Molecular dynamics simulation of the hydration shell of a B-DNA decamer reveals two main types of minor-groove hydration depending on groove width

The conformation of the self-complementary B-DNA decamer C-C-A-A-C-G-T-T-G-G is known from a high-resolution x-ray crystal structure analysis. Molecular dynamics simulation of the hydration shell of the decamer has revealed two main types of minor-groove hydration, depending on groove width. The narrow part of the minor groove has a spine of hydration analogous to that described for the A + T-rich center of the minor groove in the dodecamer C-G-C-G-A-A-T-T-C-G-C-G. In contrast, in the wide part of the minor groove, each base in hydrated individually, water molecules lying predominantly in the base plane. The observed pattern agrees with available crystallographic data and with our earlier calculation. The results confirm the assumption that preferred positions of water oxygens in the minor groove depend predominantly on groove width rather than on base sequence. The authors suggest a simple explanation of water-spine formation in the narrow minor groove of a random DNA sequence. The spine of hydration may be a property of the minor groove of overwound variants of B-DNA, the C and D forms, for which the middle part of the decamer C-C-A-A-C-G-T-T-G-G can serve as a model