Study on the interaction of Yohimbine with duplex oligonucleotide using spectroscopic and computational tools

DNA-interactions with multivalent ligand(s) have increasingly become the subject of substantial research. For several small-molecules with therapeutic-potential, nucleic-acids serve as their primary molecular-target. Such interaction has been shown to affect transcription, and replication, ultimately leading to apoptotic cell-death. Thus, researchers are becoming increasingly interested in understanding ligand-interaction with oligonucleotides making it possible to develop new, DNA-specific drugs. Yohimbe (Yh), a bioactive indole-alkaloid, has been thoroughly investigated for its pharmaceutical qualities, but the mechanism of DNA-binding is still ambiguous. This research adopted computational and multi-spectroscopic methods to investigate the molecular-mechanism between Yohimbine and hairpin-duplex oligonucleotide at physiological-conditions. The occurrence of slight hypochromic and bathochromic deviations in fluorescence intensity indicates that Yh interacts with hairpin-duplex. Employing the McGhee-von Hipple approach, the Scatchard-plot analyses indicated non-cooperative interaction with 10 ⁵ M ^-1 binding affinities. The temperature-dependent fluorescence data suggested positive entropy and negative enthalpy supporting the exothermic binding. Salt-dependent fluorescence revealed that non-polyelectrolytic forces governed the DNA-ligand association. The findings of the urea-denaturation, dye-displacement, and molecular-docking analysis, iodide-quenching confirmed groove-binding. Therefore, biophysical tools and in silico modeling were utilized to identify the structural-alteration and energetic-profiling of Yh’s interaction with oligonucleotides which can be employed for the development of DNA-targeted therapeutics.