On binding mechanism exploration of organic amphoteric dye Rhodamine B with natural polymeric DNA

Abstract Nucleic acids, like DNA and RNA, are molecules that are present in any life form. Their most notable function is to encode biological information. DNA also has unique material properties, which attract material scientists, nanotechnologists, and engineers. The study and investigation of the structural and dynamical properties of complex biological systems have attracted considerable interest among scientists in general and physicists and biologists in particular.The alteration in DNA due to the introduction of any small molecule changes the overall function and stability of DNA. So quantitative information about the effects of such ligand binding on the structure and function of DNAs, are very much required. In this study, the interaction between natural polymeric DNA (deoxyribonucleic acid sodium salt from herring testes; derived from the sperm of herring fish) and organic amphoteric dye molecule (fluorescent, biomarker), Rhodamine B, has been studied quantitatively. An overview of the overall changes occurring in the macromolecule was estimated using multi-spectroscopic methods and complemented with computational analyses. The results obtained provide an understanding of the binding affinity, stoichiometry, and structural details of the ligand-DNA complex, followed by an estimation of associated binding thermodynamics. Finally, structure–function relationships and molecular aspects of ligand binding to DNA have been established in the current piece of research work, which can have multifaceted applications in drug development and pharmacology.