Spectroscopic studies on the binding interaction of phenothiazinium dyes, azure A and azure B to double stranded RNA polynucleotides

• Azure A and azure B bind to the RNA duplexes by intercalation.
• The binding of the dyes to AU nucleotide was strongly intercalative whereas weak intercalation was found to occur with CG and IC sequence.
• The binding affinity of both the dyes varied as poly(A).poly(U) > poly(C).poly(G) > poly(I).poly(C).
• The RNA conformation was perturbed with induction of optical activity in the dyes.

This manuscript presents spectroscopic characterization of the interaction of two phenothiazinium dyes, azure A and azure B with double stranded (ds) ribonucleic acids, poly(A).poly(U), poly(C).poly(G) and poly(I).poly(C). Absorbance and fluorescence studies revealed that these dyes bind to the RNAs with binding affinities of the order 106 M−1 to poly(A).poly(U), and 105 M−1 to poly(C).poly(G) and poly(I).poly(C), respectively. Fluorescence quenching and viscosity data gave conclusive evidence for the intercalation of the dyes to these RNA duplexes. Circular dichroism results suggested that the conformation of the RNAs was perturbed on interaction and the dyes acquired strong induced optical activity on binding. Azure B bound to all the three RNAs stronger than azure A and the binding affinity varied as poly(A).poly(U) > poly(C).poly(G) > poly(I).poly(C) for both dyes.

Figure optionsDownload as PowerPoint slide