO NPs treatments altered the expression patterns of all studied enzyme systems. Collectively, results from this work will help to further understand the phytotoxic effects of nanomaterials.

Photophysical and thermodynamic evaluation on the in vitro and in silico binding profile of Camptothecin with DNA

Camptothecin (CMT) is an anti-tumour alkaloid drug exhibiting selective topoisomerase-I inhibitory activity by eventually hindering dynamic functions of DNA duplex via initiating apoptosis. Unravelling the binding mechanism of CMT with bio macromolecular systems can offer fundamental information regarding the mechanism of actions which can lead to the design of rational proactive drugs. This study endeavoured the binding interactions of CMT with calf thymus DNA (ct-DNA) along with the structural alterations attained by the DNA duplex owing to CMT interactions through multi-spectroscopic, calorimetric and molecular docking studies. The UV-visible absorbance and fluorescence quenching studies revealed the binding strength of CMT with ct-DNA, evident from the binding constants K₁ = 3.79 × 10³ M^-1 and Kq = 2 × 10³ M^-1. The time-resolved lifetime measurements inferred that the quenching was static due to the non-fluorescent ground state complex formation. The dye displacement study, temperature melting and viscosity measurements established a typical non-intercalative binding mode of CMT with ct-DNA. The binding isotherm deduced from ITC was found to be spontaneous and exothermic exerting a promising ΔG value of -6.2 kcal mol^-1. The thermal kinetic parameters implied that the forces primarily involved in the CMT-ct-DNA complexation are hydrogen bonding and van der Waals interactions. Moreover, the structural alterations of DNA duplex reflected in the CD and FTIR spectra could undeniably confirm the groove binding manner of CMT. The in silico extra precision docking study explored more accurate molecular illustrations of sequence specific minor groove binding mechanism evolved between CMT and DNA corroborating well with the experimental results. These innovative findings may shorten the path towards the development of novel and more effective CMT drug derivatives.

Titania-Based Hybrid Materials with ZnO, ZrO₂ and MoS₂: A Review

Titania has properties that enable it to be used in a variety of applications, including self-cleaning surfaces, air and water purification systems, hydrogen evolution, and photoelectrochemical conversion. In order to improve the properties of titanium dioxide, modifications are made to obtain oxide/hybrid systems that are intended to have the properties of both components. In particular, zinc oxide, zirconia and molybdenum disulfide have been proposed as the second component of binary systems due to their antibacterial, electrochemical and photocatalytic properties. This paper presents a review of the current state of knowledge on the synthesis and practical utility of TiO₂-ZnO and TiO₂-ZrO₂ oxide systems and TiO₂-MoS₂ hybrid materials. The first part focuses on the hydrothermal method; then a review is made of the literature on the synthesis of the aforementioned materials using the sol-gel method. In the last section, the literature on the electrospinning method of synthesis is reviewed. The most significant physico-chemical, structural and dispersive-morphological properties of binary hybrid systems based on TiO₂ are described. A key aim of this review is to indicate the properties of TiO₂-ZnO, TiO₂-ZrO₂ and TiO₂-MoS₂ hybrid systems that have the greatest importance for practical applications. The variety of utilities of titania-based hybrid materials is emphasized.

Fluorescent ZnO-Au Nanocomposite as a Probe for Elucidating Specificity in DNA Interaction

In this work, we report the interaction of a fluorescent ZnO-Au nanocomposite with deoxyribonucleic acid (DNA), leading to AT-specific DNA interaction, which is hitherto not known. For this study, three natural double-stranded (ds) DNAs having different AT:GC compositions were chosen and a ZnO-Au nanocomposite has been synthesized by anchoring a glutathione-protected gold nanocluster on the surface of egg-shell-membrane (ESM)-based ZnO nanoparticles. The ESM-based bare ZnO nanoparticles did not show any selective interaction toward DNA, whereas intrinsic fluorescence of the ZnO-Au nanocomposite shows an appreciable blue shift (Δλ_max = 18 nm) in the luminescence wavelength of 520 nm in the presence of ds calf thymus (CT) DNA over other studied DNAs. In addition, the interaction of the nanocomposite through fluorescence studies with single-stranded (ss) CT DNA, synthetic polynucleotides, and nucleobases/nucleotides (adenine, thymine, deoxythymidine monophosphate, deoxyadenosine monophosphate) was also undertaken to delineate the specificity in interaction. A minor blue shift (Δλ_max = 5 nm) in the emission wavelength at 520 nm was observed for single-stranded CT DNA, suggesting the proficiency of the nanocomposite for discriminating ss and ds CT DNA. More importantly, fluorescence signals from the nano-bio-interaction could be measured directly without any modification of the target, which is the foremost advantage emanated from this study compared with other previous reports. The AT base-pair-induced enhancement was also found to be highest for the melting temperature of CT DNA (ΔT_mCT = 6.7 °C). Furthermore, spectropolarimetric experiments followed by calorimetric analysis provided evidence for specificity in AT-rich DNA interaction. This study would lead to establish the fluorescent ZnO-Au nanocomposite as a probe for nanomaterial-based DNA-binding study, featuring its specific interaction toward AT-rich DNA.

Adsorption of Phosphate and Polyphosphate on Nanoceria Probed by DNA Oligonucleotides

Phosphate-containing molecules exist in many forms in biology and the environment, and their interaction with metal oxides is an important aspect of their chemistry and biochemistry. In this work, phosphates with different degrees of polymerization (e.g., orthophosphate, pyrophosphate (PPi), sodium triphosphate (STPP), sodium trimetaphosphate (STMP), and polyphosphate with 25 phosphate units) and phosphates with one or two capping groups were studied. CeO₂ nanoparticles (nanoceria) were used as a model metal oxide. DNA is also a polyphosphate, and a fluorescently labeled DNA oligonucleotide was mixed with nanoceria. These phosphate species were individually added to displace the adsorbed DNA. Longer phosphate chains were more efficient when each molecule was used at the same molar concentration, whereas PPi and STPP were most efficient at the same total phosphorus atom concentration. By capping the phosphate with organic groups, the affinity was significantly decreased. Isothermal titration calorimetry (ITC) was also performed to quantitatively measure thermodynamic parameters. Although STMP was very slow at displacing DNA, it was still adsorbed very strongly by nanoceria from ITC, indicating kinetic effects likely due to its ring structure. This observation allowed us to use the DNA as a probe to study the hydrolysis of STMP to form STPP. In summary, this study provides a systematic understanding of phosphate species interacting with metal oxides, and interestingly, it demonstrates an analytical application as well.