Spectroscopic and molecular docking studies of the interactions of monomeric unsymmetrical polycationic fluorochromes with DNA and RNA

The photophysical properties of a series of unsymmetrical di- and tricationic monomethine cyanine dyes were studied in the presence of nucleic acids using combined spectroscopic techniques and molecular docking. The analysis of the UV-visible absorption and the fluorescence spectra revealed a strong association of the title cyanines with nucleic acids, while the interaction magnitude is notably higher for the double-stranded DNA, compared to that of the single-stranded RNA. The binding parameters of the cyanine dyes were determined in terms of the McGhee & von Hippel neighboring site-exclusion model. Cumulatively, the results from the optical spectroscopy measurements along with those from the molecular docking analysis were found to be consistent, presuming minor groove binding motif as predominant between the examined cyanines and deoxyribonucleic acid, whereas external binding upon biocomplexation with ribonucleic acid.