A combined molecular dynamics/density-functional theoretical study on the structure and electronic properties of hydrating water molecules in the minor groove of decameric DNA duplex

Takayuki Tsukamoto; Yasuyuki Ishikawa; Takayuki Natsume; Kenichi Dedachi; Noriyuki Kurita

doi:10.1016/j.cplett.2007.05.009

A combined molecular dynamics/density-functional theoretical study on the structure and electronic properties of hydrating water molecules in the minor groove of decameric DNA duplex

Chem Phys Lett. 2007 Jun 1;441(1-3):136-142. doi: 10.1016/j.cplett.2007.05.009.

Authors

Takayuki Tsukamoto¹, Yasuyuki Ishikawa, Takayuki Natsume, Kenichi Dedachi, Noriyuki Kurita

Affiliation

¹ Department of Knowledge-based Information Engineering, Toyohashi University of Technology, Tenpaku-cho, Toyohashi, Aichi 441-8580, Japan.

Abstract

A combined molecular dynamics/density-functional theoretical study was carried out to address the propensity of ambient water to form cross-strand bridging water (CSBW) and their effects on the electronic properties of a fully hydrated DNA duplex 5'-d(CCATTAATGG)(2)-3'. The simulation shows ubiquitous presence of up to five CSBWs along the minor groove, each with residence time ranging from 400 ps to 750 ps. The molecular orbitals localized on these CSBWs are nearly degenerate in energy with the highest occupied molecular orbital of DNA localized on guanine bases, strongly indicating that the hole transport along the guanines is mediated by the ubiquitous CSBWs.

Abstract

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