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

DNA bending and "structural" waters in major and minor grooves of A-tracts. Monte Carlo computer simulations