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

• Published in: Chemical physics letters 2006-10, Vol.429 (4), p.563-569
• Main Authors: Tsukamoto, Takayuki, Ishikawa, Yasuyuki, Vilkas, Marius J., Natsume, Takayuki, Dedachi, Kenichi, Kurita, Noriyuki
• Format: Article
• Language: English
• ISSN: 0009-2614; 1873-4448
• DOI: 10.1016/j.cplett.2006.08.112

We have theoretically examined the effect of hydration on the electronic properties of a decameric DNA duplex including the hydrating water molecules. The electronic properties of the wet DNA duplex are remarkably sensitive to hydrating water molecules, and strongly indicate that the hole transfer in hydrated DNA duplex is water-mediated. 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.