  To elucidate the possible role of structural waters in stabilizing bent DNA,
various conformations of AT-containing decamers, (A5T5)2 and A10:T10, were
studied by Monte Carlo simulations. The duplexes were constrained to reproduce
the NMR inter-proton distances for the A-tracts at two temperatures: 5 and 35C.
Analysis of the water shell structures revealed a strong correlation between
the groove widths on the one hand, and the types of hydration patterns and
their probabilities on the other hand. Depending on the minor groove width, the
following patterns were observed in this groove: either an interstrand
"hydration spine", or interstrand two-water bridges, or a double ribbon of
intrastrand sugar-base "water strings". Hydration shell in the major groove is
less regular than in the minor groove, which agrees with crystallographic data.
As in previous studies, energetically advantageous hydration is found for the
A-tract conformations with narrow minor groove and wide major groove (B'-like
DNA), known to be correlated with DNA bending and curvature. In addition, our
calculations indicate that the advantage of such DNA conformations is coupled
with the increase in adenine N7 hydration in the major groove. As the major
groove is opened wider, its hydration shell is enriched by energetically
favorable "trident waters" hydrogen bonded to three hydrophilic centers
belonging to two adjacent adenines: two N7 atoms and one amino-proton H(N6).
Based on these results, we suggest that formation of the novel hydration
pattern in the major groove is one of the factors responsible for stabilization
of the B'-like conformations of A-tracts at low temperature in the absense of
dehydrating agents, leading in turn to the strong intrinsic curvature of DNA
containing alternating A-tracts and "mixed" GC-rich sequences.
