Density Functional Study of the Structure of Guanine Octets in Aqueous Medium

Abstract

The structures and energies of guanine quartets and octets in water were determined by DFT (Density Functional Theory) calculations using M06-2X functional and 6-31G(d, p) basic set. Guanine quartets in vacuum were found to have not only the Hoogsteen or bifurcated, but also mixed system of hydrogen bonds; in water the latter two forms are transformed into the classic Hoogsteen-type structure. Four stable configurations of G-octets with D4, C4 and S4 symmetry formed by the pairs of guanine quartets with Hoogsteen, bifurcated or mixed system of H-bonds were identified. The most advantageous structure of the G-octet molecular system in aqueous medium was shown to be S4-symmetric structure consisting of the pair of mixed Hoogsteen-bifurcated type G-quartets