Complicated water orientations in the minor groove of the B-DNA decamer d(CCATTAATGG) observed by neutron diffraction measurements

Arai, Shigeki; Chatake, Toshiyuki*; Ohara, Takashi; Kurihara, Kazuo; Tanaka, Ichiro*; Suzuki, Nobuhiro*; Fujimoto, Zui*; Mizuno, Hiroshi*; Niimura, Nobuo

Nucleic Acids Research, 33(9), p.3017 - 3024, 2005/05

https://doi.org/10.1093/nar/gki616

It has long been suspected that the structure and function of a DNA duplex can be strongly dependent on its degree of hydration. By neutron diffraction experiments, we have succeeded in determining most of the hydrogen (H) and deuterium (D) atomic positions in the d(CCATTAATGG) duplex. Moreover, the D positions in 27 DO molecules have been determined. In particular, the complex water network in the minor groove has been observed in detail. By a combined structural analysis using 2.0 Å resolution X-ray and 3.0 Å resolution neutron data, it is clear that the spine of hydration is built up, not only by a simple hexagonal hydration pattern (as reported in prior X-ray studies), but also by many other water bridges hydrogen-bonded to the DNA strands. The complexity of the hydration pattern in the minor groove is derived from an extraordinary variety of orientations displayed by the water molecules.