Title
Exploring the interaction of phenothiazinium dyes methylene blue, new methylene blue, azure A and azure B with tRNAPhe : Spectroscopic, thermodynamic, voltammetric and molecular modeling approach
Author
Puja Paul, Soumya Sundar Mati, Subhash Chandra Bhattacharya, Gopinatha Suresh Kumar
Year
2017
Journal
Physical Chemistry Chemical Physics
Abstract
This study focuses to understand the interaction of phenothiazinium dyes methylene blue (MB), new methylene blue (NMB), azure A (AZA) and azure B (AZB) with tRNAPhe with particular emphasis on deciphering mode and energetics of the binding. Strong intercalative binding to tRNAPhe was observed for MB, NMB and AZB, bound by a partial intercalative mode. AZA has shown groove binding characteristics. From spectroscopic studies binding affinity values of the order 105 M-1 were deduced for these dyes; the trend varied as MB > NMB > AZB > AZA. The binding was characterized by an increase of thermal melting temperatures and perturbation in the circular dichroism spectrum of tRNA. All the dyes acquired optical activity on binding to tRNA. The binding was predominantly entropy driven with a favorable enthalpy term that increased with temperature in all the cases. Dissection of the Gibbs energy to polyelectrolytic and non- polyelectrolytic terms revealed a major role for the non-electrostatic forces to the binding. The small but significant heat capacity changes and the observed enthalpy-entropy compensation phenomenon confirmed the involvement of multiple weak non-covalent forces driving the interaction. The mode of binding was confirmed from quenching, viscosity and cyclic voltammetric results. Using density functional theory, ground state optimized structures of the dyes were calculated to provide insight into theoretical docking studies to correlate the experimental approaches. Modeling results verified the binding location as well as binding energy of the complexation. Results may provide new insights to structure- activity relationship useful in the designing effective RNA targeted therapeutic agents.
Instrument
J-815
Keywords
Circular dichroism, Induced CD, DNA structure, Ligand binding, Chemical stability, Biochemistry