Spectroscopic studies on the binding interaction of phenothiazinium dyes toluidine blue O, azure A and azure B to DNA

Biochemical Composition and Seasonal Variations of the Madagascar Algae Eucheuma denticulatum (Solieriaceae, Rhodophyta)

Although the density and diversity of seaweeds in Madagascar is particularly high, these resources are underexploited and they are not part of the local population's eating habits. No study has been carried out on the nutritional properties and seasonal variation of Eucheuma species harvested in Madagascar. In this study, Eucheuma denticulatum was harvested monthly over two years (2021 and 2022) on the northeast coast of Madagascar (Sainte Marie Island). The compositional analysis revealed prominent sugars and minerals up to 41.0 and 39.5% dw, respectively. E. denticulatum showed slight variability over the seasons in the macroelements and oligoelements (Ca, K, Na, Mg, Fe, Mn) ranging from 22.8 ± 0.2 to 25.3 ± 0.1% dw in 2021 and 22.1 ± 0.3 to 26.5 ± 0.3% dw in 2022. Total amino acids varied from 2.3 ± 0.6 to 2.5 ± 0.6% dw during the two years. Seaweed extracts showed antioxidant activity by the in vitro method ranging from 2026 ± 2 to 2998 ± 4 μg.mL-1 in 2021, and from 1904 ± 2 to 2876 ± 4 μg.mL-1 in 2022. Finally, the principal component analysis (PCA) showed a correlation between protein content and environmental parameters. The nutritional characteristics therefore confirmed that E. denticulatum could potentially be used as a nutritious and functional food and could be incorporated in the diet of local populations.

Nature-Inspired Synthesis of Yeast Capsule Replicas Encased with Silica-Vinyl Functionality: New Fluorescent Hollow Hybrid Microstructures

Yeast capsules (YCs) produced from Saccharomyces cerevisiae with encapsulated fluorescent phenosafranin and azure dyes were used as catalytic template guides for developing hybrid functional organic/inorganic hollow microstructures with silica (SiO2) deposited on their surface generated in the imidazole-buffered system without the addition of any cationic surfactant. YCs-doped with SiO2 act as fluorescence emitters maintaining dye-loaded materials by sealing the microporous surface of YCs. We used vinyltrimethoxysilane as a precursor of SiO2 endowed with functional vinyl groups facilitating their further modification without disturbing the polysaccharide wall integrity. Consequently, the hybrid fluorescent polysaccharide/silica microcapsules (YC@dye@SiO2) are promising for wide-ranging optoelectronic applications in electrochromic and OLED devices with biocompatibility and biodegradability properties.

Romanowsky staining: history, recent advances and future prospects from a chemistry perspective

Romanowsky staining was an important methodological breakthrough in diagnostic hematology and cytopathology during the late 19th and early 20th centuries; it has facilitated for decades the work of biologists, hematologists and pathologists working with blood cells. Despite more than a century of studying Romanowsky staining, no systematic review has been published that explains the chemical processes that produce the "Romanowsky effect" or "Romanowsky-Giemsa effect" (RGE), i.e., a purple coloration arising from the interaction of an azure dye with eosin and not due merely to their simultaneous presence. Our review is an attempt to build a bridge between chemists and biomedical scientists and to summarize the available data on methylene blue (MB) demethylation as well as the related reduction and decomposition of MB to simpler compounds by both light and enzyme systems and microorganisms. To do this, we analyze modern data on the mechanisms of MB demethylation both in the presence of acids and bases and by disproportionation due to the action of light. We also offer an explanation for why the RGE occurs only when azure B, or to a lesser extent, azure A is present by applying experimental and calculated physicochemical parameters including dye-DNA binding constants and electron density distributions in the molecules of these ligands. Finally, we discuss modern techniques for obtaining new varieties of Romanowsky dyes by modifying previously known ones. We hope that our critical literature study will help scientists understand better the chemical and physicochemical processes and mechanisms of cell staining with such dyes.

Bismuthene - Tetrahedral DNA nanobioconjugate for virus detection

In this work, we present an electrochemical sensor for fast, low-cost, and easy detection of the SARS-CoV-2 spike protein in infected patients. The sensor is based on a selected combination of nanomaterials with a specific purpose. A bioconjugate formed by Few-layer bismuthene nanosheets (FLB) and tetrahedral DNA nanostructures (TDNs) is immobilized on Carbon Screen-Printed Electrodes (CSPE). The TDNs contain on the top vertex an aptamer that specifically binds to the SARS-CoV-2 spike protein, and a thiol group at the three basal vertices to anchor to the FLB. The TDNs are also marked with a redox indicator, Azure A (AA), which allows the direct detection of SARS-CoV-2 spike protein through changes in the current intensity of its electrolysis before and after the biorecognition reaction. The developed sensor can detect SARS-CoV-2 spike protein with a detection limit of 1.74 fg mL-1 directly in nasopharyngeal swab human samples. Therefore, this study offers a new strategy for rapid virus detection since it is versatile enough for different viruses and pathogens.

A multifunctional DNA tetrahedron for imaging, gene therapy, and chemotherapy-phototherapy combination: Binding affinity and anticancer activity

Imaging, silencing cancer-related microRNA, and chemotherapy-phototherapy (CTPT) combination therapy are crucial for cancer diagnosis and drug resistance overcoming. In this study, we designed a multifunctional DNA tetrahedron (MB-MUC1-TD) for the targeted delivery of combined daunorubicin (DAU) + toluidine blue O (TBO). The detection limit of miRNA-21 was determined to be 0.91 nM. The intercalation of DAU and TBO into MB-MUC1-TD was proved by spectroscopic and calorimetric methods. The thermodynamic parameters for the interactions of DAU and/or TBO with MB-MUC1-TD confirmed high drug loading. The first addition of TBO in the ternary system achieved a higher loading of both drugs and a more stable complex structure. Deoxyribonuclease I (DNase I) accelerated the release of DAU and/or TBO loaded in MB-MUC1-TD. Confocal laser scanning microscope demonstrated that MB-MUC1-TD exhibited good imaging ability for miRNA-21 to accurately identify cancer cells, and DAU/TBO was predominantly distributed within the nucleus of cancer cells. In vitro cytotoxicity showed better gene therapy efficacy of MB on MCF-7 cells, better biocompatibility of loaded DAU and TBO on LO2 cells, and stronger synergistic cytotoxicity of DAU + TBO on MCF-7/ADR cells. This study may establish a theoretical foundation for co-loading CTPT combination drugs based on multifunctional DNA nanostructures.

Effect of the combined binding of topotecan and catechin/protocatechuic acid to a pH-sensitive DNA tetrahedron on release and cytotoxicity: Spectroscopic and calorimetric studies

The therapeutic efficacy of chemotherapy drugs can be effectively improved through the dual effects of their combination with natural polyphenols and the delivery of targeted DNA nanostructures. In this work, the interactions of topotecan (TPT), (+)-catechin (CAT), or protocatechuic acid (PCA) with a pH-sensitive DNA tetrahedron (MUC1-TD) in the binary and ternary systems at pHs 5.0 and 7.4 were investigated by fluorescence spectroscopy and calorimetry. The intercalative binding mode of TPT/CAT/PC to MUC1-TD was confirmed, and their affinity was ranked in the order of PCA > CAT > TPT. The effects of the pH-sensitivity of MUC1-TD and different molecular structures of CAT and PCA on the loading, release, and cytotoxicity of TPT were discussed. The weakened interaction under acidic conditions and the co-loading of CAT/PCA, especially PCA, improved the release of TPT loaded by MUC1-TD. The targeting of MUC1-TD and the synergistic effect with CAT/PCA, especially CAT, enhanced the cytotoxicity of TPT on A549 cells. For L02 cells, the protective effect of CAT/PCA reduced the damage caused by TPT. The single or combined TPT loaded by MUC1-TD was mainly concentrated in the nucleus of A549 cells. This work will provide key information for the combined application of TPT and CAT/PCA loaded by DNA nanostructures to improve chemotherapy efficacy and reduce side effects.

Contamination of textile dyes in aquatic environment: Adverse impacts on aquatic ecosystem and human health, and its management using bioremediation

Textile dyes are the burgeoning environmental contaminants across the world. They might be directly disposed of from textile industries into the aquatic bodies, which act as the direct source for the entire ecosystem, ultimately impacting the human beings. Hence, it is essential to dissect the potential adverse outcomes of textile dye exposure on aquatic plants, aquatic fauna, terrestrial entities, and humans. Analysis of appropriate literature has revealed that textile dye effluents could affect the aquatic biota by disrupting their growth and reproduction. Various aquatic organisms are targeted by textile dye effluents. In such organisms, these chemicals affect their development, behavior, and induce oxidative stress. General populations of humans are exposed to textile dyes via the food chain and drinking contaminated water. In humans, textile dyes are biotransformed into electrophilic intermediates and aromatic amines by the enzymes of the cytochrome family. Textile dyes and their biotransformed products form the DNA and protein adducts at sub-cellular moiety. Moreover, these compounds catalyze the production of free radicals and oxidative stress, and trigger the apoptotic cascades to produce lesions in multiple organs. In addition, textile dyes modulate epigenetic factors like DNA methyltransferase and histone deacetylase to promote carcinogenesis. Several bioremediation approaches involving algae, fungi, bacteria, biomembrane filtration techniques, etc., have been tested and some other hybrid systems are currently under investigation to treat textile dye effluents. However, many such approaches are at the trial stage and require further research to develop more efficient, cost-effective, and easy-to-handle techniques.

Fluorescent hydrophobic ion pairs: A powerful tool to investigate cellular uptake of hydrophobic drug complexes via lipid-based nanocarriers

HYPOTHESIS

Hydrophobic ion pairs (HIPs) between two fluorescent components and incorporation into nanoemulsions (NE) allows tracking in cellular uptake studies.

EXPERIMENTS

HIPs were formed between propidium iodide and 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-(7-nitro-2-1,3-benzoxadiazol-4-yl) (NBD-PE), azure A chloride and NBD-PE or coumarin 343 and 4-(4-dihexadecylaminostyryl)-N-methylpyridinium iodide) (DiA). Fluorescence spectra of the resulting complexes were recorded. HIPs were loaded into zwitterionic NE and their size, stability in different media, haemolytic properties and cytotoxicity were evaluated. Furthermore, cellular uptake at 37 °C and 4 °C was investigated via flow cytometry and confocal microscopy.

FINDINGS

HIP-formation increased lipophilicity of the hydrophilic model drugs. NE exhibited a size between 80 and 150 nm and were not toxic in concentrations up to 0.1 % but showed high haemolytic properties. Cellular uptake of propidium, azure A and coumarin 343 were 8-fold, 115-fold and 1.3-fold improved by the formation of HIPs and up to 59-fold, 120-fold and 50-fold by incorporating these HIPs in NE, respectively. Lower uptake was observed at 4 °C. In case of propidium/ NBD-PE and azure A/ NBD-PE HIPs, propidium and azure A were delivered into the cytosol, whereas NBD-PE was unable to enter cells. In case of coumarin 343/ DiA HIPs, both components accumulated in the cell membrane. Therefore, HIPs between two fluorescent compounds are a powerful tool to investigate cellular uptake of hydrophobic complexes via nanocarriers by visualization of their cellular distribution.

Binding, brightness, or noise? Extracting temperature-dependent properties of dye bound to DNA

We present a method for extracting temperature-dependent thermodynamic and photophysical properties of SYTO-13 dye bound to DNA from fluorescence measurements. Together, mathematical modeling, control experiments, and numerical optimization enable dye binding strength, dye brightness, and experimental noise (or error) to be discriminated from one another. By focusing on the low-dye-coverage regime, the model avoids bias and can simplify quantification. Utilizing the temperature-cycling capabilities and multi-reaction chambers of a real-time PCR machine increases throughput. Significant well-to-well and plate-to-plate variation is quantified by using total least squares to account for error in both fluorescence and nominal dye concentration. Properties computed independently for single-stranded DNA and double-stranded DNA by numerical optimization are consistent with intuition and explain the advantageous performance of SYTO-13 in high-resolution melting and real-time PCR assays. Distinguishing between binding, brightness, and noise also clarifies the mechanism for the increased fluorescence of dye in a solution of double-stranded DNA compared to single-stranded DNA; in fact, the explanation changes with temperature.

Deep targeted sequencing of cytological tumor cells using whole genome amplification

BACKGROUND

Genomic profiling in lung cancer is essential for precision medicine. Cytological specimens provide an alternative to formalin-fixed paraffin-embedded (FFPE) samples for comprehensive genomic analysis. However, this approach remains challenging when a limited number of tumor cells are available. We applied whole genome amplification (WGA) to cytology specimens to overcome this limitation.

METHODS

Using a lung cancer panel targeting 58 genes, we performed next-generation sequencing of whole genome-amplified DNA extracted from cytological specimens containing 10-20 tumor cells (cyto-WGA) and DNA from corresponding FFPE tumor tissue. We compared sequencing data from cyto-WGA and FFPE samples to examine the detection accuracy of copy number variations and oncogenic and drug-matched variants.

RESULTS

The DNA quality and quantity from cyto-WGA were higher than those from FFPE samples (p < .0005 and p < .05, respectively). Sequencing metrics of cyto-WGA and FFPE tissues showed no difference in the number of mapped reads and mean coverage depth, but there were significant differences in the on-target rate (p < .05) and uniformity (p < .0005). Copy number variations in cyto-WGA samples (n = 211) were higher than in FFPE samples (n = 9) (p < .0001). Fourty nine oncogenic variants were detected in cyto-WGA and 39 in FFPE. Of these variants, 34 (63%) were present in both samples. In addition, all 16 drug-matched variants were detected in FFPE and cyto-WGA samples with 100% concordance.

CONCLUSION

Cyto-WGA can be a feasible and alternative method to detect oncogenic and drug-matched variants.

Host-assisted delivery of a model drug to genomic DNA: Key information from ultrafast spectroscopy and in silico study

Intended drug delivery to a target without adverse effect is one of the major criteria for its acceptance in real use. Herein, we have made an attempt to explore the delivery efficacy of SDS surfactant in a monomer and micellar stage during the delivery of model drug, Toluidine Blue (TB) from micellar cavity to DNA. Molecular recognition of pre-micellar SDS encapsulated TB with DNA occurs at a rate constant (k1~652 s-1). On the contrary, no significant release of encapsulated TB at micellar concentration was observed within the experimental time frame. This originated from the higher binding affinity of TB towards the nano cavity of SDS at micellar concentration which doesn't allow the delivery of TB from the nano cavity of SDS micelle to DNA. Thus, molecular recognition controls the extent of DNA recognition by TB which in turn modulates the rate of delivery of TB from SDS in a concentration dependent morphology.

Arylamine Analogs of Methylene Blue: Substituent Effect on Aggregation Behavior and DNA Binding

The synthesis of new phenothiazine derivatives, analogs of Methylene Blue, is of particular interest in the design of new drugs, as well as in the development of a new generation of agents for photodynamic therapy. In this study, two new derivatives of phenothiazine, i.e., 3,7-bis(4-aminophenylamino)phenothiazin-5-ium chloride dihydrochloride (PTZ1) and 3,7-bis(4-sulfophenylamino)phenothiazin-5-ium chloride (PTZ2), are synthesized for the first time and characterized by NMR, IR spectroscopy, HRMS and elemental analysis. The interaction of the obtained compounds PTZ1 and PTZ2 with salmon sperm DNA is investigated. It is shown by UV-Vis spectroscopy and DFT calculations that substituents in arylamine fragments play a crucial role in dimer formation and interaction with DNA. In the case of PTZ1, two amine groups promote H-aggregate formation and DNA interactions through groove binding and intercalation. In the case of PTZ2, sulfanilic acid fragments prevent any dimer formation and DNA binding due to electrostatic repulsion. DNA interaction mechanisms are studied and confirmed by UV-vis and fluorescence spectroscopy in comparison with Methylene Blue. The obtained results open significant opportunities for the development of new drugs and photodynamic agents.

Interactions between natural organic matter (NOM) and the cationic dye toluidine blue at varying pHs and ionic strengths: Effects of NOM charges and Donnan gel potentials

This study examined effects of charges of molecules of natural organic matter (NOM) on its interactions with organic cations represented by toluidine blue (TB). NOM was exemplified in this study by Suwannee River (SR) and South Platte (SP) NOM. TB/NOM interactions were probed in the range of pH 3 to 11, DOC concentrations 0-10.6 mg L^-1 and ionic strengths 0.001-0.1 mol L^-1. Changes of TB absorbance at indicative wavelengths of 640 and 550 nm located in the characteristic absorbance band of TB and their ratio R_640/550 were used to quantify TB/NOM binding and the formation of TB dimers and possibly higher order aggregates in the Donnan volume of NOM molecules. These effects were interpreted based on the modeling of NOM charges and their Donnan gel potentials (ψ_D). The spectroscopic and modeling data showed that TB/NOM binding can be quantified via a complexation model that reflects the extent of electrostatic attraction between TB cations and anionic NOM molecules. The dependence of the apparent formation constant vs. ionic strength was shown to be qualitatively correlated with the ψ_D potentials of NOM molecules.

DNA-based bioassay of legionella pneumonia pathogen using gold nanostructure: A new platform for diagnosis of legionellosis

The specific diagnosis of hard-growing bacteria is one of the most important concerns of medical bacteriology. Legionella pneumophila is one of the most important bacteria in hard growth. In spite remarkable trends in bacteriology, now day, culture is the gold standard for detection of L. pneumophila. This work is an attempt to quantification of L. pneumophila bacteria using a bioassay. The fabrication of a new electrochemical DNA-based bioassay using gold nano architecture combined with as a transducer substrate combined with toluidine blue (TB) as a redox marker was performed successful. Also, the mixture of beta‑cyclodextrin and dopamine as Poly (dopamine‑β‑Cyclodextrin) was used to proper a biointerface for stabilization of gold nanoparticles optimum immobilize of pDNA sequence (5-SH-TCGA TAC TCT CCC CGC CCC TT T TGTATCGACG-3). So, a specific thiolated pDNA was immobilized on the transducer substrate and DNA hybridization was followed by C-DNA sequence (5-ACA AAA GGG GCG GGG AGA GTA-3) using square wave voltammetry and differential pulse voltammetry. At the optimum conditions, linear range was 1 μM to 1 ZM and low limit of quantification (LLOQ) was 1 Zepto-molar. L. pneumophila were sensitively distinguished by the planned DNA sensor. Finally, the engineered DNA based bioassay could be used for identifying the L. pneumophila samples from patients or environments.

Structural Heterogeneity in Polynucleotide-Facilitated Assembly of Phenothiazine Dyes

The assembly of stacked dyes on DNA is of interest for electron transfer, light harvesting, sensing, and catalysis applications. A combination of UV/vis absorption, linear dichroism (LD), and circular dichroism (CD) was applied to characterize thoroughly the aggregation with DNA of the phenothiazine dyes methylene blue, azure B, and thionine. Aggregates of each dye with [poly(dG-dC)]₂, [poly(dA-dT)]₂, and calf thymus DNA were explored at high dye:DNA binding ratios, where excess dye groove-binds after all intercalation sites are filled. The organization of the aggregates (dimers, trimers, and multimers) with polydeoxynucleotides displays a structural diversity that depends on DNA sequence, extent of methylation of dye exocyclic amine groups, and ionic strength. The dyes typically form right-handed H-aggregates having negative LD, consistent with stepped stacking along the minor groove. However, aggregates in some dye:DNA aggregates show left-handed chirality or positive LD, indicating unusual modes of aggregation such as formation of adventitious dimers between intercalated and minor groove bound dye. In terms of sequence-dependence, methylene blue shows more extensive aggregation with [poly(dA-dT)]₂, while thionine aggregates more with [poly(dG-dC)]₂. Azure B has distinctive behavior that is unlike either other dyes. Thus, although these phenothiazine dyes possess a common tricyclic framework, the organization of their polynucleotide-facilitated aggregates depends sensitively on the extent of methylation of the exocyclic amines.

Database of Absorption and Fluorescence Spectra of >300 Common Compounds for use in PhotochemCAD

The design of new molecules for photochemical studies typically requires knowledge of spectral features of pertinent chromophores beginning with the absorption spectrum (λabs ) and accompanying molar absorption coefficient (ε, m-1  cm-1 ) and often extending to the fluorescence spectrum (λem ) and fluorescence quantum yield (Φf ), where the fluorescence properties may be of direct relevance or useful as proxies to gain insight into the nature of the first excited singlet state. PhotochemCAD databases, developed over a period of 30 years, are described here. The previous databases for 150 compounds have been expanded to encompass 339 compounds for which absorption spectra (including ε values), fluorescence spectra (including Φf values) and references to the primary literature have been included where available (552 spectra altogether). The compounds exhibit spectra in the ultraviolet, visible and/or near-infrared spectral regions. The compound classes and number of members include acridines (21), aromatic hydrocarbons (41), arylmethane dyes (11), azo dyes (18), biomolecules (18), chlorins/bacteriochlorins (16), coumarins (14), cyanine dyes (19), dipyrrins (7), heterocycles (26), miscellaneous dyes (13), oligophenylenes (13), oligopyrroles (6), perylenes (5), phthalocyanines (11), polycyclic aromatic hydrocarbons (16), polyenes/polyynes (10), porphyrins (34), quinones (24) and xanthenes (15). A database of 31 solar spectra also is included.

Real-Time Visualization of Lysosome Destruction Using a Photosensitive Toluidine Blue Nanogel

Breaking the lysosome helps its sequestered payloads access their molecular targets in cells and thus enhances the intracellular drug delivery. Current strategies for lysosomal escape involve direct physical interactions with the lipid membrane. These interactions pose a systemic toxicity and uncontrolled membrane rupture risk. Here, we report a light-detonated lysosome disruption using a hyaluronan (HA) nanogel packed with toludine blue (TB). The HA/TB nanogel is concentrated within the lysosomes. The applied light assists TB in generating reactive oxygen species and destroying the lysosome in situ, both in cells and isolated lysosomes. Real time fluorescent tracking reveals that quenched TB fluorescence recovers along with lysosome explosion, relocates to the nucleus, and is presented as a fluorescent sparkling in cells. This HA/TB, composed of all clinically approved materials, represents a biocompatible and facile strategy to "bomb" lysosomes in a spatiotemporally controlled fashion.

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.

Exploring the interaction of phenothiazinium dyes methylene blue, new methylene blue, azure A and azure B with tRNAPhe: spectroscopic, thermodynamic, voltammetric and molecular modeling approach

RNA targeting by small molecules.

Binding interaction of phenothiazinium dyes with double stranded RNAs: Spectroscopic and calorimetric investigation

RNA targeting through small molecules is an emerging and promising therapeutic route that necessitates identification of small molecules that can selectively target specific RNA structures. In this context a comparative study of the interaction of two phenothiazinium dyes thionine (THN) and toluidine blue O (TBO) with three double stranded RNA polynucleotides (ds RNAs) viz. poly(I).poly(C), poly(A).poly(U) and poly(C).poly(G) was conducted by various biophysical techniques. A higher binding of THN with poly(I).poly(C) over poly(A).poly(U) and poly(C).poly(G) was observed. The intercalative binding and RNA induced fluorescence quenching of the dyes through a static mechanism was confirmed by viscosity studies and steady state polarization anisotropy experiments. Binding induced structural perturbation in the RNA polynucleotides was confirmed from circular dichroism spectroscopy. DSC and thermal melting experiments confirmed that the binding resulted in strong thermal stabilization. The binding affinity of THN with poly(I).poly(C) was the highest followed by that to poly(A).poly(U) and poly(C).poly(G). The trend was the same for TBO also, but THN bound stronger than TBO. The binding of the dyes was characterized by strong negative enthalpy changes with minimum positive entropy changes indicating typical intercalative interaction. The results presented here may be useful to design new types of RNA binding antitumor, antibacterial and anticancer agents.

Spectroscopic and calorimetric investigations on the binding of phenazinium dyes safranine-O and phenosafranine to double stranded RNA polynucleotides

RNA targeting through small molecules that can selectively bind specific RNA structures is an important current strategy in therapeutic drug development. Towards this strategy a comparative study on the interaction of two phenazinium dyes, safranine-O and phenosafranine to double stranded RNAs, poly(I).poly(C), poly(A).poly(U) and poly(C).poly(G) was performed. Spectrophotometric and spectrofluorimetric studies revealed non-cooperative binding of the dyes to the duplex RNA with binding constants of the order 10(5)M(-1) with a higher affinity of safranine-O to poly(I).poly(C) followed by poly(A).poly(U) and poly(C).poly(G). Anisotropy and fluorescence quenching results confirmed an intercalation mode of binding for the dyes on these RNAs. Binding induced conformational changes in the RNA polynucleotides were revealed from circular dichroism data. Thermal melting study and DSC experiments demonstrated stabilization of dye-RNA complexes. Calorimetric studies revealed that the binding was accompanied by a large positive entropy term with a small negative enthalpy contributions. Significant hydrophobic forces in the complexation of the double stranded RNAs with the dyes were confirmed from the negative heat capacity changes. Enthalpy-entropy compensation was also observed in the binding. Parsing of the Gibbs energy suggested a larger non-electrostatic contribution in all the cases. The results presented here may be helpful to design new types of RNA-based therapeutic agents.

Spectroscopic studies on the binding interaction of phenothiazinium dyes, azure A and azure B to double stranded RNA polynucleotides

This manuscript presents spectroscopic characterization of the interaction of two phenothiazinium dyes, azure A and azure B with double stranded (ds) ribonucleic acids, poly(A).poly(U), poly(C).poly(G) and poly(I).poly(C). Absorbance and fluorescence studies revealed that these dyes bind to the RNAs with binding affinities of the order 10(6)M(-1) to poly(A).poly(U), and 10(5)M(-1) to poly(C).poly(G) and poly(I).poly(C), respectively. Fluorescence quenching and viscosity data gave conclusive evidence for the intercalation of the dyes to these RNA duplexes. Circular dichroism results suggested that the conformation of the RNAs was perturbed on interaction and the dyes acquired strong induced optical activity on binding. Azure B bound to all the three RNAs stronger than azure A and the binding affinity varied as poly(A).poly(U)>poly(C).poly(G)>poly(I).poly(C) for both dyes.

Photophysical and calorimetric investigation on the structural reorganization of poly(A) by phenothiazinium dyes azure A and azure B

Poly(A) has significant relevance to mRNA stability, protein synthesis and cancer biology. The ability of two phenothiazinium dyes azure A (AA) and azure B (AB) to bind single-stranded poly(A) was studied by spectroscopic and calorimetric techniques. Strong binding of the dyes and the higher affinity of AA over AB were ascertained from absorbance and fluorescence experiments. Significant perturbation of the circular dichroism spectrum of poly(A) in the presence of these molecules with formation of induced CD bands in the 300-700 nm region was observed. Strong emission polarization of the bound dyes and strong energy transfer from the adenine base pairs of poly(A) suggested intercalative binding to poly(A). Intercalative binding was confirmed from fluorescence quenching experiments and was predominantly entropy driven as evidenced from isothermal titration calorimetry data. The negative values of heat capacity indicated involvement of hydrophobic forces and enthalpy-entropy compensation suggested noncovalent interactions in the complexation for both the dyes. Poly(A) formed a self-assembled structure on the binding of both the dyes that was more favored under higher salt conditions. New insights in terms of spectroscopic and thermodynamic aspects into the self-structure formation of poly(A) by two new phenothiazinium dyes that may lead to structural and functional damage of mRNA are revealed from these studies.

Unraveling the binding interaction of Toluidine blue O with bovine hemoglobin – a multi spectroscopic and molecular modeling approach

Toluidine blue O (TBO) is a cationic photosensitizer that belongs to the class of phenothiazinium dyes.

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.

Self-structure formation in polyadenylic acid by small molecules: new insights from the binding of planar dyes thionine and toluidine blue O

Thionine and toluidine blue targeting poly(A).

In vitro investigation of domain specific interactions of phenothiazine dye with serum proteins by spectroscopic and molecular docking approaches

In the present study the interaction of the chemotherapeutic agent, Azure A (AZA) with Human Serum Albumin (HSA) and Bovine Serum Albumin (BSA) was investigated by multi spectroscopic and molecular docking methods.

A new analytical bench assay for the determination of arylsulfatase a activity toward galactosyl-3-sulfate ceramide: implication for metachromatic leukodystrophy diagnosis

Here, we present the design and validation of a new assay for the diagnosis of metachromatic leukodystrophy. The method is highly specific, simple, reproducible, and straightforward. In our spectrophotometric method, the determination of arylsulfatase A (ARSA) activity toward the natural substrate, galactosyl-3-sulfate ceramide (or sulfatide), is performed using neat sulfatide without chemical modification. This confers to the assay high analytical specificity. The hydrolyzed sulfatide is monitored upon inclusion of the colorimetric reagent Azure A. The nonhydrolyzed sulfatide-Azure A is recovered and measured at a wavelength of λ = 650 nm. Thus, ARSA activity toward the sulfatide is obtained by subtracting the nonhydrolyzed sulfatide from the total sulfatide used in the enzyme reaction (sulfatide-Azure A present in a parallel assay performed in the absence of ARSA). Within a clinical context, our method definitely discriminated between healthy subject samples and metachromatic leukodystrophy patient samples, and, therefore, it is suitable for diagnostic applications and for monitoring the efficacy of therapeutic treatments in patients or animal models.