Minor groove binding of the food colorant carmoisine to DNA: spectroscopic and calorimetric characterization studies

In-silico and in-vitro assessment of the antibiofilm potential of azo dye, carmoisine against Pseudomonas aeruginosa

Biofilm is a community of microorganisms attached to the substrate and plays a significant role in microbial pathogenesis and medical device-related infection. Pseudomonas aeruginosa (PA) is a highly infectious gram-negative opportunistic biofilm-forming bacterium with high antibiotic resistance. Several reports underscore the antimicrobial activity of natural and synthetic food coloring agents, including carmoisine, turmeric dye, red amaranth dye, and phloxine B. However, their ability to suppress the PA biofilm is not clearly understood. Carmoisine is a red-colored synthetic azo dye containing naphthalene subunits and sulfonic groups and is widely used as a food coloring agent. This study investigated the antibiofilm potential and possible mechanism of biofilm inhibition by carmoisine against PA. Computational studies through molecular docking revealed that carmoisine strongly binds to QS regulator LasR (-12.7) and relatively less strongly but significantly with WspR (-6.9). Further analysis of the docked LasR-carmoisine complex using 100 ns MD simulation (Desmond, Schrödinger) validated the bonding strength and stability. Crystal violet assay, triphenyl tetrazolium chloride salt assay, and confocal microscopic studies were adopted for biofilm quantification, and the results indicated the dose-dependent antibiofilm activity of carmoisine against PA. We hypothesise that the carmoisine-mediated reduction of biofilm in PA is due to its interaction with LasR and interference with the QS system. The computational and biochemical analysis of another compound, 1,2-naphthoquinone-4-sulphonic acid, reiterated the role of the naphthalene ring in biofilm inhibition. Hence, this work will pave the way for the future discovery of antibiofilm drugs based on naphthalene ring-based lead compounds.Communicated by Ramaswamy H. Sarma.

Targeting genomic DNAs and oligonucleotide on base specificity: A comparative spectroscopic, computational and in vitro study

Drug discovery in targeted nucleic acid therapeutics encompass several stages and rigorous challenges owing to less specificity of the DNA binders and high failure rate in different stages of clinical trials. In this perspective, we report newly synthesized ethyl 4-(pyrrolo[1,2-a]quinolin-4-yl)benzoate (PQN) with minor groove A-T base pair binding selectivity and encouraging in cell results. This pyrrolo quinolin derivative has shown excellent groove binding ability with three of our inspected genomic DNAs (cpDNA 73 % AT, ctDNA58% AT and mlDNA 28 % AT) with varying A-T and G-C content. Notably in spite of similar binding patterns PQN have strong binding preference with A-T rich groove of genomic cpDNA over the ctDNA and mlDNA. Spectroscopic experiments like steady state absorption and emission results have established the relative binding strengths (K_abs = 6.3 × 10⁵ M^-1, 5.6 × 10⁴ M^-1, 4.3 × 10⁴ M^-1 and K_emiss = 6.1 × 10⁵ M^-1, 5.7 × 10⁴ M^-1 and 3.5 × 10⁴ M^-1 for PQN-cpDNA, PQN-ctDNA and PQN-mlDNA respectively) whereas circular dichroism and thermal melting studies have unveiled the groove binding mechanism. Specific A-T base pair attachment with van der Waals interaction and quantitative hydrogen bonding assessment were characterized by computational modeling. In addition to genomic DNAs, preferential A-T base pair binding in minor groove was also observed with our designed and synthesized deca-nucleotide (primer sequences 5^/-GCGAATTCGC-3^/ and 3^/-CGCTTAAGCG-5^/). Cell viability assays (86.13 % in 6.58 μM and 84.01 % in 9.88 μM concentrations) and confocal microscopy revealed low cytotoxicity (IC₅₀ 25.86 μM) and efficient perinuclear localization of PQN. We propose PQN with excellent DNA-minor groove binding capacity and intracellular permeation properties, as a lead for further studies encompassing nucleic acid therapeutics.

Unveiling the tartrazine binding mode with ds-DNA by UV-visible spectroscopy, electrochemical, and QM/MM methods

Here, we studied the interaction between the food colorant tartrazine (TZ) and double stranded DNA (dsDNA), using spectroscopic, electrochemical, and computational methods such as QM/MM combined with TD-DFT. Despite the UV-vis spectroscopy is widely used to study the interaction between molecules, for the case of TZ there are discrepancies in the analyses presented in the literature available, presenting both hyperchromic and hypochromic effects and consequently different rationalizations for their results. Herein we propose the combination of UV-vis experiments with the design of high-level computational models capable of reproducing the experimental behavior to finally define the proper binding mode at the molecular scale together with the rationalization of the experimental optical response due to the complex formation. To complement the UV-vis experiments, we propose the use of electrochemical measurements, to support the results obtained through UV-vis spectroscopy, as it has been successfully used for the determination of interaction modes between small molecules and biomolecules in any condition. Our UV-vis spectroscopy experiments showed only a hypochromic effect of the absorption spectra of TZ after interaction with DNA, indicative of TZ being deeply buried in the DNA structure. The effect of ionic strength in the experimental procedures led to the dissociation of TZ, thus indicating that the interaction mode was groove binding. On the other hand, the electrochemical studies showed an irreversible reduction peak of TZ, which after the interaction with DNA exhibited a positive shift in potential that can be attributed to groove binding. The binding constant for TZ-DNA was calculated as 4.45x10⁴M^-1 (UV-vis) and 5.75x10⁴M^-1 (electrochemistry), in line with other groove binder azo dyes. Finally, through the QM/MM calculations we found that the minor-groove binding mode interacting in zones rich in adenine and thymine was the model best suited to reproduce the experimental UV-vis response.

Molecular spectroscopic and molecular simulation studies on the interaction of oral contraceptive drug Ormeloxifene with CT-DNA

The interaction between oral contraceptive drug Ormeloxifene (ORM) and calf thymus DNA (CT-DNA) was studied using UV-Vis, fluorescence, circular dichroism (CD) and ¹H NMR spectral techniques under physiological buffer (pH 7.4). Competitive binding assays with ethidium bromide (EB) and Hoechst 33258, viscosity measurements, KI quenching studies, molecular docking and metadynamics simulation studies were also substantiated the spectroscopic results. ORM is found to binds in the minor groove of CT-DNA as evidenced by: (1) non-displacement of EB from EB/CT-DNA complex; (2) appreciable displacement of Hoechst 33258 from its CT-DNA complex; (3) slight alteration in the CD signal; (4) small shifts (Δδ < 0.033 ppm) without broadening in ¹H NMR signals and (5) the nearly equal extent of quenching of fluorescence of ORM by KI in the absence and presence of CT-DNA. Negative values of both enthalpy and entropy changes pointed out that the interaction between ORM and CT-DNA is governed mainly by H-bonding and van der Waals forces. Negative free energy change suggested a spontaneous interaction between ORM and CT-DNA. The free energy landscape of the binding process was computed using metadynamics simulation. The simulation study results disclosed that ORM binds to the minor groove of DNA through H-bonding and π-π stacking interactions. The results of molecular docking and simulation studies corroborate the available experimental data.

Economical gold recovery cycle from bio-sensing AuNPs: an application for nanowaste and COVID-19 testing kits

We report the controlled growth of biologically active compounds: gold nanoparticles (AuNPs) in various shapes, including their green synthesis, characterization, and studies of their applications towards biological, degradation and recycling. Using spectroscopic methods, studies on responsive binding mechanisms of AuNPs with biopolymers herring sperm deoxyribonucleic acid (hsDNA), bovine serum albumin (BSA), dyes degradation study, and exquisitely gold separation studies/recovery from nanowaste, COVID-19 testing kits, and pregnancy testing kits are discussed. The sensing ability of the AuNPs with biopolymers was investigated via various analytical techniques. The rate of degradation of various dyes in the presence and absence of AuNPs was studied by deploying stirring, IR, solar, and UV-Vis methods. AuNPs were found to be the most active cytotoxic agent against human breast cancer cell lines such as MCF-7 and MDAMB-468. Furthermore, an economical process for the recovery of gold traces from nanowaste, COVID-19 detection kits, and pregnancy testing kits was developed using inexpensive and eco-friendly α-cyclodextrin sugar. This method was found to be easy and safest in comparison with the universally accepted cyanidation process. In the future, small gold jewelry makers and related industries would benefit from the proposed gold-recycling process and it might contribute to their socio-economic growth. The methodologies proposed are also beneficial for trace-level forensic investigation.

A Rotatable Paper Device Integrating Reverse Transcription Loop-Mediated Isothermal Amplification and a Food Dye for Colorimetric Detection of Infectious Pathogens

In this study, we developed a rotatable paper device integrating loop-mediated isothermal amplification (RT-LAMP) and a novel naked-eye readout of the RT-LAMP results using a food additive, carmoisine, for infectious pathogen detection. Hydroxyl radicals created from the reaction between CuSO₄ and H₂O₂ were used to decolor carmoisine, which is originally red. The decolorization of carmoisine can be interrupted in the presence of DNA amplicons produced by the RT-LAMP reaction due to how DNA competitively reacts with the hydroxyl radicals to maintain the red color of the solution. In the absence of the target DNA, carmoisine is decolored, owing to its reaction with hydroxyl radicals; thus, positive and negative samples can be easily differentiated based on the color change of the solution. A rotatable paper device was fabricated to integrate the RT-LAMP reaction with carmoisine-based colorimetric detection. The rotatable paper device was successfully used to detect SARS-CoV-2 and SARS-CoV within 70 min using the naked eye. Enterococcus faecium spiked in milk was detected using the rotatable paper device. The detection limits for the SARS-CoV-2 and SARS-CoV targets were both 10³ copies/µL. The rotatable paper device provides a portable and low-cost tool for detecting infectious pathogens in a resource-limited environment.

Decrypting the interaction pattern of Piperlongumine with calf thymus DNA and dodecamer d(CGCGAATTCGCG)2 B-DNA: Biophysical and molecular docking analysis

The mechanisms of interaction of DNA with pharmacological molecules are critical to understanding their therapeutic actions on physiological systems. Piperlongumine is widely studied for its anticancer potential. Multi-spectrometry, calorimetry and in silico studies were employed to study the interaction of piperlongumine and calf thymus DNA. UV-Vis spectroscopy illustrated a hyperchromic pattern in spectra of the calf thymus DNA-piperlongumine complex, while fluorescent quenching was observed in emission spectral studies. Competitive displacement assay demonstrated higher displacement and binding constant for DNA-rhodamine B complex by piperlongumine than DNA-methylene blue complex. Differential scanning calorimetry presented non-significant changes in melting temperature and molecular docking presented the precise interaction site of piperlongumine with calf thymus DNA at minor groove. Further, piperlongumine treatment did not result in pBluescript KS plasmid DNA cleavage as revealed from the DNA topology assay. All these experiments confirmed the binding of piperlongumine with DNA through minor groove binding mode.

Deciphering the sensing of α-amyrin acetate with hs-DNA: a multipronged biological probe

In this study, we focus on the biomimetic development of small molecules and their biological sensing with DNA. The binding of herring sperm deoxyribonucleic acid (hs-DNA) with naturally occurring bioactive small molecule α-amyrin acetate (α-AA), a biomimetic - isolated from the leaves of Ficus (F.) arnottiana is investigated. Collective information from various imaging, spectroscopic and biophysical experiments provides evidence that α-AA is a minor groove sensor of hs-DNA and preferentially binds to the A-T-rich regions. Interactions of different concentrations of small molecule α-AA with hsDNA were evaluated via various analytical techniques such as UV-Vis, circular dichroism (CD) and fluorescence emission spectroscopy. Fluorescence emission spectroscopy results suggest that α-AA decreases the emission level of hsDNA. DNA minor groove sensor Hoechst 33258 and intercalative sensor EB, melting transition analysis (T M) and viscosity analysis clarified that α-AA binds to hs-DNA via a groove site. Biophysical chemistry and molecular docking studies show that hydrophobic interactions play a major role in this binding. The present research deals with a natural product biosynthesis-linked chemical-biology interface sensor as a biological probe for α-AA: hs-DNA.

The protective effect of natural phenolic compound on the functional and structural responses of inhibited catalase by a common azo food dye

In this research retrieval effects of natural yellow (NY) on the performance of carmoisine (CAR) inhibited bovine liver catalase (BLC) was studied using multispectral and theoretical methods. Kinetic studies showed that CAR inhibited BLC through competitive inhibition (IC₅₀ value of 2.24 × 10^-6 M) while the addition of NY recover the activity of CAR-BLC up to 82% in comparison with the control enzyme. Circular dichroism data revealed that NY can repair the structural changes of BLC, affected by CAR. Furthermore, an equilibrium dialysis study indicated that NY could reduce the stability of the CAR-catalase complex. The surface plasmon resonance (SPR) data analysis indicated a high affinity of NY to BLC compared to CAR and the binding of NY led to a decrease in the affinity of the enzyme to the inhibitor. On the other hand, fluorescence and molecular docking studies showed that the quenching mechanism of BLC by CAR occurs through a static quenching process, and van der Waals forces and hydrogen bonding play a crucial role in the binding of CAR to BLC. MLSD data demonstrated that NY could increase the binding energy of CAR-BLC complex from -7.72 kJ mol^-1 to -5.9 kJ mol^-1, leading to complex instability and catalase activity salvage.

Molecular photoswitches in aqueous environments

Molecular photoswitches enable dynamic control of processes with high spatiotemporal precision, using light as external stimulus, and hence are ideal tools for different research areas spanning from chemical biology to smart materials. Photoswitches are typically organic molecules that feature extended aromatic systems to make them responsive to (visible) light. However, this renders them inherently lipophilic, while water-solubility is of crucial importance to apply photoswitchable organic molecules in biological systems, like in the rapidly emerging field of photopharmacology. Several strategies for solubilizing organic molecules in water are known, but there are not yet clear rules for applying them to photoswitchable molecules. Importantly, rendering photoswitches water-soluble has a serious impact on both their photophysical and biological properties, which must be taken into consideration when designing new systems. Altogether, these aspects pose considerable challenges for successfully applying molecular photoswitches in aqueous systems, and in particular in biologically relevant media. In this review, we focus on fully water-soluble photoswitches, such as those used in biological environments, in both in vitro and in vivo studies. We discuss the design principles and prospects for water-soluble photoswitches to inspire and enable their future applications.

Molecular complexes of calf thymus DNA with various bioactive compounds: Formation and characterization

The interaction between biomacromolecules and ligands has attracted great interest because of their biological properties. Calf thymus DNA (ctDNA) can interact with bioactive compounds to form complexes. Here, ctDNA-ligand complexes were studied using fluorescence, absorption, and infrared spectroscopy, circular dichroism, ABTS assay and competitive displacement. The binding constants of bioactive compounds at the intercalative site of ctDNA ranked in order kaempferol > apigenin > quercetin > curcumin > riboflavin, while the binding constants at minor groove sites ranked quercetin > kaempferol > naringenin ~ apigenin > hesperetin > curcumin ~ resveratrol ~ riboflavin > caffeic acid. CtDNA maintained stable B-form with an enhancement of base stacking and a decrease of right-handed helicity in the presence of these bioactive compounds, except for hesperetin and caffeic acid. Bioactive compounds preferentially bound to guanine bases and tended to transfer into a more hydrophobic environment upon complexation with ctDNA. The DNA complexation did not affect the ABTS·⁺ scavenging capacity of quercetin, kaempferol, resveratrol and apigenin but increased the ones of naringenin, caffeic acid, curcumin, hesperetin and riboflavin. The data gathered here should be useful to understand the binding modes of DNA with ligands for their potential application in pharmaceutical and food industries.

Adaptable DNA-Interactive Probe Proficient at Selective Turn-On Sensing for Al3+: Insight from the Crystal Structure, Photophysical Studies, and Molecular Logic Gate

The synthesized Schiff base ligand 3-hydroxy-N'-(2-hydroxy-3-methoxybenzylidene)-2-naphthohydrazide (H₂NPV) is structurally characterized by single-crystal X-ray diffraction (XRD) and exhibits weak fluorescence in the excited state owing to the effect of excited-state-induced proton transfer (ESIPT). However, in the presence of Al³⁺, the ESIPT is blocked and chelation-enhanced fluorescence (CHEF) is induced because of complexation with the cations, resulting in turn-on emission for Al³⁺. The probe H₂NPV selectively detects Al³⁺ among the various metal ions, and the detection limit is found to be 1.70 μM. The composition and modes of complex coordination were determined by spectroscopic, theoretical studies and molecular logic gate applications. Finally, DNA binding studies were performed by spectroscopic and calorimetric methods to elucidate possible bioactivity of H₂NPV.

Adaptable DNA-Interactive Probe Proficient at Selective Turn-On Sensing for Al3+: Insight from the Crystal Structure, Photophysical Studies, and Molecular Logic Gate

The synthesized Schiff base ligand 3-hydroxy-N'-(2-hydroxy-3-methoxybenzylidene)-2-naphthohydrazide (H2NPV) is structurally characterized by single-crystal X-ray diffraction (XRD) and exhibits weak fluorescence in the excited state owing to the effect of excited-state-induced proton transfer (ESIPT). However, in the presence of Al3+, the ESIPT is blocked and chelation-enhanced fluorescence (CHEF) is induced because of complexation with the cations, resulting in turn-on emission for Al3+. The probe H2NPV selectively detects Al3+ among the various metal ions, and the detection limit is found to be 1.70 μM. The composition and modes of complex coordination were determined by spectroscopic, theoretical studies and molecular logic gate applications. Finally, DNA binding studies were performed by spectroscopic and calorimetric methods to elucidate possible bioactivity of H2NPV.

Food color 'Azorubine' interferes with quorum sensing regulated functions and obliterates biofilm formed by food associated bacteria: An in vitro and in silico approach

Quorum sensing (QS) plays a crucial role in different stages of biofilm development, virulence production, and subsequently to the growth of bacteria in food environments. Biofilm mediated spoilage of food is one of the ongoing challenge faced by the food industry worldwide as it incurs substantial economic losses and leads to various health issues. In the present investigation, we studied the interference of quorum sensing, its regulated virulence functions, and biofilm in food-associated bacteria by colorant azorubine. In vitro bioassays demonstrated significant inhibition of QS and its coordinated virulence functions in Chromobacterium violaceum 12472 (violacein) and Pseudomonas aeruginosa PAO1 (elastase, protease, pyocyanin, and alginate). Further, the decrease in the production EPS (49–63%) and swarming motility (61–83%) of the pathogens was also recorded at sub-MICs. Azorubine demonstrated broad-spectrum biofilm inhibitory potency (50–65%) against Chromobacterium violaceum, Pseudomonas aeruginosa, E. coli O157:H7, Serratia marcescens, and Listeria monocytogenes. ROS generation due to the interaction between bacteria and azorubine could be responsible for the biofilm inhibitory action of the food colorant. Findings of the in vitro studies were well supported by molecular docking and simulation analysis of azorubine and QS virulence proteins. Azorubine showed strong binding to PqsA as compared to other virulent proteins (LasR, Vfr, and QscR). Thus, it is concluded that azorubine is a promising candidate to ensure food safety by curbing the menace of bacterial QS and biofilm-based spoilage of food and reduce economic losses.

DNA intercalative trinuclear Cu(ii) complex with new trans axial nitrato ligation as an efficient catalyst for atmospheric CO2 fixation to epoxides

A trinuclear octahedral Cu^II complex was synthesized and structurally characterized by single crystal X-ray diffraction studies and behaved as a catalyst for CO₂ fixation to epoxide and as a DNA binder.

Design and synthesis of a sulphur containing Schiff base drug: DNA binding studies and theoretical calculations

The Schiff base compound MTA ((E)-5-methyl-N'-((5-methylthiophen-2-yl)methylene)-1H-pyrazole-3-carbohydrazide) derived from 2-thiophenecarboxaldehyde and 5-methylpyrazole-3-carbohydrazide has been designed to develop new sulphur containing DNA targeted molecule. The MTA has been characterized by elemental analyses, ¹H-NMR, single crystal X-ray diffraction studies as well as by geometry optimization of using DFT/B3LYP. The interaction of MTA with Calf thymus DNA (CT-DNA) was studied by spectroscopic and calorimetric techniques. The synthesized compound was found to bind with CT-DNA through groove binding mode, and the binding constant was estimated to be (4.15 ± 0.08) × 10⁴ M^-1. The negative ΔG⁰ and positive ΔS⁰ values obtained from the calorimetric technique confirmed the spontaneity of the binding of MTA with DNA.Communicated by Ramaswamy H. Sarma.

Synthesis of 5-Alkyl- and 5-Phenylamino-Substituted Azothiazole Dyes with Solvatochromic and DNA-Binding Properties

A series of new 5-mono- and 5,5'-bisamino-substituted azothiazole derivatives was synthesized from the readily available diethyl azothiazole-4,4'-dicarboxylate. This reaction most likely comprises an initial Michael-type addition by the respective primary alkyl and aromatic amines at the carbon atom C5 of the substrate. Subsequently, the resulting intermediates are readily oxidized by molecular oxygen to afford the amino-substituted azothiazole derivatives. The latter exhibit remarkably red-shifted absorption bands (λabs =507-661 nm) with high molar extinction coefficients and show a strong positive solvatochromism. As revealed by spectrometric titrations and circular and linear dichroism studies, the water-soluble, bis-(dimethylaminopropylamino)-substituted azo dye associates with duplex DNA by formation of aggregates along the phosphate backbone at high ligand-DNA ratios (LDR) and by intercalation at low LDR, which also leads to a significant increase of the otherwise low emission intensity at 671 nm.

DNA supported graphene quantum dots for Ag ion sensing

The use of graphene quantum dots can be extended for bio-sensing and metal ion detection. Synergistic combination of graphene quantum dots (GQDs) with DNA leads to high performance Ag-ion detection system. The thoroughly characterized GQDs were found to have spherical morphology, with dimensions in the range of 5-10 nm. The atomic force microscopy studies proved that the synthesized GQDs were mostly comprised of two to four graphene layers. To make the system biocompatible, GQDs/NGQDs were combined with DNA. Two properties of DNA were exploited, capacity to provide nitrogen to GQDs; and to synergistically contribute to Ag⁺ detection. In addition to Ag⁺, the strong green photoluminescence (PL) of GQDs showed significant quenching, owing to the appearance of associated Förster resonance energy transfer processes. This led to high sensing efficiencies.

Adaptable sensor for employing fluorometric detection of methanol molecules: theoretical aspects and DNA binding studies

The multifunctional ligand NO2-H2SALNN has been synthesized and employed for the selective fluorometric detection of methanol and its interaction with DNA.

hsDNA groove binding, photocatalytic activity, and in vitro breast and colon cancer cell reducing function of greener SeNPs

Selenium nanoparticles (SeNPs) have attracted great attention because of their superior optical properties and wide utilization in biological and biomedical studies. This paper reports an environmentally benign procedure of greener monodispersible SeNP synthesis using the reducing power of Trigonella foenum-graecum extract, characterization and their protective effect against unfolded (Herring sperm DNA) hsDNA. We investigated the anti-cancer activity of SeNPs against MCF-7, MDA MB 435 and COLO-205 cells. The photocatalytic activity of SeNPs was investigated for the degradation of a Sunset Yellow FCF (SYFCF) dye using ultraviolet-B light. The reduction of the Se ion to SeNPs was monitored by ultraviolet-visible spectroscopy (UV-vis). The size and morphology of the SeNPs were characterized by high resolution transmission electron microscopy (HRTEM), X-ray diffraction (XRD), and Dynamic Light Scattering (DLS). The SeNPs were stable, and the diameter was homogeneous at around 5-12 nm. Interactions of various concentrations of SeNPs with hsDNA were systematically investigated by UV-vis, fluorescence, circular dichroism (CD), polarimetry and FTIR spectroscopy under physiological conditions. The results from fluorescence spectroscopy indicated that SeNPs quenched the fluorescence intensity of hsDNA with increasing concentrations. The modified Stern-Volmer quenching rate constant Ksv, binding constant K and binding sites n at different temperatures and the corresponding thermodynamic parameters ΔH°, ΔG° and ΔS° were calculated. Hoechst 33258 and methyl green (MG) site markers, melting experiment (Tm), viscosity measurements and sequence specificity verification by DNA bases clarified that SeNPs bind to hsDNA via a groove site. The rate of photocatalytic degradation of the SYFCF dye in the presence and absence of photocatalysts (SeNPs) was studied using UV-vis, the results showed appreciable degradation of the SYFCF dye. Our results suggested that nano Se can be used as a promising selenium species with potential application in cancer treatment. These nanoparticles were found to be the most active cytotoxic agent prepared in a new green synthesis manner, causing >50% inhibition of MCF-7, MDA MB-435 and COLO-205 cell proliferation at concentrations <10(-7) M. Hence these SeNPs could be recognized as promising materials for biomedical applications.

Rhodamine based turn-on chemosensor for Fe3+ in aqueous medium and interactions of its Fe3+ complex with DNA

A novel di-coordinating rhodamine-based chemosensor, HL with NO donor atoms, selectively and rapidly recognizes Fe³⁺ in the presence of all biologically relevant as well as toxic metal ions and numerous anions and also with other reactive oxygen and nitrogen species.

Interaction between azo dye Acid Red 14 and pepsin by multispectral methods and docking studies

The interaction of synthetic azo dye Acid Red 14 with pepsin was studied by fluorescence spectroscopy, UV-vis spectroscopy, circular dichroism and molecular docking. Results from the fluorescence spectroscopy show that Acid Red 14 has a strong capability to quench the intrinsic fluorescence of pepsin with static quenching. Binding constant, number of the binding sites and thermodynamic parameters were measured at different temperatures. The result indicates that Acid Red 14 interact with pepsin spontaneously by hydrogen bonding and van der Waals interactions. Three-dimensional fluorescence spectra and circular dichroism spectra reveal that Acid Red 14 could slightly change the structure of pepsin. The hydrogen bond is formed between Acid Red 14 and Tyr-189 and Thr-218 residues of pepsin. Furthermore, the binding between Acid Red 14 and pepsin inhibits pepsin activity. The study can provide a way to analyze the biological safety of Acid Red 14 on digestive proteases or other proteins.

Interaction between 8-methoxypsoralen and trypsin: Monitoring by spectroscopic, chemometrics and molecular docking approaches

8-Methoxypsoralen (8-MOP) is a naturally occurring furanocoumarin with various biological activities. However, there is little information on the binding mechanism of 8-MOP with trypsin. Here, the interaction between 8-MOP and trypsin in vitro was determined by multi-spectroscopic methods combined with the multivariate curve resolution-alternating least squares (MCR-ALS) chemometrics approach. An expanded UV-vis spectral data matrix was analysed by MCR-ALS, the concentration profiles and pure spectra for the three reaction species (trypsin, 8-MOP and 8-MOP-trypsin) were obtained to monitor the interaction between 8-MOP and trypsin. The fluorescence data suggested that a static type of quenching mechanism occurred in the binding of 8-MOP to trypsin. Hydrophobic interaction dominated the formation of the 8-MOP-trypsin complex on account of the positive enthalpy and entropy changes, and trypsin had one high affinity binding site for 8-MOP with a binding constant of 3.81×10⁴Lmol^-1 at 298K. Analysis of three dimensional fluorescence, UV-vis absorption and circular dichroism spectra indicated that the addition of 8-MOP induced the rearrangement of the polypeptides carbonyl hydrogen-bonding network and the conformational changes in trypsin. The molecular docking predicted that 8-MOP interacted with the catalytic residues His57, Asp102 and Ser195 in trypsin. The binding patterns and trypsin conformational changes may result in the inhibition of trypsin activity. This study has provided insights into the binding mechanism of 8-MOP with trypsin.

Interaction and inhibitory influence of the azo dye carmoisine on lysozyme amyloid fibrillogenesis

The azo dye carmoisine has a significant inhibitory effect on fibrillogenesis in lysozyme.

Unraveling the Interaction of Silver Nanoparticles with Mammalian and Bacterial DNA

The focus of this study was to understand and unravel the interaction of silver nanoparticles (AgNPs) with different types of Deoxyribonucleic acid (DNA), mammalian and bacterial, having different base pair compositions. Binding of spherical silver nanoparticles (AgNPs) to Calf thymus (CT) DNA, Escherichia coli (EC) DNA and Micrococcus lysodeikticus (ML) DNA has been studied to gain insights into their mode of interaction and specificity. Interaction of AgNPs with synthetic DNA has also been carried out. On the basis of absorption, thermal melting, isothermal calorimetry and viscosity studies, we could establish the mode of binding and specificity of the synthesized silver nanoparticles with mammalian and bacterial DNA. Thermal melting (Tm) studies indicated a decrease in the Tm of all the DNAs, confirming the destabilization of DNA stacks on interaction with AgNPs. Comparative interaction studies with single stranded (ss) and double stranded (ds) DNAs further confirmed the specificity of the particles toward ds DNA. On the basis of the results we could confirm that the synthesized AgNPs could be used for selective detection of DNA through their DNA binding mechanism. In addition, the AgNPs-DNA complexes exhibited distinct differences in the SERS spectra making it an interesting SERS platform for identifying ds DNA. The optical and physical properties of AgNPs help in differentiating the DNAs of different base pair compositions through their binding affinity and specificity.

Synthesis, Characterization, Molecular Modeling, and DNA Interaction Studies of Copper Complex Containing Food Additive Carmoisine Dye

A copper complex of carmoisine dye; [Cu(carmoisine)2(H2O)2]; was synthesized and characterized by using physico-chemical and spectroscopic methods. The binding of this complex with calf thymus (ct) DNA was investigated by circular dichroism, absorption studies, emission spectroscopy, and viscosity measurements. UV-vis results confirmed that the Cu complex interacted with DNA to form a ground-state complex and the observed binding constant (2× 10(4) M(-1)) is more in keeping with the groove bindings with DNA. Furthermore, the viscosity measurement result showed that the addition of complex causes no significant change on DNA viscosity and it indicated that the intercalation mode is ruled out. The thermodynamic parameters are calculated by van't Hoff equation, which demonstrated that hydrogen bonds and van der Waals interactions played major roles in the reaction. The results of circular dichroism (CD) suggested that the complex can change the conformation of DNA from B-like form toward A-like conformation. The cytotoxicity studies of the carmoisine dye and its copper complex indicated that both of them had anticancer effects on HT-29 (colon cancer) cell line and they may be new candidates for treatment of the colon cancer.

In vitro DNA binding studies of antiretroviral drug nelfinavir using ethidium bromide as fluorescence probe

Understanding the interaction of small molecules with DNA has become an active research area at the interface between biology and chemistry. In the present work, we investigated the mode of interaction of nelfinavir (NFV) with herring sperm DNA (hs DNA) under physiological conditions using various biophysical techniques. Analysis of UV-absorption and fluorescence spectra indicates the formation of complex between NFV and hs DNA. According to the fluorescence results, the binding constant (K) between NFV and hs DNA was found to be 3.30 × 10(4)LM(-1). The calculated thermodynamic parameters (ΔH° and ΔS°) suggested that hydrogen bonding plays a major role in binding between them. Phosphate group binding studies revealed that there was no electrostatic interactions occurred between NFV and hs DNA. Circular dichroism (CD) and DNA melting curve were employed to measure the conformational change of hs DNA in the presence of NFV, which verified the minor groove binding mode. These results were further supported by viscosity measurements and competitive displacement assay study using Hoechst 33258. According to the sequence specificity experiments, NFV binds to A-T rich region of hs DNA.

Characterization of the interaction between resmethrin and calf thymus DNA in vitro

Resmethrin preferentially binds to the G–C rich region of the ctDNA groove, and the UV-vis spectral matrix is decomposed by MCR-ALS.

Partial intercalative binding of the food colorant erythrosine to herring sperm DNA

Erythrosine partially inserts into the G–C rich region of hsDNA and induces moderate conformational perturbation of the DNA.

Intercalation binding of food antioxidant butylated hydroxyanisole to calf thymus DNA

The binding properties of food antioxidant butylated hydroxyanisole (BHA) associated with calf thymus DNA (ctDNA) in physiological buffer (pH 7.4) were investigated. Experimental results based on fluorescence, UV-vis absorption, circular dichroism (CD), viscosity measurements and autodocking techniques confirmed the intercalation binding between BHA and ctDNA. The changes in Fourier transform infrared spectra of ctDNA induced by BHA suggested that BHA was more prone to bind to G-C rich region of ctDNA, which was further ascertained with the molecular docking studies. Analysis of the CD spectra indicated that this binding interaction led to a transformation from B-like DNA structure toward A-like conformation. The complexation of BHA with ctDNA was driven mainly by hydrogen bonds and hydrophobic forces. The binding constants of the BHA-ctDNA complex were calculated to be 2.03 × 10(4), 1.92 × 10(4) and 1.59 × 10(4)L mol(-1) at 298, 304 and 310 K, respectively. Gel electrophoresis results suggested that intercalated BHA molecules did not significantly affect plasmid DNA. Moreover, the concentration profiles and the spectra for the three reaction components (BHA, ctDNA, and BHA-ctDNA complex) of the system by resolving the augmented UV-vis spectral data matrix with the use of multivariate curve resolution-alternating least squares approach provided quantitative data to estimate the progress of BHA-ctDNA interaction. This study is expected to provide new insights into the mechanism of interaction between BHA and ctDNA.

Targeting proteins with toxic azo dyes: a microcalorimetric characterization of the interaction of the food colorant amaranth with serum proteins

The interaction of amaranth with two homologous serum albumins from human and bovine (HSA and BSA) was studied by microcalorimetry. The binding stoichiometry for the complexation of amaranth to both BSA and HSA was around 1, and the equilibrium constants were (5.79 ± 0.07) × 10(5) and (1.76 ± 0.05) × 10(5) M(-1), respectively. The binding reaction to HSA at 298.15 K was driven by a large negative enthalpic contribution and a small but positive entropic contribution, while to BSA, it was entirely enthalpy-driven and the entropic contribution was unfavorable. Parsing of the standard molar Gibbs energy revealed that the complexation was dominated by non-polyelectrolytic forces. Temperature-dependent isothermal titration calorimetry studies revealed that the enthalpic contribution increased and the entropic contribution decreased with the rise in the temperature but the Gibbs energy change remained almost unaltered. Differential scanning calorimetry results revealed that the binding reaction stabilized the serum albumins significantly against thermal unfolding.