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

Publication date: Available online 25 January 2020Source: Journal of Photochemistry and Photobiology B: BiologyAuthor(s): Puja Paul, Soumya Sundar Mati, Gopinatha Suresh KumarAbstractThe ubiquitous influence of double stranded RNAs in biological events makes it imperative to gather data based on specific binding procedure of small molecules to various RNA conformations. Particular interest may be attributed to situation wherein small molecules target RNAs altering their structures and causing functional modifications. The main focus of the study is to delve into the interactive pattern of two small molecule phenothiazinium dyes methylene blue and new methylene blue with three duplex RNA polynucleotides-poly(A).poly(U), poly(C).poly(G) and poly(I).poly(C) by spectroscopic as well as molecular modeling techniques. Analysis of data as per Scatchard and Benesi-Hildebrand methodologies revealed highest affinity of these dyes to poly(A).poly(U) and least to poly(I).poly(C). In addition to fluorescence quenching, viscometric studies also substantiated that the dyes follow different modes of binding to different RNA polynucleotides. Distortion in the RNA structures with induced optical activity in the otherwise optically inactive dye molecules were evidenced from circular dichroism results. Dye-induced RNA structural modification occurred from extended conformation to compact particles visualized by atomic force microscopy. Molecular docking results revealed different binding pattern...
Source: Journal of Photochemistry and Photobiology B: Biology - Category: Speech-Language Pathology Source Type: research