Pyronin Y as a fluorescent stain for paraffin sections

Improving the Brightness of Pyronin Fluorophore Systems through Quantum-Mechanical Predictions

The pyronin class of fluorophores serves a critical role in numerous imaging applications, particularly involving preferential staining of RNA through base pair intercalation. Despite this important role in molecular staining applications, the same set of century-old pyronins (i.e., pyronin Y (PY) and pyronin B (PB)), which possess relatively low fluorophore brightness, are still predominantly being used due to the lack of methodology for generating enhanced variants. Here, we use TD-DFT calculations of interconversion energies between structures on the S1 surface as a preliminary means to evaluate fluorophore brightness for a proposed set of pyronins containing variable substitution patterns at the 2, 3, 6, and 7 positions. Using a nucleophilic aromatic substitution/hydride addition approach, we synthesized the same set of pyronins and demonstrate that quantum-mechanical computations are useful for predicting fluorophore performance. We produced the brightest series of pyronin fluorophores described to date, which possess considerable gains over PY and PB.

Hierarchical supramolecular co-assembly formation employing multi-component light-harvesting charge transfer interactions giving rise to long-wavelength emitting luminescent microspheres

Charge transfer (CT) interaction induced formation of a hierarchical supramolecular assembly has attracted attention due to its wide diversity of structural and functional characteristics. In the present work, we report the generation of green luminescent microspheres from the charge transfer interaction induced co-assembly of a bis-naphthyl dipicolinic amide (DPA) derivative with tetracyanobenzene (TCNB) for the first time. The properties of these self-assemblies were studied both in solution and the solid-state using spectroscopic and a variety of microscopy techniques. The X-ray crystal structure analysis showed a mixed stack arrangement of DPA and TCNB. The molecular orbital and energy level calculations confirm the charge transfer complex formation between DPA and TCNB. Furthermore, energy transfer was observed from the green luminescent CT complex to a red-emitting dye, pyronin Y, in the microsphere matrix, leading to the formation of a light-harvesting tri-component self-assembly.

The Toolbox of Methods for Multidirectional Characterization of Dietary Nucleic Acids; Verification for Raw and Processed Food Products

Currently, the nutritional value of food is associated mainly with components such as proteins, carbohydrates, and lipids. However, another important macromolecules present in many foods are dietary nucleic acids (dietNA), i.e., DNA as well as both coding and non-coding RNAs. In the context of food chemistry and nutrition, dietNA are nowadays vastly neglected. In consequence, there are no dedicated methodologies to characterize dietNA. In this study, using raw or processed meat and plant products as model foodstuffs, we developed a toolbox of methods borrowed from other fields (histology, toxicology, molecular biology) that enable the initial characterization of dietNA as a necessary step on the way to systematic evaluation of their nutritional role. The proposed set of methods embraces (i) paraffin embedding of food samples and their staining to visualize the distribution and variety of dietNA in situ; (ii) comet assay to assess integrity of nuclear DNA with possible detection of DNA damage; (iii) dietNA isolation with and without RNAse digestion to determine the content of both DNA and RNA; (iv) electrophoretic separation of isolates to profile dietNA fragments. Such a combined methodological approach revealed clear differences between dietNA derived from raw and processed food products. We believe that the presented set of methods will encourage the broader research on dietNA to understand their role as a nutritionally relevant food component.

Cytomorphometric analysis of oral submucous fibrosis and leukoplakia using methyl green-pyronin Y, Feulgen staining and exfoliative brush cytology

The incidence of potentially malignant oral pathology such as leukoplakia, oral submucous fibrosis and squamous cell carcinoma has increased in India. We investigated whether cytoplasmic diameter, nuclear diameter and nucleus:cytoplasm ratio in exfoliative cytology are reliable indicators of potentially malignant lesions. We also investigated methyl green-pyronin Y and Feulgen staining as simple time saving and cost effective staining techniques for diagnostic exfoliative cytology. Cell and nuclear diameters of squamous cells of normal buccal mucosa, oral leukoplakia and oral submucous fibrosis were measured using an ocular micrometer disc. The nucleus:cytoplasm ratios in pathological cells were compared to age, sex and site matched controls. We found a significant reduction in the mean cytoplasmic and nuclear diameter in the experimental groups compared to normal controls. Methyl green-pyronin Y stained smears were clearer than Feulgen stained cells. We suggest that a decreased mean cytoplasmic diameter of exfoliated buccal mucosal cells could serve as an early indicator of dysplastic change in lesions that otherwise appear benign. Methyl green-pyronin Y may be useful for identifying premalignant and malignant transformations before a lesion is visible. The simplicity of the technique makes its routine use feasible.

A fast, low cost, and highly efficient fluorescent DNA labeling method using methyl green

The increasing need for multiple-labeling of cells and whole organisms for fluorescence microscopy has led to the development of hundreds of fluorophores that either directly recognize target molecules or organelles, or are attached to antibodies or other molecular probes. DNA labeling is essential to study nuclear-chromosomal structure, as well as for gel staining, but also as a usual counterstain in immunofluorescence, FISH or cytometry. However, there are currently few reliable red to far-red-emitting DNA stains that can be used. We describe herein an extremely simple, inexpensive and robust method for DNA labeling of cells and electrophoretic gels using the very well-known histological stain methyl green (MG). MG used in very low concentrations at physiological pH proved to have relatively narrow excitation and emission spectra, with peaks at 633 and 677 nm, respectively, and a very high resistance to photobleaching. It can be used in combination with other common DNA stains or antibodies without any visible interference or bleed-through. In electrophoretic gels, MG also labeled DNA in a similar way to ethidium bromide, but, as expected, it did not label RNA. Moreover, we show here that MG fluorescence can be used as a stain for direct measuring of viability by both microscopy and flow cytometry, with full correlation to ethidium bromide staining. MG is thus a very convenient alternative to currently used red-emitting DNA stains.

Simultaneous quantification of nucleoproteins and comparison of methyl green-pyronin Y and Feulgen staining in sections of oral squamous cell carcinoma, dysplastic lesions and normal mucosa

A fundamental difference between normal cells and tumor cells is the proliferative activity of the nucleus and nucleolus, which increases progressively from normal to oral dysplastic mucosa to oral squamous cell carcinoma (OSCC). This activity is evaluated routinely using hematoxylin and eosin (H & E) staining, but in some cases, inter-observer variability occurs among pathologists. We evaluated cellular proliferation by staining sections with the methyl green-pyronin Y procedure and the Feulgen reaction. We also compared the efficacy of methyl green-pyronin Y and Feulgen staining for studying nuclear and nucleolar features in oral dysplastic mucosa and in different grades of OSCC. Sections cut from formalin fixed, paraffin embedded blocks of five normal mucosa, 15 dysplastic mucosa, 10 well-differentiated OSCC, 10 moderately differentiated OSCC and five poorly differentiated OSCC cases were stained with Hematoxylin and Eosin, methyl green-pyronin Y and the Feulgen reaction. The mean diameters of the nuclei and number of nucleoli showed significant differences. A progressive increase in diameter of the nucleus and number of nucleoli was observed from normal mucosa through poorly differentiated OSCC. We observed that methyl green-pyronin Y stain is more useful than Feulgen and hematoxylin and eosin for simultaneous quantitative assessment of both RNA and DNA. The simplicity of this technique makes it a valuable tool even for daily routine examination.

The effect of poly(vinyl alcohol) on the photophysical properties of pyronin dyes in aqueous solution: a spectroscopic study

The photophysical properties of pyronin B (PyB) and pyronin Y (PyY) in water and poly(vinyl alcohol) (PVA) aqueous solutions were studied by using absorption, steady-state fluorescence and time-resolved fluorescence spectroscopy techniques at room temperature. The spectroscopic and photophysical properties of pyronin dyes in the concentrated PVA aqueous solution were different than those found in water. The aggregation of the pyronin dyes in the concentrated PVA aqueous solution was prevented with ease while the dye aggregation was generally formed in water with high dye concentration. The decrease in the aggregation tendency of pyronin dyes in the concentrated PVA aqueous solution caused an increase in radiative transitions. The addition of PVA into the aqueous solution induced the enhancement in the fluorescence intensity of the dyes compared to those in water. As a result, the quantum yields of the dyes were improved by the addition of PVA at high loading. The time-resolved fluorescence study revealed that the fluorescence decay of dyes in all solutions were found to be single-exponential and the fluorescence lifetime of pyronin dyes in the concentrated PVA aqueous solution were also higher than those found in water.

Alcian Blue and Pyronine Y histochemical stains permit assessment of multiple parameters in pulmonary disease models

Utilization of a combined Alcian Blue and Pyronine Y histochemical method for the assessment of multiple parameters in the respiratory tract of various species is described. Acidic mucins were deep blue (sialylated mucins), red (sulfated mucins), or variably purple (mixture of sialylated/sulfated mucins), and differential mucus production was readily detected in a murine respiratory syncytial virus vaccine model of pulmonary inflammation. Elastic fibers stained red in the walls of pulmonary arteries, connecting airways, alveolar septa, and subpleural interstitium. Mast cells had red to red-purple granular cytoplasmic staining. Nuclei were ubiquitously counterstained pale blue. Representative staining was detected in tissues from multiple species, including inbred mice, rats, ferrets, cats, dogs, sheep, and pigs. The fluorescent property of the stained tissues offers additional modalities with which to analyze tissue sections. This histochemical technique detects multiple critical parameters in routine paraffin sections of lung tissue, reduces the need for repeated serial sectioning and staining, and is cost-effective and simple to perform.