alcian-blue and pyridine

This work concerns an analysis of the binding mechanism of a copper phthalocyanine (Alcian Blue-tetrakis(methylpyridinium) chloride, ABTP) to natural calf thymus DNA, G-quadruplexes (G4) and synthetic RNA polynucleotides in the form of double polyriboadenylic·polyribouridylic acid (poly(A)·poly(U)) or triple strands polyriboadenylic·2polyribouridylic acid (poly(A)·2poly(U)). ABTP is a well know dye that might undergo novel applications, but its interaction with DNA is scarcely studied and we lack information on possible RNA or G4 binding. This might be related to system complexity due to the presence of supramolecular dye-dye aggregates. Despite this, we show here that apparent parameters can be calculated, which provide information on the binding mechanism. Absorbance titrations in the presence of biosubstrate excess, melting and circular dichroism experiments show that ABTP binds to both RNAs and DNA. External/groove binding is the main feature for RNAs, whereas partial intercalation is the major binging mode for DNA. ABTP externally binds to both hybrid, parallel and anti-parallel G4s but seem to show a slightly different binding mode and a preference for anti-parallel structures. The thermodynamic features of the different systems are also discussed in the frame of the enthalpy-entropy compensation phenomenon.

Topics: Alcian Blue; Binding Sites; Circular Dichroism; DNA; G-Quadruplexes; Pyridines; RNA; Spectrophotometry, Ultraviolet; Substrate Specificity; Thermodynamics

We compared the staining performance, dye content, solubility, and visual absorption maximum of two batches of alcian blue pyridine variant and of five batches of alcian blue 8GX (C.I. 74240). Whenever possible, we also compared results to those obtained with the same dye batches produced at an earlier date to provide information concerning dye stability. Both alcian blue pyridine variant batches were of high dye content, stable, of satisfactory solubility, and performed well in both the routine Mowry mucin stain and in the critical electrolyte concentration (CEC) stain. Of the five alcian blue 8GX samples, some were also of appropriate dye content, were sufficiently stable, and gave good staining in the two procedures. Two batches, however, were unstable, and three batches were unsatisfactory in staining performance and solubility in the CEC stain. Consequently alcian blue pyridine variant is a superior substitute for alcian blue 8GX.

Topics: Alcian Blue; Coloring Agents; Drug Stability; Humans; Intestines; Larynx; Pyridines; Solubility; Staining and Labeling; Trachea