Insights on the interaction of phenothiazinium dyes methylene blue and new methylene blue with synthetic duplex RNAs through spectroscopy and modeling

Spectroscopic and calorimetric study of the interaction between Nile blue and double-stranded RNA

Nile blue has been widely used in histological staining, fluorescence labeling, and DNA probing, with its intercalation behavior into the DNA helix being well documented. Here, we present a comprehensive investigation to address a current knowledge gap regarding the binding properties of Nile blue to two types of double-stranded RNA (dsRNA): poly(A·U) and poly(I·C), using various biophysical techniques. Absorption and fluorescence spectroscopic studies suggest a significant binding interaction between Nile blue and the two designated dsRNAs, specifically indicating an intercalation binding mode with poly(A·U) and demonstrating a noticeably higher binding affinity compared to poly(I·C). The binding stoichiometry was further determined by Job's plot to be 0.47 for poly(A·U) and 1.0 for poly(I·C). The increased relative viscosity and changes in the circular dichroism (CD) ellipticity of dsRNA after interacting with Nile blue indicate the stacking of Nile blue dyes between the RNA duplexes. These changes suggest a conformational alteration of the dsRNAs and confirm the intercalation mode of binding. The thermal dynamic analysis demonstrates that both binding were favored by negative enthalpy and primarily driven by the hydrophobic effect.

Peptide nucleic acid-clicked Ti3C2Tx MXene for ultrasensitive enzyme-free electrochemical detection of microRNA biomarkers

We report the engineering and synthesis of peptide nucleic acid-functionalized Ti3C2Tx MXene nanosheets as a novel transducing material for amplification-free, nanoparticle-free, and isothermal electrochemical detection of microRNA biomarkers. Through bio-orthogonal copper-free click chemistry, azido-modified MXene nanosheets are covalently functionalized with clickable peptide nucleic acid probes targeting prostate cancer biomarker hsa-miR-141. The platform demonstrates a wide dynamic range, single-nucleotide specificity, and 40 aM detection limit outperforming more complex, amplification-based methods. Its versatility, analytical performance, and stability under serum exposure highlight the immense potential of this first example of click-conjugated MXene in the next generation of amplification-free biosensors.

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.

Deciphering the binding site and mechanism of new methylene blue with serum albumins: A multispectroscopic and computational investigation

Herein, the interaction mechanism of new methylene blue (NMB) with human serum albumin (HSA) and bovine serum albumin (BSA) was carefully investigated both experimentally and conceptually, employing experimental and insilico analysis. The steady-state emission spectral studies showed that the emission intensity of HSA and BSA was quenched significantly by NMB. The findings of the Stern-Volmer and double logarithmic plot revealed that the observed emission quenching process was through a static quenching mechanism and the measured binding constant values (K_b) for HSA-NMB and BSA-NMB are 2.766 and 1.187 × 10⁵ dm³ mol^-1 respectively. The time-resolved fluorescence lifetime measurement and UV-vis absorption investigation further verify the complex formation between NMB and HSA/BSA. The assessment of thermodynamic parameters disclosed the binding process was spontaneous driven by hydrogen bonds (H-bond) and van der Waals interactions, which contributed a significant role in the complexation. Moreover, the secondary structural conformation and microenvironment of HSA/BSA were modified in the presence of NMB, as evidenced by circular dichroism and synchronous fluorescence data. Molecular docking study predicted a plausible binding mode of NMB inside the binding pocket of HSA and BSA. These results demonstrated that the stabilized NMB is found at the Subdomain IIA (site I) of both the proteins and the results were correlated well with the competitive binding assay. Additionally, the principal components analysis revealed less variation of docked poses for HSA, while, more dispersed docked poses were observed for the BSA model. This also highlights the effects of docking towards a modeled protein (BSA). Molecular dynamic (MD) simulation based binding free energy (ΔG_mmgbsa) estimation obtained at 298, 303, 308 and 313 K, were in good agreement with our experimental (ΔG_bind) values.

pH-Induced Biophysical Perspectives of Binding of Surface-Active Ionic Liquid [BMIM][OSU] with HSA and Dynamics of the Formed Complex

The influence of pH on the human serum albumin (HSA) interaction with ionic liquid (IL)1-butyl 3-methylimidazolium octyl sulfate ([BMIM][OSU]) at its sub-micellar concentration of 5 mM (well below CMC ∼31 mM at 25 °C) in aqueous solution has been monitored employing different methods, viz., circular dichroism (CD), fluorescence, electrokinetic determination of the zeta potential (ZP), nuclear magnetic resonance (NMR), small-angle neutron scattering (SANS), and molecular docking (MD). CD analysis indicated a noticeable reduction of the α-helical content of HSA by IL at pH 3. A significant interaction of the anionic part of IL with HSA was evident from the ¹H chemical shifts and saturation transfer difference (STD) NMR. A strong binding between IL and HSA was observed at pH 3 relative to pH 5, revealing the importance of electrostatic and hydrophobic interactions assessed from global binding affinities and molecular correlation times derived from STD NMR and a combined selective/nonselective spin-relaxation analysis, respectively. ZP data supported the electrostatic interaction between HSA and the anionic part of IL. The nature of IL self-diffusion with HSA was assessed from the translational self-diffusion coefficients by pulse field gradient NMR. SANS results revealed the formation of prolate ellipsoidal geometry of the IL-HSA complex. MD identified the preferential binding sites of IL to the tryptophan centers on HSA. The association of IL with HSA was supported by fluorescence measurements, in addition to the structural changes that occurred in the protein by the interaction with IL. The anionic part of IL contributed a major interaction with HSA at the pH levels of study (3, 5, 8, and 11.4); at pH > 8 (effectively 11.4), the protein also interacted weakly with the cationic component of IL.

Influence of Green Synthesized Zinc Oxide Nanoparticles on Molecular Interaction and Comparative Binding of Azure Dye with Chymotrypsin: Novel Nano-Conjugate for Cancer Phototherapy

Till date, different types of conventional drugs have been used to fight tumors. However, they have significant flaws, including their usage being constrained because of their low bioavailability, poor supply, and serious side effects. The modern combination therapy has been viewed as a potent strategy for treating serious illnesses, including cancer-type feared diseases. The nanoparticles are a promising choice for cancer therapeutic and diagnostic applications because of their fascinating optoelectronic and physicochemical features. Among the metallic nanoparticles, Zinc oxide nanoparticles possess interesting physicochemical and anti-cancer characteristics, such as ROS generation, high retention, enhanced permeability etc., making them attractive candidates for the treatment and diagnosis of cancer. Zinc oxide nanoparticles showed anti-cancer property via excessive reactive oxygen species (ROS) production, and by the destruction of mitochondrial membrane. Here, we have synthesized organic/inorganic hybrid nanosystem composed of chymotrypsin protein (Chymo) with AzureC (AzC) conjugated with Zinc oxide nanoparticles (ZnONPs). The conjugation of AzureC with ZnONPs was confirmed by transmission electron microscopy (TEM), zeta potential, and dynamic light scattering (DLS) experiment. The interaction of Chymo with AzC alone and AzC-ZnONPs was investigated, and it was observed that the interaction was enhanced in the presence of ZnONPs, which was concluded by the results obtained from different spectroscopic techniques such as UV-Visible spectroscopy, fluorescence spectroscopy and circular dichroism in combination with molecular docking. UV-Visible spectroscopic studies and the corresponding binding parameters showed that the binding of AzC-ZnONPs complex with Chymo is much higher than that of AzC alone. Moreover, the fluorescence measurement showed enhancement in static quenching during titration of Chymo with AzC-ZnONPs as compared to dye alone. In addition to this, circular dichroism results show that the dye and dye-NPs conjugate do not cause much structural change in α-Chymo. The molecular docking and thermodynamic studies showed the predominance of hydrogen bonding, Van der Waal force, and hydrophobic forces during the interactions. After correlation of all the data, interaction of Chymo with AzC-ZnONPs complex showed strong interaction as compared to dye alone. The moderate binding with chymo without any alteration in the structure makes it desirable for the distribution and pharmacokinetics. In addition, the in vitro cytotoxicity of the AzC-ZnONPs was demonstrated on A-549 adenocarcinoma cell line. Our findings from physiochemical investigations suggested that the chymotrypsin coated AzC conjugated ZnONPs could be used as the novel nanoconjugates for various cancer phototherapies.

Improved Bladder Tumor RNA Isolation from Archived Tissues Using Methylene Blue for Normalization, Multiplex RNA Hybridization, Sequencing and Subtyping

Methylene blue (MB) is a dye used for histology with clinical importance and intercalates into nucleic acids. After MB staining of formalin fixed paraffin embedded (FFPE) muscle invasive bladder cancer (MIBC) and normal urothelium, specific regions could be microdissected. It is not known if MB influences RNA used for gene expression studies. Therefore, we analyzed MIBC using five different RNA isolation methods comparing patient matched FFPE and fresh frozen (FF) tissues pre-stained with or without MB. We demonstrate a positive impact of MB on RNA integrity with FF tissues using real time PCR with no interference of its chemical properties. FFPE tissues showed no improvement of RNA integrity, which we propose is due to formalin induced nucleotide crosslinks. Using direct multiplex RNA hybridization the best genes for normalization of MIBC and control tissues were identified from 34 reference genes. In addition, 5SrRNA and 5.8SrRNA were distinctive reference genes detecting <200 bp fragments important for mRNA analyses. Using these normalized RNAs from MB stained MIBC and applying multiplex RNA hybridization and mRNA sequencing, a minimal gene expression panel precisely identified luminal and basal MIBC tumor subtypes, important for diagnosis, prognosis and chemotherapy response.

New Methylene Blue Covalently Functionalized Graphene Oxide Nanocomposite as Interfacial Material for the Electroanalysis of Hydrogen Peroxide

New methylene blue (NMB), a phenothiazine dye, was covalently bonded to graphene oxide (GO) using glutaraldehyde as a crosslinking agent, which was characterized by spectroscopic techniques and electrochemistry. The obtained GO-NMB nanocomposite was used as interface material to construct a novel electrochemical sensor for the determination of hydrogen peroxide (H₂O₂). The electrochemical sensor based on GO-NMB nanocomposite exhibited excellent electrocatalytic activity for the reduction of hydrogen peroxide (H₂O₂), which was also enhanced by GO within the GO-NMB nanocomposite. With the optimized experimental conditions, the developed sensor showed high sensitivity (79.4 μA mM^-1 cm^-2) for electrocatalytic determination of H₂O₂ at the applied potential of -0.50 V in the concentration range of 0.000333 to 2.28 mΜ. The low limit of detection (1.35 μM), good reproducibility, and high stability of the sensor suggests that the electrochemical sensor based on the GO-NMB nanocomposite possesses obvious advantages, which paves a new avenue to functionalize GO for obtaining electrode interface materials.

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.