Understanding the binding interaction mechanism of i-motif with fluorophores: A biophysical approach

Abstract

DNA exists in many canonical and non-canonical forms. i-motif: a non-canonical, tetraplex, antiparallel strand rich in cytosine, formed by hemi protonated cytosine- cytosine+ base pairs under slightly acidic pH levels, i-motifs are utilised in the study of numerous fields of applications. These i-motif tend to exhibit the property of switching the fluorescent nature of ligands such as thiazole orange, crystal violet and berberine upon interaction. This work is focussed on a basic overview of i-motif and its interactions with ligands to form fluorescence probes which could be useful in bio imaging. Herein, we are trying to find the electronic properties of small molecules upon interacting with i-motif. In order to find the active binding site in i-motif, Molecular Docking simulation was performed. The best docked pose obtained from the docking studies were subjected to molecular dynamics simulations. Further, DFT studies, optimization and single point energy calculations were carried out for freeligands and those bounded with the secondary DNA structures to understand the intermolecular interaction and to study their electronic properties.