Density-functional theoretical study on hydrated DNA duplex: Effect of hydrating water molecules on HOMO distribution in DNA

Abstract

The effect of hydration on the electronic properties of DNA is investigated by density-functional calculations for the decameric 5′-d(CCATTAATGG) 2-3′ DNA duplex with hydrating water molecules identified by neutron diffraction analysis. Energetically, the three highest occupied molecular orbitals (HOMO) of the hydrated DNA duplex are nearly degenerate. These MOs are spatially distributed on the guanine bases and a cluster of water molecules hydrating the minor groove of the DNA duplex, indicating that these specific water molecules are directly involved in radical cation transport through DNA. The water molecules bound to the DNA backbones have no noticeable effects on the HOMO distribution.