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

Abstract

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 [Drew, H. R. & Dickerson, R. E. (1981) J. Mol. Biol. 151, 535-556], the first hydration layer of which contains one water molecular per base pair. In contrast, in the wide part of the minor groove, each base is hydrated individually, water molecules lying predominantly in the base plane. In intermediate-width regions, preferred water-molecule sites are shifted away from the base plane in a 3'-to-5' direction. This shift becomes more pronounced as the minor groove narrows, until the two water molecules lie approximately midway between base pairs. If the minor groove is narrowed still further, it accommodates only one water molecule, and the hydration transforms to the well-known water spine. The observed pattern agrees with available crystallographic data and with our earlier calculations. 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. However, the location of water hydrogens, and the network of hydrogen bonding, can depend on base sequence. We 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.