The binding properties of photosensitizer methylene blue to herring sperm DNA: a spectroscopic study

Establishment of an amplification strategy - specific binding - convenient processing integrated aflatoxin B1 detection method based on Fe3O4-NH4/AuNPs/apt-S1

Aflatoxin B1 (AFB1) is a potent toxin in food, necessitating rapid, instant, and sensitive detection. We have engineered an electrochemical sensor to monitor AFB1 using a system composed of Fe3O4-NH4/AuNPs/apt-S1. The aptamer specifically recognizes AFB1, while 'S1' is functionalized with methylene blue to enhance the current. The RecJf exonuclease promotes the formation of the electrochemical strategy. The Fe3O4 component, with its magnet properties, enables a rapid separation of solids and liquids without the need for instrumentation. The sensor exhibits a linear range for AFB1 ranging from 1 ng to 10 μg. The regression equation is I(nA) = 446.8 × logc+2085 (where I and c represent the peak current and AFB1 concentration, respectively). The correlation coefficient is 0.9508, and the detection limit is 3.447 nM. The relative standard deviation of AFB1 in peanut oil ranges from 4.80% to 6.80%. These results demonstrate that the sensor has high sensitivity, stability, repeatability, and specificity for AFB1 detection.

Association of Papacarie Duo® and low-level laser in antimicrobial photodynamic therapy (aPDT)

Dental caries is a multifactorial, non-communicable disease. Effective treatment options for minimally invasive removal of carious tissue include Papacarie Duo® gel and antimicrobial photodynamic therapy (aPDT). aPDT involves a combination of a light source and photosensitizer. Given that Papacarie Duo® contains a percentage of blue dye, this study aims to explore the antimicrobial potential of Papacarie Duo® when associated with a light source against Streptococcus mutans strains. The chosen light source was a low-power diode laser (λ = 660 nm, E = 3 J, P = 100 mW, t = 30 s). To assess antimicrobial capacity, planktonic suspensions of Streptococcus mutans were plated on Brain Heart Infusion Agar (BHI) to observe the formation of inhibition halos. The studied groups included methylene blue (0.005%), Papacarie Duo®, distilled water (negative control), 2% chlorhexidine (positive control), Papacarie Duo® + laser, and methylene blue (0.005%) + laser. Following distribution onto plates, each group was incubated at 37 °C for 48 h under microaerophilic conditions. Inhibition halos were subsequently measured using a digital caliper. The results showed that chlorhexidine had the greatest antimicrobial effect followed by the group of irradiated methylene blue and irradiated Papacarie Duo®. All experimental groups demonstrated antimicrobial potential, excluding the negative control group. The study concludes that Papacarie Duo® exhibits antimicrobial properties when associated with a low-power diode laser.

Nanometer Resolution Mass Spectro-Microtomography for In-Depth Anatomical Profiling of Single Cells

Visually identifying the molecular changes in single cells is of great importance for unraveling fundamental cellular functions as well as disease mechanisms. Herein, we demonstrated a mass spectro-microtomography with an optimal voxel resolution of ∼300 × 300 × 25 nm³, which enables three-dimensional tomography of chemical substances in single cells. This mass imaging method allows for the distinguishment of abundant endogenous and exogenous molecules in subcellular structures. Combined with statistical analysis, we demonstrated this method for spatial metabolomics analysis of drug distribution and subsequent molecular damages caused by intracellular drug action. More interestingly, thanks to the nanoprecision ablation depth (∼12 nm), we realized metabolomics profiling of cell membrane without the interference of cytoplasm and improved the distinction of cancer cells from normal cells. Our current method holds great potential to be a powerful tool for spatially resolved single-cell metabolomics analysis of chemical components during complex biological processes.

Photodynamic therapy mediated by a red LED and methylene blue inactivates resistant Leishmania amazonensis

Cutaneous leishmaniasis is a neglected parasitic disease that leads to destructive lesions. The emergence of drug resistance has been a global concern over the past years. Photodynamic therapy (PDT) mediated by a red LED and methylene blue (MB) involves the overproduction of oxidative stress, which oxidizes several cellular biomolecules and prevents the selection of resistant strains. Herein, we investigated the potential of PDT mediated by MB against wild-type and miltefosine-resistant strains of Leishmania amazonensis. As a result, both strains were susceptible to PDT, thus encouraging us to seek the best conditions to overcome the drug resistance problem in cutaneous leishmaniasis.

Generation of singlet oxygen by porphyrin and phthalocyanine derivatives regarding the oxygen level

Background. The principle of photodynamic effect is based on the combined action of photosensitiser, molecular oxygen and light, which produce various reactive oxygen species and are associated with significant cellular damage. Singlet oxygen is one of the most serious representatives, which is characterised by powerful oxidising properties. Moreover, concomitant hyperbaric oxygen treatment can support these effects. Therefore, the subject of our study was to compare the yields of singlet oxygen for four different photosensitizers in dependency on the oxygen concentration. Material and methods. Four different photosensitizers 5,10,15,20-tetrakis(1-methyl-4-pyridinio)porphyrin tetra(p-toluenesulfonate), tetramethylthionine chloride, 5,10,15,20-tetrakis(4-sulfonatophenyl)porphyrin zinc(II) and zinc phthalocyanine disulfonate were investigated to determine the yield of singlet oxygen in PBS by Singlet Oxygen Sensor Green reagent under different partial pressures of oxygen (0.4 and 36 mg/l). Results. There were no noticeable shifts in the excitation and emission fluorescence spectra regarding the oxygen concentration. Concerning the same molar concentration of photosensitizers the production of singlet oxygen was highest for 5,10,15,20-tetrakis(4-sulfonatophenyl)porphyrin zinc(II), where the rate of the fluorescence change was more than 3 times higher than that obtained for 5,10,15,20-tetrakis(1-methyl-4-pyridinio)porphyrin tetra(p-toluenesulfonate). On the other hand, zinc phthalocyanine disulfonate showed the lowest yield in singlet oxygen production. Conclusions. Singlet oxygen production, within the range of oxygen concentrations achievable in tissues under normoxia or hyperoxia, does not depend on these concentrations. However, the singlet oxygen generation is significantly influenced by the type of photosensitizer, with the highest yield belonging to 5,10,15,20-tetrakis(4-sulfonatophenyl)porphyrin zinc(II).

A New Insight into the Mechanisms Underlying the Discoloration, Sorption, and Photodegradation of Methylene Blue Solutions with and without BNOx Nanocatalysts

Methylene blue (MB) is widely used as a test material in photodynamic therapy and photocatalysis. These applications require an accurate determination of the MB concentration as well as the factors affecting the temporal evolution of the MB concentration. Optical absorbance is the most common method used to estimate MB concentration. This paper presents a detailed study of the dependence of the optical absorbance of aqueous methylene blue (MB) solutions in a concentration range of 0.5 to 10 mg·L^-1. The nonlinear behavior of optical absorbance as a function of MB concentration is described for the first time. A sharp change in optical absorption is observed in the range of MB concentrations from 3.33 to 4.00 mg·L^-1. Based on the analysis of the absorption spectra, it is concluded that this is due to the formation of MB dimers and trimers in the specific concentration range. For the first time, a strong, thermally induced discoloration effect of the MB solution under the influence of visible and sunlight was revealed: the simultaneous illumination and heating of MB solutions from 20 to 80 °C leads to a twofold decrease in the MB concentration in the solution. Exposure to sunlight for 120 min at a temperature of 80 °C led to the discoloration of the MB solution by more than 80%. The thermally induced discoloration of MB solutions should be considered in photocatalytic experiments when tested solutions are not thermally stabilized and heated due to irradiation. We discuss whether MB is a suitable test material for photocatalytic experiments and consider this using the example of a new photocatalytic material-boron oxynitride (BNO_x) nanoparticles-with 4.2 and 6.5 at.% of oxygen. It is shown that discoloration is a complex process and includes the following mechanisms: thermally induced MB photodegradation, MB absorption on BNO_x NPs, self-sensitizing MB photooxidation, and photocatalytic MB degradation. Careful consideration of all these processes makes it possible to determine the photocatalytic contribution to the discoloration process when using MB as a test material. The photocatalytic activity of BNO_x NPs containing 4.2 and 6.5 at.% of oxygen, estimated at ~440 μmol·g^-1·h^-1. The obtained results are discussed based on the results of DFT calculations considering the effect of MB sorption on its self-sensitizing photooxidation activity. A DFT analysis of the MB sorption capacity with BNO_x NPs shows that surface oxygen defects prevent the sorption of MB molecules due to their planar orientation over the BNO_x surface. To enhance the sorption capacity, surface oxygen defects should be eliminated.

Surfactin-methylene blue complex under LED illumination for antibacterial photodynamic therapy: Enhanced methylene blue transcellular accumulation assisted by surfactin

Recently, increased attention has been focused on antibacterial photodynamic therapy (APDT) to treat multidrug-resistant bacterial infection due to the antibiotic abuse. Methylene blue has been used as a kind of efficient and cheap commercial photosensitizer in APDT. However, due to high hydrophilicity, methylene blue is not able to be transcellular intaken and accumulated efficiently. To promote accumulation and APDT efficiency of methylene blue, lipopeptide surfactin-methylene blue complex has been prepared through electrostatic interaction. The complex under LED irradiation was found to effectively reduce 5.0 Log₁₀ CFU and 7.6 Log₁₀ CFU for P. aeruginosa and S. aureus, respectively. The bacterial reduction efficiency is slightly higher than free methylene blue. The photosensitizers accumulation and APDT targeting protein have been characterized by fluorescence spectroscopy, fluorescence microscopy and protein electrophoresis techniques. These results demonstrated that more surfactin-methylene blue complex could be accumulated more into the cell, and inactivate bacteria through destroying intracellular protein under LED illumination. In comparison, free methylene blue under light could inactivate bacteria through destroying membrane protein and lipid structures. These results would provide valuable insight for developing advanced clinical medicine and designing photo-drug for photodynamic therapy.

DNA-Triggered Enhancement of Singlet Oxygen Production by Pyridinium Alkynylanthracenes

There is an ongoing interest in ¹ O₂ sensitizers, whose activity is selectively controlled by their interaction with DNA. To this end, we synthesized three isomeric pyridinium alkynylanthracenes 2 o-p and a water-soluble trapping reagent for ¹ O₂ . In water and in the absence of DNA, these dyes show a poor efficiency to sensitize the photooxygenation of the trapping reagent as they decompose due to electron transfer processes. In contrast, in the presence of DNA ¹ O₂ is generated from the excited DNA-bound ligand. The interactions of 2 o-p with DNA were investigated by thermal DNA melting studies, UV/vis and fluorescence spectroscopy, and linear and circular dichroism spectroscopy. Our studies revealed an intercalative binding with an orientation of the long pyridyl-alkynyl axis parallel to the main axis of the DNA base pairs. In the presence of poly(dA : dT), all three isomers show an enhanced formation of singlet oxygen, as indicated by the reaction of the latter with the trapping reagent. With green light irradiation of isomer 2 o in poly(dA : dT), the conversion rate of the trapping reagent is enhanced by a factor >10. The formation of ¹ O₂ was confirmed by control experiments under anaerobic conditions, in deuterated solvents, or by addition of ¹ O₂ quenchers. When bound to poly(dG : dC), the opposite effect was observed only for isomers 2 o and 2 m, namely the trapping reagent reacted significantly slower. Overall, we showed that pyridinium alkynylanthracenes are very useful intercalators, that exhibit an enhanced photochemical ¹ O₂ generation in the DNA-bound state.

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.

The photosensitiser azure A disrupts mitochondrial bioenergetics through intrinsic and photodynamic effects

Azure A (AA) is a cationic molecule of the class of phenothiazines that has been applied in vitro as a photosensitising agent in photodynamic antimicrobial chemotherapy. It is a di-demethylated analogue of methylene blue (MB), which has been demonstrated to be intrinsically and photodynamically highly active on mitochondrial bioenergetics. However, as far as we know, there are no studies about the photodynamic effects of AA on mammalian mitochondria. Therefore, this investigation aimed to characterise the intrinsic and photodynamic acute effects of AA (0.540 μM) on isolated rat liver mitochondria, isolated hepatocytes, and isolated perfused rat liver. The effects of AA were assessed by evaluating several parameters of mitochondrial bioenergetics, oxidative stress, cell viability, and hepatic energy metabolism. The photodynamic effects of AA were assessed under simulated hypoxic conditions, a suitable way for mimicking the microenvironment of hypoxic solid tumour cells. AA interacted with the mitochondria and, upon photostimulation (10 min of light exposure), produced toxic amounts of reactive oxygen species (ROS), which damaged the organelle, as demonstrated by the high levels of lipid peroxidation and protein carbonylation. The photostimulated AA also depleted the GSH pool, which could compromise the mitochondrial antioxidant defence. Bioenergetically, AA photoinactivated the complexes I, II, and IV of the mitochondrial respiratory chain and the F1FO-ATP synthase complex, sharply inhibiting the oxidative phosphorylation. Upon photostimulation (10 min of light exposure), AA reduced the efficiency of mitochondrial energy transduction and oxidatively damaged lipids in isolated hepatocytes but did not decrease the viability of cells. Despite the useful photobiological properties, AA presented noticeable dark toxicity on mitochondrial bioenergetics, functioning predominantly as an uncoupler of oxidative phosphorylation. This harmful effect of AA was evidenced in isolated hepatocytes, in which AA diminished the cellular ATP content. In this case, the cells exhibited signs of cell viability reduction in the presence of high AA concentrations, but only after a long time of incubation (at least 90 min). The impairments on mitochondrial bioenergetics were also clearly manifested in intact perfused rat liver, in which AA diminished the cellular ATP content and stimulated the oxygen uptake. Consequently, gluconeogenesis and ureogenesis were strongly inhibited, whereas glycogenolysis and glycolysis were stimulated. AA also promoted the release of cytosolic and mitochondrial enzymes into the perfusate concomitantly with inhibition of oxygen consumption. In general, the intrinsic and photodynamic effects of AA were similar to those of MB, but AA caused some distinct effects such as the photoinactivation of the complex IV of the mitochondrial respiratory chain and a diminution of the ATP levels in the liver. It is evident that AA has the potential to be used in mitochondria-targeted photodynamic therapy, even under low oxygen concentrations. However, the fact that AA directly disrupts mitochondrial bioenergetics and affects several hepatic pathways that are linked to ATP metabolism, along with its ability to perturb cellular membranes and its little potential to reduce cell viability, could result in significant adverse effects especially in long-term treatments.

The photodynamic and direct actions of methylene blue on mitochondrial energy metabolism: A balance of the useful and harmful effects of this photosensitizer

According to the literature, methylene blue (MB) is a photosensitizer (PS) with a high affinity for mitochondria. Therefore, several studies have explored this feature to evaluate its photodynamic effects on the mitochondrial apoptotic pathway under normoxic conditions. We are aware only of limited reports regarding MB's photodynamic effects on mitochondrial energy metabolism, especially under hypoxic conditions. Thus, the purposes of this study were to determine the direct and photodynamic acute effects of MB on the energy metabolism of rat liver mitochondria under hypoxic conditions and its direct acute effects on several parameters linked to energy metabolism in the isolated perfused rat liver. MB presented a high affinity for mitochondria, irrespective of photostimulation or proton gradient formation. Upon photostimulation, MB demonstrated high in vitro oxidizing species generation ability. Consequently, MB damaged the mitochondrial macromolecules, as could be evidenced by the elevated levels of lipid peroxidation and protein carbonyls. In addition to generating a pro-oxidant environment, MB also led to a deficient antioxidant defence system, as indicated by the reduced glutathione (GSH) depletion. Bioenergetically, MB caused uncoupling of oxidative phosphorylation and led to photodynamic inactivation of complex I, complex II, and F₁F_O-ATP synthase complex, thus decreasing mitochondrial ATP generation. Contrary to what is expected for an ideal PS, MB displayed appreciable dark toxicity on mitochondrial energy metabolism. The results indicated that MB acted via at least three mechanisms: direct damage to the inner mitochondrial membrane; uncoupling of oxidative phosphorylation; and inhibition of electron transfer. Confirming the impairment of mitochondrial energy metabolism, MB also strongly inhibited mitochondrial ATP production. In the perfused rat liver, MB stimulated oxygen consumption, decreased the ATP/ADP ratio, inhibited gluconeogenesis and ureogenesis, and stimulated glycogenolysis, glycolysis, and ammoniagenesis, fully corroborating its uncoupling action in intact cells, as well. It can be concluded that even under hypoxic conditions, MB is a PS with potential for photodynamic effect-induced mitochondrial dysfunction. However, MB disrupts the mitochondrial energy metabolism even in the dark, causing energy-linked liver metabolic changes that could be harmful in specific circumstances.

Study on the interactions between B-norcholesteryl benzimidazole compounds with ct-DNA

The study of molecule-DNA interaction is very important for designing an improved therapeutic agent. In previous studies, we synthesized some B-norcholesteryl benzimidazole compounds, and the tests on cancer cells showed that these compounds had good in vitro anti-cancer activities. In order to further investigate mechanism of their actions, three different B-norcholesteryl benzimidazole compounds were selected and interaction of these compounds with the calf thymus DNA (ct-DNA) was monitored by using various methods including UV-Vis and fluorescence spectroscopic techniques, viscosity measurement, and circular dichroism (CD). The results proved a hypochromic effect accompanied with a slight red-shift due to the interaction of the molecules with ct-DNA. According to the UV-Vis and fluorescence spectra, the mentioned compounds were bound to DNA, preferentially through partial intercalation into the DNA helix. Moreover, the ethidium bromide (EB) and Hoechst 33258 competitive binding experiments were also used to confirm the interaction mode of the compounds with ct-DNA. In the Hoechst 33258 displacement experiment, no significant change in the fluorescence intensity was observed. Additional assays such as iodide quenching, viscosity, and CD spectroscopy further confirmed that intercalation should be the major binding mode of the selected compounds with DNA. The cytotoxicity of these three compounds was also evaluated by MTT method, and the results confirmed that binding ability of these compounds to DNA was consistent with their cytotoxicity behavior. The experimental results indicated a higher binding affinity for compound 3 compared to the other compounds. This research provided a better understanding on the molecular mechanism of the interaction between B-norcholesteryl benzimidazole compounds and tumor cells, and offered a beneficial perspective to the designation of novel B-norsteroidal anticancer compounds.

Evaluation of the effect of Tb(IV)-NR complex on herring sperm DNA genetic information by mean of spectroscopic

The interaction between Tb(IV)-NR complex and herring sperm DNA in buffer solution of Tris-HCl was investigated with the use of acridine orange(AO) as a spectral probe. The binding modes and other information were provided by the UV-spectrophotometry and fluorescence spectroscopy. The thermodynamic functions expressed that the binding constants of Tb(IV)-NR complex with DNA was K^θ_298.15K = 4.03 × 10⁵ L·mol^-1, K^θ_310.15K =1.30 × 10⁷ L·mol^-1, and the Δ_rGθ m _298.15 K＝-3.20 × 10⁴ J·mol^-1. The scatchard equation suggested that the interaction mode between Tb(IV)-NR complex and herring sperm DNA is electrostatic and weak intercalation bindings. FTIR spectroscopy results also indicate that there is a specific interaction between the Tb(IV)-NR complex and the A and G bases of DNA.

NMR studies on oligonucleotide - Methylene blue conjugates targeting double-helical nucleic acids

Methylene blue (MB) - nucleic acid interactions are of considerable interest due to the photosensitizing activity of the dye with potential applications in medicine and biotechnology. Covalent attachment of the MB to an oligonucleotide through a flexible heptamethylene linker enabled a positioning of the dye moiety to specific sites through triplex formation with a target duplex. NMR studies demonstrated interactions of MB with the nucleic acids. In sequences with the MB moiety facing the triplex-duplex junction with an alternating CG duplex overhang next to a T·A·T triple-helical tract, proton resonances experienced severe linebroadening upon MB binding and point to kinetically labile complexes with exchange among different binding modes. For sequences with the MB moiety facing a terminal T·A·T base triad of the triplex tract, structural heterogeneity decreased when compared to a triplex without MB attached to the third strand. Also, the thermal stability of the latter construct increased significantly in the presence of MB, indicating external end stacking as predominant binding mode. Without any obvious disruptions of sequential imino-imino NOE contacts within the triplex and duplex tracts, a most favorable intercalation between T·A·T base triples or CG base pairs is not supported by the present data under our experimental conditions.

DNA binding studies of antibiotic drug cephalexin using spectroscopic and molecular docking techniques

The purpose of this study was to explore an accurate characterization of the binding interaction of antibiotic drug cephalexin with calf thymus DNA (CT-DNA) as a relevant biological target by using UV absorption, fluorescence spectroscopy and circular dichroism (CD) in vitro under simulated physiological conditions (pH = 7.4) and also through a molecular modeling study. The results showed that the drug interacts with the DNA helix via a minor groove binding mode. The thermodynamic parameters were calculated and showed that the reaction between the drug and CT-DNA was exothermic. In addition, the drug enforced traceable changes in the viscosity of DNA. The molecular modeling results indicated that cephalexin forcefully binds to the minor groove of DNA with a relative binding energy of -21.02 kJ mol^-1. The obtained theoretical results were in good agreement with those obtained from experimental studies.

Intercalating Electron Dyes for TEM Visualization of DNA at the Single-Molecule Level

Staining compounds containing heavy elements (electron dyes) can facilitate the visualization of DNA and related biomolecules by using TEM. However, research into the synthesis and utilization of alternative electron dyes has been limited. Here, we report the synthesis of a novel DNA intercalator molecule, bis-acridine uranyl (BAU). NMR spectroscopy and MS confirmed the validity of the synthetic strategy and gel electrophoresis verified the binding of BAU to DNA. For TEM imaging of DNA, two-dimensional DNA origami nanostructures were used as a robust microscopy test object. By using scanning transmission electron microscopy (STEM) imaging, which is favored over conventional wide-field TEM for improved contrast, and therefore, quantitative image analysis, it is found that the synthesized BAU intercalator can render DNA visible, even at the single-molecule scale. For comparison, other staining compounds with a purported affinity towards DNA, such as dichloroplatinum, cisplatin, osmium tetroxide, and uranyl acetate, have been evaluated. The STEM contrast is discussed in terms of the DNA-dye association constants, number of dye molecules bound per base pair, and the electron-scattering capacity of the metal-containing ligands. These findings pave the way for the future development of electron dyes with specific DNA-binding motifs for high-resolution TEM imaging.

Studies on the Interaction of [SnMe2Cl2(bu2bpy)] Complex with ct-DNA Using Multispectroscopic, Atomic Force Microscopy (AFM) and Molecular Docking

The interaction of SnMe₂Cl₂(bu₂bpy)complex with calf thymus DNA (ct-DNA) has been explored following, using spectroscopic methods, viscosity measurements, Atomic force microscopy, Thermal denaturation and Molecular docking. It was found that Sn(IV) complex could bind with DNA via intercalation mode as evidenced by hyperchromism and bathochromic in UV-Vis spectrum; these spectral characteristics suggest that the Sn(IV) complex interacts with DNA most likely through a mode that involves a stacking interaction between the aromatic chromophore and the base pairs of DNA. In addition, the fluorescence emission spectra of intercalated methylene blue (MB) with increasing concentrations of SnMe₂Cl₂(bu₂bpy) represented a significant increase of MB intensity as to release MB from MB-DNA system. Positive values of ΔH and ΔS imply that the complex is bound to ct-DNA mainly via the hydrophobic attraction. Large complexes contain the DNA chains with an average size of 859 nm were observed by using AFM for Sn(IV) Complex-DNA. The Fourier transform infrared study showed a major interaction of Sn(IV) complex with G-C and A-T base pairs and a minor perturbation of the backbone PO₂ group. Addition of the Sn(IV)complex results in a noticeable rise in the Tm of DNA. In addition, the results of viscosity measurements suggest that SnMe₂Cl₂(bu₂bpy) complex may bind with the classical intercalative mode. From spectroscopic and hydrodynamic studies, it has been found that Sn(IV)complex interacts with DNA by intercalation mode. Optimized docked model of DNA-complex mixture confirmed the experimental results.

Drug Effect of Thulium(III)-Arsenazo III Complex on Herring Sperm DNA

To assess the potential cytostatic properties of the thulium(III)-arsenazo III complex as a probe of rare earth complex antitumor drugs, the interaction information of the thulium(III)-arsenazo III complex with DNA was obtained by using spectroscopy, viscosity measurements, and voltammetric methods. The thermodynamic functions demonstrated that the binding constants of the thulium(III)-arsenazo III complex with DNA were Kθ298.15K = 4.84 × 106 L·mol−1 and Kθ308.15K = 4.48 × 106 L·mol−1, and the binding process was enthalpy driven. The increase in relative viscosity of DNA with the addition of the thulium(III)-arsenazo III complex and the results from Scatchard and voltammetric methods showed that the interaction mode between the thulium(III)-arsenazo III complex and DNA was groove binding along with weak intercalative binding.

Superstructure-Dependent Loading of DNA Origami Nanostructures with a Groove-Binding Drug

DNA origami nanostructures are regarded as powerful and versatile vehicles for targeted drug delivery. So far, DNA origami-based drug delivery strategies mostly use intercalation of the therapeutic molecules between the base pairs of the DNA origami's double helices for drug loading. The binding of nonintercalating drugs to DNA origami nanostructures, however, is less studied. Therefore, in this work, we investigate the interaction of the drug methylene blue (MB) with different DNA origami nanostructures under conditions that result in minor groove binding. We observe a noticeable effect of DNA origami superstructure on the binding affinity of MB. In particular, non-B topologies as for instance found in designs using the square lattice with 10.67 bp/turn may result in reduced binding affinity because groove binding efficiency depends on groove dimensions. Also, mechanically flexible DNA origami shapes that are prone to structural fluctuations may exhibit reduced groove binding, even though they are based on the honeycomb lattice with 10.5 bp/turn. This can be attributed to the induction of transient over- and underwound DNA topologies by thermal fluctuations. These issues should thus be considered when designing DNA origami nanostructures for drug delivery applications that employ groove-binding drugs.

Evaluation of aluminum phthalocyanine chloride and DNA interactions for the design of an advanced drug delivery system in photodynamic therapy

The aim of this study was to evaluate the interaction of aluminum phthalocyanine chloride (AlClPc) with double-stranded DNA. Absorption and fluorescence spectra, resonance light scattering, and circular dichroism were evaluated in water and water/ethanol mixtures with different concentrations of DNA or AlClPc. AlClPc showed a high ability to bind to DNA in both water and 4/6 water/ethanol mixture (v/v), with a majority of monomeric and aggregated initial forms of AlClPc, respectively. In this interaction, AlClPc bound preferentially to the grooves of DNA. The monomeric/aggregate state of AlClPc in DNA was dependent on the AlClPc/DNA ratio. At low concentrations of AlClPc, the interaction of AlClPc with few DNA sites caused a curvature in the DNA structure that provided a favorable environment for the intercalation of AlClPc aggregates. Increase in AlClPc concentration induced interactions with a high number of binding sites on DNA, which prevented bending and therefore aggregation of AlClPc molecules throughout the double-stranded DNA. These results are relevant to the understanding of the behavior and interaction of AlClPc with double-stranded DNA in the design of novel drug delivery systems for clinical application in photodynamic therapy as a new approach to treat skin or oral cancer, scars, or wound healing.

Binding studies of guggulsterone-E to calf thymus DNA by multi-spectroscopic, calorimetric and molecular docking studies

Guggulsterone, a sterol found in plants is used as an ayurvedic medicine for many diseases such as obesity, internal tumors, ulcers etc. E and Z are two isoforms of guggulsterone, wherein guggulsterone-E (GUGE) has also been shown to have anticancer potential. Most of the anticancer drugs target nucleic acids. Therefore, we studied the mode of interaction between ctDNA and GUGE using UV-Vis, fluorescence and CD spectroscopy, isothermal calorimetry along with molecular docking studies. Hoechst 3325, ethidium bromide and rhodamine-B displacement experiments confirms that GUGE binds in the minor groove of DNA. ITC results further suggest these interactions to be feasible and spontaneous with hydrogen bond formation and van der waals interactions. Lastly, molecular docking also suggests GUGE to be a minor groove binder interacting through a single hydrogen bond formation between OH group of GUGE and nitrogen (N3) of adenosine (A6).

Spectroscopic and molecular docking studies on the interaction of antiviral drug nevirapine with calf thymus DNA

The interaction of calf thymus DNA with nevirapine at physiological pH was studied by using absorption, circular dichroism, viscosity, differential pulse voltammetry, fluorescence techniques, salt effect studies and computational methods. The drug binds to ct-DNA in a groove binding mode, as shown by slight variation in the viscosity of ct-DNA. Furthermore, competitive fluorimetric studies with Hoechst 33258 indicate that nevirapine binds to DNA via groove binding. Moreover, the structure of nevirapine was optimized by DFT calculations and was used for the molecular docking calculations. The molecular docking results suggested that nevirapine prefers to bind on the minor groove of ct-DNA.

Synthesis, DNA binding and in-vitro cytotoxicity studies on novel bis-pyrazoles

A new series of bis-pyrazoles 6a-t were synthesized from 3,5-dimethyl pyrazole using sequential approach. All these compounds were characterized by IR, ¹H NMR, ¹³C NMR and mass spectral data. The interaction of newly synthesized bis-pyrazoles with DNA was investigated through molecular docking and absorption spectroscopic technique. Among all bis-pyrazoles compounds, the 6h compound showed lower conformational energy through in silico analysis. The interaction of each molecule in this series 6a-t with the various concentrations of DNA was examined through the UV-visible spectroscopic studies. The UV-visible spectroscopy studies on the specific binding of compound 6a, 6b, 6g, 6h, 6d, 6i, 6k, 6n, 6s with DNA have exhibited spectral shifts and the results were discussed. In further the compounds 6a-t were subjected to the in-vitro cytotoxicity studies against human pancreatic adenocarcinoma, human non-small cell lung carcinoma cell lines. Among the screened compounds, N-(3-isopropoxy-1-isopropyl-4-(3,5-dimethyl-1H-pyrazol-1-yl)-1H-pyrazol-5-yl)cyclobutane carboxamide and N-(5'-Isopropoxy-2'-isopropyl-3,5-dimethyl-2'H-[1,4'] bipyrazolyl-3'-yl)-dimethane sulfonamide were found as lead molecules since they have exhibited promising activity against both the cancer cell lines used in this study, whereas the compounds 4-(trifluoromethyl)-N-(3-isopropoxy-1-isopropyl-4-(3,5-dimethyl-2H-pyrrol-2-yl)-1H-pyrazol-5-yl)benzamide and 2,6-difluoro-N-(3-isopropoxy-1-isopropyl-4-(3,5-dimethyl-2H-pyrrol-2-yl)-1H-pyrazol-5-yl) benzamide were found to be active against the pancreatic cell line only. Rest all the other compounds were found to exhibit moderate to good activity towards both the cell lines.

Detection of a few DNA copies by real-time electrochemical polymerase chain reaction

In the current work, accurate quantification over 10 to 10⁸ DNA copies has been successfully achieved for the first time by real-time electrochemical PCR.

Supermolecules of poly(N-isopropylacrylamide) complexating Herring sperm DNA with bio-multiple hydrogen bonding

In this study we used the poly(N-isopropylacrylamide) (PNIPAAm) as a medium to blend with an organic DNA, herring sperm DNA (HSD), to generate PNIPAAm-HSD supramolecular complexes. Bio-multiple hydrogen bonding (BMHB) between PNIPAAm and HSD was investigated that changed the temperature responsiveness of PNIPAAm relatively to the HSD concentrations. With blending the HSD into PNIPAAm matrix, the phase separation in solution is completely opposite from that of neat PNIPAAm. Surface property in static water contact angle (SWCA) is also opposite from that of pure PNIPAAm upon increasing HSD content over 60%. In addition, we found that the PNIPAAm and HSD self-assembled a specific triangle-like structure at a PNIPAAm-to-HSD weight ratio of 1:4 at 25°C; while the triangle-like structure disappeared with increasing temperature to 45°C. Furthermore, both PNIPAAm and HSD could be regarded as insulator, but it transformed into a semiconductive matter after blending with the HSD. Incorporation of organic DNA with hydrogel could significantly change their properties, which might facilitate their use as novel materials in bioelectronics.

Spectroscopic Study of CpG Alternating DNA-Methylene Blue Interaction for Methylation Detection

Recognition of methylated DNA sites would be useful strategy due to the important roles of methylation in disease occurrence and developmental processes. The interaction of CpG rich methylated and unmethylated DNA hybrid with methylene blue (MB) as an optical probe has been investigated by absorption, emission, circular dichorism and fluorescence anisotropy analysis. Titration of MB with both sequences caused a hypsochromism and decreased the absorption of MB that indicating an intercalative mode of interaction. The experimental results revealed that MB as the optical indicator could distinguish between the methylated and unmethylated DNA sequences. Under optimum conditions, upon the addition of methylated dsDNA, the fluorescence intensity increased in linear range from 1.0 × 10(-9) to 1.0 × 10(-6) M with detection limit of 7.2 × 10(-10) M and on the other hand, the intensity of MB showed no change with addition of unmethylated dsDNA.

Real-time electrochemical LAMP: a rational comparative study of different DNA intercalating and non-intercalating redox probes

The main objective of this study is provide guidelines in the search for ideal redox-active reporters in real-time electrochemical LAMP.

Pharmacological investigation of 2-aminobenzothiazolium-4-methylbenzenesulphonate: Synthesis, spectral characterization and structural elucidation

An organic charge transfer complex, 2-aminobenzothiazolium-4-methylbenzenesulphonate (ABPTS) was synthesized and single crystals grown by slow solvent evaporation solution growth technique at ambient temperature. The single crystal X-ray diffraction analysis was carried out to establish the molecular structure of the title crystal. FT-IR spectral study was carried out to identify the various functional groups present in the crystal. The (1)H and (13)C spectra were recorded to further confirm the molecular structure of the CT complex. The TG/DTA analyses were carried out to establish the thermal stability of the complex. The antibacterial and antifungal activities of synthesized complex were examined against various bacteria and fungi strains, to identify the antibacterial and antifungal activity. The DNA binding profile of the complex has been investigated through absorption spectroscopy and complex has intrinsic binding constant 3.6 × 10(4) M(-1). A gel electrophoresis assay demonstrated the ability of the complex to cleave the pBR322 DNA. The free radical scavenging activity of the complex has been determined against DPPH, OH and ABTS radicals.