Electron density analysis of the ionized states of Watson-Crick GC base pair: A novel approach to investigate the cause of altered base pairing

Abstract

Using electron density analysis, we present a model study to investigate the effect of ionization on the structure of the guanine-cytosine (GC) base pair. The structures of G, C, GC, GC–, and GC+ were optimized using DFT. NBO analysis were made to compare the interaction energies and the H-bond strengths in GC, GC–, and GC+. Electron difference density map (EDDM) of GC, GC–, and GC+ were plotted in the hydrogen bonding plane of GC. EDDM map shows the electronic density redistribution upon ionization which locate the important regions that controls the strength of hydrogen bonds in GC base pair. EDDM along with the optimized structures of G, C and GC confirms the localization of positive charge on G and negative charge on C in GC+ and GC–, respectively. Using this novel approach, it has been shown pictorially the cause of induced instability on hydrogen bonding interaction upon ionization. This deviates the linearity and planarity of the structure, providing an opportunity to alter the base pairing.