Spectroscopic studies on the interaction between carbaryl and calf thymus DNA with the use of ethidium bromide as a fluorescence probe

Algal toxicity and food chain transport characteristics of three common bisphenols and their mixtures

Various bisphenols (BPs) have been frequently detected in the aquatic environment and coexist in the form of mixtures with potential huge risks. As we all know, food chain is a media by which BPs mixtures and their mixtures probably enter the organisms at different trophic levels due to their environmental persistence. As a result, the concentrations of BPs and their mixtures may continuously magnify to varying degrees, which can produce higher risks to different levels of organisms, and even human health. However, the related researches about mixtures are few due to the complexity of mixtures. So, the ternary BP mixtures were designed by the uniform design ray method using bisphenol A (BPA), bisphenol S (BPS) and bisphenol F (BPF) to investigate their food chain effects including bioconcentration and biomagnification. Here, Chlorella pyrenoidosa (C. pyrenoidosa) and Daphnia magna (D. magna) were selected to construct a food chain. The toxic effects of single BPs and their mixtures were also systematically investigated by the time-dependent microplate toxicity analysis (t-MTA) method. Toxicity interaction within the ternary mixture was analyzed by the concentration addition model (CA) and the deviation from the CA model (dCA). The results show that the C. pyrenoidosa and D. magna had obvious bioconcentration and biomagnification effects on BPs and their mixture. The mixture had the potential to enrich at higher nutrient levels. And BPF had the largest bioconcentration effect (BCF1 = 481.86, BCF2 = 772.02) and biomagnification effect (BMF = 1.6). Three BPs were toxic to C. pyrenoidosa by destroying algal cells and decreasing protein and chlorophyll contents, and their toxicity order was BPF > BPA > BPS. Moreover, their ternary mixture exhibits synergism with time/concentration-dependency. The obtained results are of significant reference value for objectively and accurately assessing the ecological and environmental risks of bisphenol pollutants.

Anti-Inflammatory and Antioxidant Pyrrolo[3,4-d]pyridazinone Derivatives Interact with DNA and Bind to Plasma Proteins-Spectroscopic and In Silico Studies

From the point of view of the search for new pharmaceuticals, pyridazinone derivatives are a very promising group of compounds. In our previous works, we have proved that newly synthesized ligands from this group have desirable biological and pharmacokinetic properties. Therefore, we decided to continue the research evaluating the activity of pyrrolo[3,4-dpyridazinone derivatives. In this work, we focused on the interactions of five pyridazinone derivatives with the following biomolecules: DNA and two plasma proteins: orosomucoid and gamma globulin. Using several of spectroscopic methods, such as UV-Vis, CD, and fluorescence spectroscopy, we proved that the tested compounds form stable complexes with all biomacromolecules selected for analysis. These findings were also confirmed by the results obtained by molecular modeling. All tested pyridazinone derivatives bind to the ctDNA molecule via groove binding mechanisms. All these molecules can also be bound and transported by the tested plasma proteins; however, the stability of the complexes formed is lower than those formed with serum albumin.

Differences in the response of Chlorella pyrenoidosa to three antidepressants and their mixtures in different light-dark start cycles

The use of antidepressants is increasing along with the continuing spike in the prevalence of depression worldwide. As a result, more and more antidepressants are entering the water and probably does harm to the aquatic organisms and even human health. Therefore, three antidepressants, including fluoxetine (FLU), citalopram (CIT), and aspirin (APC), were selected to investigate the toxic risks of antidepressants and their mixtures to a freshwater green alga Chlorella pyrenoidosa (C. pyrenoidosa). Due light is critical for the growth of green algae, six different light-dark cycle experiments were constructed to investigate the differences in toxicity and interaction responses of C. pyrenoidosa to antidepressants and their ternary mixture designed by the uniform design ray method. The toxic effects of individual antidepressants and their mixtures on C. pyrenoidosa were systematically investigated by the time-dependent microplate toxicity analysis (t-MTA) method. Toxicity interactions (synergism or antagonism) within mixtures were analyzed by the concentration addition (CA) and the deviation from the CA model (dCA) models. The results showed that the toxicities of the three antidepressants were different, and the order was FLU > APC > CIT. Light-dark cycles obviously affect the toxicity of three antidepressants and their combined toxicity interaction. Toxicity of the three antidepressants increases with the duration of light but decreases with the duration of darkness. The ternary antidepressant mixture exhibits antagonism, and the longer the initial lighting is, the stronger the antagonism. The antagonism of the ternary mixture is also affected by exposure time and mixture components' pi as well as exposure concentration.

Design, characterization and green synthesis of samarium-decorated magnetic Fe3O4 nanoparticles: cytotoxicity and DNA binding studies

In this study, we have successfully synthesized magnetic Fe3O4 nanoparticles adorned with samarium (Sm-MNPs) utilizing ginger extract for the very first time. Furthermore, a comprehensive characterization of the nanoparticles along with an exploration of their physicochemical attributes was conducted. The biological functionalities of the synthesized nanoparticles were investigated through a thorough examination of their interaction with calf thymus DNA (ctDNA) using diverse spectroscopic techniques encompassing ultraviolet-visible (UV-Vis) and fluorescence spectroscopy at varying temperatures. Subsequently, we evaluated the cytotoxicity of the magnetic nanoparticles using a colorectal cancer cell model (HCT116 cells) and a tetrazolium colorimetric assay (MTT assay). The characterization of the ginger extract-coated magnetic nanoparticles (ginger-Sm-MNPs) revealed their superparamagnetic nature, nanocrystalline structure, spherical morphology, hydrodynamic size of 155 nm, and uniform distribution. The outcomes from UV-Vis and fluorescence spectroscopy affirmed the binding of ginger-Sm-MNPs with ctDNA. Additionally, the MTT assay demonstrated that the cytotoxicity of ginger-Sm-MNPs surpassed that of both magnetite nanoparticles and ginger extract. Notably, the inhibitory concentrations (IC50) for the green-synthesized nanoparticles after 24 and 48 h of incubation were determined as 198.1 and 135.8 μg/mL, respectively. In conclusion, our study findings suggest the potential utility of ginger-Sm-MNPs as a promising candidate for various biomedical applications.Communicated by Ramaswamy H. Sarma.

In vitro and in silico binding studies of phytochemical isochroman with calf thymus DNA using multi-spectroscopic and computational modelling techniques

A wide range of therapeutic molecules uses deoxyribonucleic acid (DNA) as an intracellular target. The interaction of small molecules to DNA is a key feature in pharmacology and plays a vital role in the development of novel and more efficient drugs with increased selective activity and enhanced therapeutic effectiveness. Isochroman (IC) is a constituent of Olea europea plant, which has been shown to exhibit several beneficial pharmacological activities. At present, its interaction studies using calf thymus DNA (ct-DNA) have not been explained. A set of multi-spectroscopic techniques has been performed to determine the interaction mechanism of isochroman with ct-DNA. Absorption spectra and quenching in fluorescence studies show that isochroman and ct-DNA form a complex. The static mode of quenching was determined by the Stern-Volmer plot. The value of binding constant, Kb = 4.0 × 103 M-1 revealed moderate type of binding. Effects of single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and ionic strength were studied to examine the isochroman binding to ct-DNA. Potassium iodide (KI) quenching effects and competitive binding studies clearly showed that isochroman binds in the minor groove of ct-DNA. Circular dichroic and DNA melting experiments also confirmed these results. The experimental outputs were further corroborated via in silico computational modelling studies. Lipinski's rule of 5 and SwissADME showed drug-likeness and oral bioavailability scores. Protox ІІ online software predicts oral and organ toxicity.Communicated by Ramaswamy H. Sarma.

Effect of Soybean Protein Concentrate Preparation on Copy Numbers and Structural Characteristics of DNA from Genetically Modified Soybean

To regulate the degradation of transgenic DNA and lay theoretical foundations for the rational utilization of genetically modified (GM) products, variations in copy numbers and structural characteristics of DNA from GM soybean event GTS 40-3-2 during soybean protein concentrate (SPC) preparation were evaluated. Results showed that defatting and the first ethanol extraction were key procedures inducing DNA degradation. After these two procedures, copy numbers of the lectin and cp4 epsps targets decreased by more than 4 × 10⁸, occupying 36.88-49.30% of the total copy numbers from raw soybean. Atomic force microscopy images visually revealed the degradation of DNA that thinned and shortened during SPC preparation. Circular dichroism spectra suggested a lower helicity of DNA from defatted soybean kernel flour and a conformation transition of DNA from B-type to A-type after ethanol extraction. The fluorescence intensity of DNA decreased during SPC preparation, verifying the DNA damage along this preparation chain.

Interaction of bifunctional peptide-carbazole complexes with DNA and antimicrobial activity

Two peptide-carbazole conjugates, CTAT and CNLS, were designed and synthesized using carbazole Schiff base to modify the cell membrane penetrating peptide TAT (47-57) and the nuclear localization peptide NLS at the N terminus. The interaction with ctDNA was investigated by multispectral and agarose gel electrophoresis. And the effects of CNLS and CTAT on the G-quadruplex structure were explored by circular dichroism titration experiments. The results show that both CTAT and CNLS interact with ctDNA in a minor groove binding manner. Both conjugates bind more tightly to DNA than the individual substances CIBA, TAT and NLS. In addition, CTAT and CNLS are capable of unfolding parallel G-quadruplex structures and are potential G-quadruplex unfolding agents. Finally, broth microdilution was performed to test the antimicrobial activity of the peptides. The results showed that CTAT and CNLS had a 4-fold increase in antimicrobial activity compared with the parent peptides TAT and NLS. They could exert antimicrobial activity by disrupting the integrity of cell membrane bilayer and binding to DNA, and could be used as novel antimicrobial peptides for the development of novel antimicrobial antibiotics.

Cytotoxic and genotoxic evaluation of bisphenol S on onion root tips by Allium cepa and comet tests

Bisphenol S (BPS) is an analog of bisphenol A, which is used as substitute of BPA in many products like airport luggage tags, baby bottles, plastics, and epoxy resins etc. Bisphenol S can cause toxic effects in different organisms, i.e., mice, rat, zebrafish, and C.elegans, etc. Bisphenol S is also known as "endocrine disruptor" due to its ability to mimic the endocrine receptors. So, the aim of this study was to evaluate the cytotoxic and genotoxic effects of bisphenol S on meristematic cells present in onion root tips through Allium cepa (A.cepa) and comet tests. Root growth inhibition was evaluated by root growth inhibition assay. Mitotic index (MI) and chromosomal aberrations (CAs) were assessed by A.cepa assay. DNA damage was evaluated by comet assay. Root growth of A.cepa was inhibited due to bisphenol S. LC50 value calculated by root growth inhibition assay for bisphenol S was (2.6±0.63, 50 μg/ml). Mitotic index was reduced, and chromosomal aberrations were observed, i.e., stickiness, polyploidy, and disturbed ana-telophase in anaphase and telophase stages of mitosis. In case of comet assay, DNA damage was increased in statistically significant manner (p ≤ 0.05). It was concluded that bisphenol S constitutes cytotoxic and genotoxic effects on A. cepa root meristematic cells. Moreover, it is suggested to explore more toxicity studies of bisphenol S at molecular level.

Understanding the binding behavior of Malathion with calf thymus DNA by spectroscopic, cell viability and molecular dynamics simulation techniques: binary and ternary systems comparison

The interaction between calf thymus DNA (ctDNA) and Malathion in the absence and presence of Histone 1 has been enquired by the means of spectroscopic, viscometry, molecular modeling, and cell viability assay techniques. Malathion is capable of quenching the fluorescence of ct DNA in the absence and presence of H1. The binding constants of Malathion-ctDNA complex in the absence of H1 have been calculated to be 6.62 × 10⁴, 4.31 × 10⁴ and 1.93 × 10⁴ M^-1 at 298, 303, and 308 K, respectively that revealed static quenching in complex formation. The observed negative values of enthalpy and entropy changes indicate that the main binding interaction forces were van der Waals force and hydrogen bonding. The binding constant between Malathion and single-stranded ctDNA (ss ctDNA) seemed to be much weaker than that of Malathion and double-stranded ctDNA (ds ctDNA). Furthermore, Malathion can induce detectable alterations in the CD spectrum of ctDNA, along with changes in its viscosity. In the presence of H1, fluorescence quenching of ctDNA-Malathion complex displays dynamic behavior and binding constants were perceived to be 1.66 × 10⁴, 2.93 × 10⁴ and 5.77 × 10⁴ M^-1 at 298, 303, and 308 K, respectively. The different of interaction behavior between ctDNA and Malathion in the absence and presence of H1 clearly revealed H1 role in the complex formation and forces change between ctDNA and Malathion. The positive values of enthalpy and entropy changes have suggested that binding process is primarily driven by hydrophobic interactions. The tendency to interact with ss ctDNA, reduced viscosity have designated that the Malathion bound to ctDNA in the presence of H1 is groove binding. The results of molecular docking and molecular dynamics simulation also confirmed potent interactions between Malathion and the macromolecules in the binary and ternary systems.Communicated by Ramaswamy H. Sarma.

Investigating binding of insecticide buprofezin to DNA by experimental and metadynamics simulation studies

Buprofezin (BUP) is an insecticide which belongs to the thiadiazine structural family and known to damage DNA in mice. Though its toxic effect on human is not known clearly, understanding the mechanism of interaction of BUP with DNA can prove useful when required. Multi-spectroscopic experiments such as UV-Vis, fluorescence, circular dichroism (CD) and ¹H NMR coupled with viscosity measurements, urea effect and voltametric studies were performed to ascertain the mode of binding of BUP with calf thymus DNA (CT-DNA). Analysis of UV-Vis and fluorescence spectra indicated the formation of a complex between BUP and CT-DNA. Other experiments such as competitive binding assays with ethidium bromide (EB) and Hoechst 33258, viscosity measurements, effect of urea, CD, voltammetric studies and ¹H NMR spectral analysis suggested that BUP intercalates into the base pairs of CT-DNA. All these results revealed that the binding mode of BUP with CT-DNA should be intercalation and the binding constant is in the order of 10⁴ M^-1. The ΔH^o < 0 and ΔS^o < 0 suggested that H-bonding or van der Waals force was the main binding force between BUP and CT-DNA. The proposed mode of binding of BUP with CT-DNA has been visualized using in silico molecular docking and metadynamics simulation studies, which showed that the phenyl ring of BUP binds to CT-DNA via π-π stacking interaction in addition to H-bond formation.Communicated by Ramaswamy H. Sarma.

A study of structure-activity relationship and anion-controlled quinolinyl Ag(I) complexes as antimicrobial and antioxidant agents as well as their interaction with macromolecules

In this communication, we feature the synthesis and in-depth characterization of a series of silver(I) complexes obtained from the complexation of quinolin-4-yl Schiff base ligands ((E)-2-((quinolin-4-ylmethylene)amino)phenol L_a, 2-(quinolin-4-yl)benzo[d]thiazole L_b, (E)-N-(2-fluorophenyl)-1-(quinolin-4-yl)methanimine L_c, (E)-N-(4-chlorophenyl)-1-(quinolin-4-yl)methanimine L_d, (E)-1-(quinolin-4-yl)-N-(p-tolyl)methanimine L_e, (E)-1-(quinolin-4-yl)-N-(thiophen-2-ylmethyl)methanimine L_f) and three different silver(I) anions (nitrate, perchlorate and triflate). Structurally, the complexes adopted different coordination geometries, which included distorted linear or distorted tetrahedral geometry. The complexes were evaluated in vitro for their potential antibacterial and antioxidant activities. In addition, their interactions with calf thymus-DNA (CT-DNA) and bovine serum albumin (BSA) were evaluated. All the complexes had a wide spectrum of effective antibacterial activity against gram-positive and gram-negative bacterial and good antioxidant properties. The interactions of the complexes with CT-DNA and BSA were observed to occur either through intercalation or through a minor groove binder, while the interaction of the complexes with BSA reveals that some of the complexes can strongly quench the fluorescence of BSA through the static mechanism. The molecular docking studies of the complexes were also done to further elucidate the modes of interaction with CT-DNA and BSA.

Binding and thermodynamic study of thalidomide with calf thymus DNA: Spectroscopic and computational approaches

The thalidomide-DNA interactions have been investigated in detail by numerous biophysical techniques such as UV-vis, dye displacement assay, viscosity, cyclic voltammetry, circular dichroism, molecular docking, molecular dynamic simulation, FT-IR and ¹H NMR spectroscopy. CD spectroscopy, thermal denaturation and viscosity measurement explained that thalidomide is groove binder. Molecular docking analysis highlighted that thalidomide binds trough minor groove of calf thymus DNA which also confirmed from dye displacement experiment. To our knowledge, this is the first instance thalidomide was shown to binds with calf thymus DNA. Molecular dynamic simulation indicated that the thalidomide-DNA system was stabilized by electrostatic attraction as the main interaction and mode of binding is minor groove. Our study provides a better understanding to the DNA-thalidomide binding affinity and it mechanism. Overall, all these in formations can be used for further understanding the pharmacological effects of thalidomide.

Effect of Juglone against Pseudomonas syringae&nbsp;pv Actinidiae Planktonic Growth and Biofilm Formation

Pseudomonas syringaepv Actinidiae (P. syringae) is a common pathogen causing plant diseases. Limoli proved that its strong pathogenicity is closely related to biofilm state. As a natural bacteriostatic agent with broad-spectrum bactericidal properties, juglone can be used as a substitute for synthetic bacteriostatic agents. To explore the antibacterial mechanism, this study was carried out to examine the inhibitory effect of juglone on cell membrane destruction, abnormal oxidative stress, DNA insertion and biofilm prevention of P. syringae. Results showed that juglone at 20 μg/mL can act against planktogenic P. syringae (10⁷ CFU/mL). Specially, the application of juglone significantly damaged the permeability and integrity of the cell membrane of P. syringae. Additionally, juglone caused abnormal intracellular oxidative stress, and also embedded in genomic DNA, which affected the normal function of the DNA of P. syringae. In addition, environmental scanning electron microscope (ESEM) and other methods showed that juglone effectively restricted the production of extracellular polymers, and then affected the formation of the cell membrane. This study provided a possibility for the development and utilization of natural juglone in plants, especially P. syringae.

Interactions in Ternary Aqueous Solutions of NMA and Osmolytes-PARAFAC Decomposition of FTIR Spectra Series

Intermolecular interactions in aqueous solutions are crucial for virtually all processes in living cells. ATR-FTIR spectroscopy is a technique that allows changes caused by many types of such interactions to be registered; however, binary solutions are sometimes difficult to solve in these terms, while ternary solutions are even more difficult. Here, we present a method of data pretreatment that facilitates the use of the Parallel Factor Analysis (PARAFAC) decomposition of ternary solution spectra into parts that are easier to analyze. Systems of the NMA–water–osmolyte-type were used to test the method and to elucidate information on the interactions between N-Methylacetamide (NMA, a simple peptide model) with stabilizing (trimethylamine N-oxide, glycine, glycine betaine) and destabilizing osmolytes (n-butylurea and tetramethylurea). Systems that contain stabilizers change their vibrational structure to a lesser extent than those with denaturants. Changes in the latter are strong and can be related to the formation of direct NMA–destabilizer interactions.

Dynamic and quantitative characterization of antagonism within disinfectant mixtures by a modified area-concentration ratio method

The coexistence of various typical disinfectant pollutants has the potential to produce toxicity interaction towards organisms in the environment. A suitable model is necessary to evaluate the interaction quantitatively. Hence, the area-concentration ratio (ACR) method was modified (MACR) by combing confidence intervals to dynamically and quantitatively evaluate the toxicity interactions within disinfectant mixture pollutants. Disinfectant mixtures were designed by the direct equipartition design ray method using three guanidine disinfectants, chlorhexidine diacetate (CD), chlorhexidine (CHL), and polyhexamethylene biguanidine (POL) and one chlorine-containing disinfectant calcium hypochlorite (CAL). The toxicities of the four disinfectants and their mixtures towards Vibrio qinghaiensis sp.-Q67 (Q67) were determined by the time-dependent toxicity microplate analysis method. And the toxicity mechanism was analyzed by determining the effects of four disinfectants and their binary mixtures on the structure of cell, DNA and proteins (Pro) for Q67. The results show that the toxicities of CD and CHL to Q67vary little with time, but POL and CAL show the obvious time-dependent toxicity. The toxicities of CD, CHL and POL to Q67 are significantly stronger than that of CAL at the same exposure time. The toxicities of three binary mixture systems don't have significant difference in different exposure time. MACR can dynamically, quantitatively and accurately characterize toxicity interactions compared with ACR. According to MACR, the antagonism intensity dynamically changes with the prolongation of exposure time for binary mixture rays of three guanidine disinfectants and CAL, and linearly correlates with the components' concentration ratios. Four disinfectants all can destroy cell membrane and cause desaturation DNA of test organism, and CAL even can destroy the structure of DNA and protein. The probably reason for the antagonism within binary mixtures is the reaction between guanidine group and ClO^-, which is called chemical antaogism.

Concentration-dependent mode of binding of drug oxatomide with DNA: multi-spectroscopic, voltammetric and metadynamics simulation analysis

The interaction between antihistaminic drug oxatomide (OXT) and calf-thymus DNA (CT-DNA) has been investigated in a physiological buffer (pH 7.4) using UV-Vis, fluorescence, ¹H NMR and circular dichroism spectral techniques coupled with viscosity measurements, KI quenching, voltammetry and in silico molecular modeling studies. OXT binds with CT-DNA in a concentration-dependent manner. At a lower [Drug]/[CT-DNA] molar ratio (0.6-0.1), OXT intercalates into the base pairs of CT-DNA, while at a higher [Drug]/[CT-DNA] molar ratio (13-6), the drug binds in the minor grooves of CT-DNA. The binding constants for the interaction are found to be in the order of 10³-10⁵ M^-1, and the groove binding mode of interaction exhibits a slightly higher binding constant than that of intercalative mode. Thermodynamic analysis of binding constants at three different temperatures suggests that both these modes of binding are mainly driven by hydrophobic interactions (ΔH^o > 0 and ΔS^o > 0). Voltammetric investigations indicate that the electro-reduction of OXT is an adsorption controlled process and shifts in reduction peak potentials reiterate the concentration-dependent mode of binding of the drug with CT-DNA. The free energy landscape obtained at the all-atom level, using metadynamics simulation studies, revealed two major binding forces: partial intercalation and minor groove binding, which corroborate well with the experimental results.Communicated by Ramaswamy H. Sarma.

Design and synthesis of fatty acid derived 4-methoxybenzylamides as antimicrobial agents

A new series of fatty acid amides viz. N-(4-methoxybenzyl)undec-10-enamide (5), (9Z, 12R)-12-Hydroxy-N-(4-methoxybenzyl)octadec-9-enamide (6) and N-(4-methoxy benzyl)oleamide (7) were synthesized by using a suitable synthetic route involving DCC and DMAP as catalysts. The synthesized compounds were characterized through FTIR, NMR spectroscopy, and mass spectrometry. DNA binding studies through spectroscopy and molecular docking were performed to evaluate the binding mechanism of molecules (5-7) with (ctDNA). The inhibition zone with reference to standards, Minimum Inhibitory Concentration (MIC) and Minimum Killing Concentration (MKC) values were determined to study the in vitro antimicrobial activity for tested compounds. Among all the tested compounds, the compound 6 containing hydroxy group at the fatty acid chain showed most powerful antifungal as well as antibacterial activity.

Investigation of biological activity of 2,3-disubstituted quinazolin-4(1H)-ones against Mycobacterium tuberculosis and DNA via docking, spectroscopy and DFT studies

Docking studies, structural data of DNA binding and molecular dynamics simulations of substituted quinazolin-4(1H)-ones.

Novel 1,3,5-triazine-based pyrazole derivatives as potential antitumor agents and EFGR kinase inhibitors: synthesis, cytotoxicity, DNA binding, molecular docking and DFT studies

The development of new 1,3,5-triazine-based pyrazole derivatives as effective anticancer agents.

Multi-spectroscopic, voltammetric and molecular docking studies on binding of anti-diabetic drug rosigiltazone with DNA

The binding of an anti-diabetic drug rosiglitazone (RG) with calf-thymus DNA (CT-DNA) in physiological buffer (pH 7.4) has been investigated using various spectral techniques such as UV-Vis, fluorescence, ¹H NMR and circular dichroism (CD) coupled with viscosity measurement and molecular docking studies. The binding of RG with CT-DNA results in small hypochromism without any change in absorption maximum and fluorescence quenching with hardly any shifts in emission maximum suggesting groove binding mode of interaction. The binding constant is found to be 4.2 × 10² M^-1 at 298 K. Thermodynamic analysis reveal that the binding is spontaneous and H-bonding and van der Waals forces play predominant role in the binding of RG with CT-DNA. Competitive interaction between RG and ethidium bromide with CT-DNA, viscosity measurements, KI quenching, ¹H NMR and CD studies substantiate the prosed mode of binding. Voltammetric investigations suggest that the electro-reduction of RG is an adsorption controlled process and shift of reduction peak to more negative potential, with a binding constant of 3.4 × 10³ M^-1, validates the groove binding mode of interaction between RG and CT-DNA. Molecular docking reveals that RG binds in the minor groove of DNA and the dominating interaction forces are H-bonding and hydrophobic interactions.

Decomposition of DNA staining agent ethidium bromide by gamma irradiation: Conditions, kinetics, by-products, biological activity, and removal from wastewater

Ethidium Bromide (Eth-Br) is an intercalating agent commonly used in medical and biological laboratories as a DNA staining dye. Despite its popular use, aqueous solutions containing Eth-Br showed high toxicity, mutagenic capacity, and deactivate DNA transcription. In this study, the removal of Eth-Br from aqueous solutions by gamma irradiation has been fully investigated. Gamma irradiation was capable of achieving a near complete removal of Eth-Br in neutral and non-buffered aqueous solutions at an absorbed dose of 15 kGy. Various experimental conditions were studied and showed that the removal efficiency is not diminished. The addition of hydrogen peroxide (2 %) to the irradiated solutions reduced the D₅₀ and D₉₀ by 50 %. Modeling Eth-Br decomposition showed that the reaction followed pseudo first-order kinetics and reaches at least 90 % removal under all experimental conditions. TOC and HPLC measurements confirmed that Eth-Br is fully mineralized when the absorbed dose reaches 15 kGy. The biological activity of Eth-Br after irradiation treatment was investigated with synthetic DNA and natural DNA. The biological activity of Eth-Br was deactivated at an absorbed dose as low as 5 kGy. Toxicity measurement with E-coli bacteria also confirmed that the absorbed dose of 5 kGy was sufficient to remove Eth-Br toxicity.

DNA Binding Characteristics and Protective Effects of Yellow Pigment from Freshly Cut Yam (Dioscorea opposita)

Yam yellow pigments (YP) are natural pigments formed during the storage of freshly cut yam (Dioscorea opposita) under certain conditions. The interaction of YP with calf thymus DNA (ctDNA) and its protective effect against DNA oxidative damage were investigated using multiple spectroscopic techniques, competitive binding experiments, viscosity measurements, and gel electrophoresis. Results showed that YP participated in intercalative binding with ctDNA. YP exhibited a protective effect against hydroxyl-induced DNA damage, which was attributed to the high hydroxyl radical scavenging activity of YP. Our findings improve our understanding of the mechanism of interaction between YP and ctDNA, and provide a theoretical basis for the application of YP in the food and drug industry.

Study of the Binding Interaction between Wortmannin and Calf Thymus DNA: Multispectroscopic and Molecular Docking Studies

INTRODUCTION

Wortmannin (WTN) is a steroid metabolite that inhibits phosphatidylinositol 3-kinase and other signaling pathways. Structurally, the WTN consists of a cyclopentanophenanthrene-like structure with several oxygen-rich moieties which have the potential to interact with deoxyribonucleic acid (DNA) molecules.

METHODS

We aim to evaluate the WTN and calf thymus DNA (ct-DNA) interaction with molecular docking using the AutoDock 4.2 software. UV and fluorescence spectroscopy and viscosity techniques were performed to confirm the in silico analysis.

RESULTS

Molecular docking showed that the WTN interacted with ct-DNA via hydrogen bonds at guanine-rich sequences. The number of hydrogen bonds between the WTN and DNA was 1-2 bonds (average 1.2) per WTN molecule. The in silico binding constant was 2 × 103 M-1. UV spectroscopy showed that the WTN induced a hyperchromic feature without wavelength shifting. The WTN and DNA interaction led to quenching of DNA-emitted fluorescence. The different concentrations of WTN had no effect on DNA viscosity. Taken together, our results demonstrated WTN interacts with DNA in the nonintercalating mode, which is considered as a new mechanism of action.

CONCLUSION

These results suggest that the WTN may exert its biological effects, at least in part, via interaction with DNA.

Binding of model polycyclic aromatic hydrocarbons and carbamate-pesticides to DNA, BSA, micelles and liposomes

The binding to biosubstrates and micellar systems of pollutants as the polycyclic aromatic hydrocarbon (PAH) derivatives 1-aminopyrene (1-PyNH₂) and 1-hydroxymethylpyrene (1-PyMeOH) and the carbamate-pesticides 1-naphthyl-N-methylcarbamate (carbaryl, CA) and methyl benzimidazol-2-ylcarbamate (carbendazim, CBZ) was analysed through an integrated strategy combining spectroscopy and quantum chemistry. As biosubstrates, natural DNA and bovine serum albumin (BSA) were taken into account for a thermodynamic analysis of the binding features through spectrophotometric and spectrofluorometric techniques. In all cases, a strong DNA interaction is present and intercalation is supposed as the major binding mode. For the PAH derivatives, DNA binding is found to be favoured under high salt conditions and BSA static quenching and binding with 1:1 stoichiometry occurs. The molecular structure and optical properties of 1-PyNH₂, CA and CBZ together with their intercalated adducts in DNA were studied also by means of quantum chemical approach. The (TD)DFT calculations on intercalated dye/DNA adducts quantitatively reproduce the experimentally observed spectroscopic changes, thus confirming the intercalation hypothesis. The theoretical approach also provides information on the adducts' geometries and on the amount of charge transfer with DNA. Moreover, ultrafiltration tests in the presence of anionic (SDS), cationic (DTAC) and neutral (Triton X) micellar aggregates and liposomes provided insights into lipophilicity and cellular membrane affinity. PAH derivatives show high retention coefficient in all cases, whereas in the case of carbamate-pesticides micellar retention might be significantly reduced and is very limited in the case of liposomes.

Exploring the potential of environment friendly silver nanoparticles for DNA interaction: Physicochemical approach

Nanosilver, being the most prominent nanoproduct has diverse bio-medical applications and hence the effects associated with their exposure need to be investigated in detail. The interaction of metal nanoparticles with DNA has become a matter of interest, as their effect on structural integrity, synthesis and replication could be explored through it. Present work aims at the facile synthesis and characterization of spherical silver nanoparticles (AgNPs) using Epipremnum aureum leaves extract. Nanoparticles were characterized using UV-Visible spectroscopy, Transmission Electron Microscopy (TEM), High Resolution X-ray Diffraction (HR-XRD) and Dynamic Light Scattering (DLS) studies. The interaction of AgNPs with Calf thymus DNA (CT-DNA) was investigated using different spectroscopic techniques like UV-Visible spectroscopy, UV-thermal melting, Circular Dichroism and fluorescence spectroscopic studies. Fluorescence results suggest van der Waals and H-bonding interactions, which are predominantly responsible for the interaction of AgNPs with CT-DNA. Circular dichroism and thermal melting studies are pointing towards the groove binding of AgNPs to CT-DNA. DNA duplex destabilization was confirmed by the decreased thermal melting temperature of CT-DNA on addition of AgNPs. Present study might open up new vistas for the study of unusual kind of DNA binders, which can destabilize DNA and may further be used for various biomedical applications.

Study on antitumor molecular mechanism of Alisols based on p53DNA

Methyl thiazolyl tetrazolium (MTT) assay, UV-vis absorption spectroscopy, fluorescence spectroscopy and molecular simulation were used to investigate the antitumor activity of alisol A, alisol B and an 1:1 mixture of both compounds, the mechanism of its interaction with anti-cancer target p53DNA and explored the antitumor mechanism of alisols. MTT assay showed that the order of antitumor activity was:alisol B > alisol A > alisol A-alisol B(1:1). Spectroscopic experiments and molecular simulation suggested that alisol A, alisol B and their mixture interact with p53DNA in by partial insertion and the strength of binding affinity was consistent with the MTT assay. The K_sv of alisol A was 9.35 × 10⁴ L·mol^-1, K_q was 9.35 × 10¹² L·mol^-1·s^-1 and the K_sv and K_q of alisol B were 11.61 × 10⁴ L·mol^-1 and 11.61 × 10¹² L·mol^-1·s^-1. The molecular simulation revealed that competitive antagonism was observed in the interaction between the alisol mixture and p53DNA. The critical groups and significant binding sites for the interaction between alisol monomers and p53DNA include C19-OH and C22-OH of the alisols; N2 and H21 of the guanine deoxynucleotide (DG8), N2-H21 of the DG7, O4' of the DG9 in the f-chain of p53DNA; and C2-O2 of the cytosine deoxynucleotide (DC16) in the e-chain of p53DNA. Also, the C-22 and C23- of the alisols and the DA18-DT5 base pairs of p53DNA were key factors in the interaction of the mixture with p53DNA.

Chlorinated emodin as a natural antibacterial agent against drug-resistant bacteria through dual influence on bacterial cell membranes and DNA

The rise in infections caused by drug-resistant pathogens and a lack of effective medicines requires the discovery of new antibacterial agents. Naturally chlorinated emodin 1,3,8-trihydroxy-4-chloro-6-methyl-anthraquinone (CE) from fungi and lichens was found to markedly inhibit the growth of Gram-positive bacteria, especially common drug-resistant bacterial strains, including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecium (VRE). CE was confirmed to cause significant potassium leakage, cell membrane depolarization and damage to the selective permeability of cell membranes in bacterial cells, resulting in bacterial cell death. In addition, CE was shown to have a strong electrostatic interaction with bacterial DNA and induce DNA condensation. Thus, CE is a promising natural antibacterial pharmacophore against Gram-positive bacteria, especially common drug-resistant MRSA and VRE isolates, with a dual antibacterial mechanism that damages bacterial cell membranes and DNA.

The magnetic properties, DNA/HSA binding and nuclease activity of manganese N-confused porphyrin

The first oxidative cleavage of DNA by manganese [Formula: see text]-confused porphyrin [chloro(2-aza-2-methyl-5,10,15,20-tetrakis([Formula: see text]-chlorophenyl)-21-carbaporphyrin)manganese(III), 1] using H2O2 as oxidant agent and its magnetic, calf thymus DNA(ct-DNA)- and human serum albumin (HSA) binding properties were investigated. The magnitude of the axial (D) zero-field splitting for the mononuclear Mn(III) center in 1 was determined to be approximately 2.71 cm[Formula: see text] by paramagnetic susceptibility measurements. The DNA- and HSA binding experimental results showed that 1 bound to ct-DNA via an outside groove binding mode and the hydrophobic cavity located in subdomain IIA of HSA with the binding constant of 4.144 × 105 M[Formula: see text] and [Formula: see text] 106 M[Formula: see text], respectively. Thermodynamic parameters revealed that both DNA- and HSA binding were spontaneous process. The main driven forces were the hydrogen bond and van der Waals for the former, but hydrophobic interaction for the latter, which were further confirmed by molecular docking modeling. Manganese [Formula: see text]-confused porphyrin 1 could cleave the supercoiled plasmid DNA efficiently in the presence of hydrogen peroxide. Hydroxyl radical ([Formula: see text]OH) was found the active species for oxidative damage of DNA.

Deciphering the groove binding modes of tau-fluvalinate and flumethrin with calf thymus DNA

Tau-fluvalinate (TFL) and flumethrin (FL), widely used in agriculture and a class of synthetic pyrethroid pesticides with a similar structure, may cause a potential security risk. Herein, the modes of binding in vitro of TFL and FL with calf thymus DNA (ctDNA) were characterized by fluorescence, UV-vis absorption, circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy with the aid of viscosity measurements, melting analyses and molecular docking studies. The fluorescence titration indicated that both TFL and FL bound to ctDNA forming complexes through hydrogen bonding and van der Waals forces. The binding constants of TFL and FL with ctDNA were in the range of 10(4)Lmol(-1), and FL exhibited a higher binding propensity than TFL. The iodide quenching effect, single/double-stranded DNA effects, and ctDNA melting and viscosity measurements demonstrated that the binding of both TFL and FL to ctDNA was groove mode. The FT-IR analyses suggested the A-T region of the minor groove of ctDNA as the preferential binding for TFL and FL, which was confirmed by the displacement assays with Hoechst 33258 probe, and the molecular docking visualized the specific binding. The changes in CD spectra indicated that both FL and TFL induced the perturbation on the base stacking and helicity of B-DNA, but the disturbance caused by FL was more obvious. Gel electrophoresis analyses indicated that both TFL and FL did not cause significant DNA cleavage. This study provides novel insights into the binding properties of TFL/FL with ctDNA and its toxic mechanisms.

Binding properties of pendimethalin herbicide to DNA: multispectroscopic and molecular docking approaches

Pendimethalin (PND) is a systemic herbicide widely used on rice, cotton, peas, wheat, potatoes, fruits, nuts and other residential and non-residential crops; however, it concurrently exerts toxic effects on beneficial organisms like earthworms, aquatic invertebrates and other non-targeted animals including humans. Most likely, the genotoxicity of agrochemicals/drugs is modulated through cellular distribution of bound DNA. Therefore, the in vitro interaction of PND with calf thymus DNA (ctDNA) has been investigated using various sensitive biophysical techniques to ascertain its binding mechanism. UV-visible absorption and fluorescence spectra suggested the formation of a complex between PND and ctDNA. The binding constant of the PND-ctDNA complex was found to be around 10(4) M(-1) using steady state fluorescence titration. The calculated positive values of enthalpy and entropy changes suggested that the binding reaction was predominantly driven by hydrophobic interactions. Competitive displacement studies using acridine orange (AO), ethidium bromide (EB) and Hoechst dye suggested intercalation of PND molecules into the double helix of ctDNA by replacing the bound AO and EB probes. An increase in the viscosity and melting temperature of ctDNA and a decrease in iodine-quenching also support the intercalative binding of PND with ctDNA. Molecular docking analysis further confirmed the specific binding mode of PND between adjacent 'G-C' base pairs of ctDNA.

Synthesis, structure, and calf-thymus DNA binding of ternary fleroxacin–Cu(ii) complexes

The interaction between the synthesized fleroxacin complexes and CT DNA was investigated.