MONTE-CARLO MODELING OF DNA HYDRATION - POLY(A)-WATER INTERACTION IN THE MAJOR GROOVE STABILIZES THE B' CONFORMATION

Hydration of two kinds of DNA duplex containing A tracts was assessed by Monte Carlo simulation. Conformations of B'-DNA with narrowed minor groove proved advantageous in the hydration energy over canonical B-D NA. The effect is mainly due to adenine-water interactions in the majo r groove. The energy of these interactions in the minor groove did not appreciably vary with groove width, while for the major groove the en ergy monotonically increased with widening at the expense of the other groove. Analysis of the H-bond networks in the duplex water jackets r evealed that such dissimilar dependences are due to the structural pec uliarities of water in the DNA grooves. Decisive for stabilization of the B' conformation is the rise in the number of water H-bonds with ad enine N7 and generation of ''triples,'' i.e., formation by one water m olecule of three H-bonds: two with N7 atoms of adjacent adenines and a third with the amino group in one of the latter.