B-DNA's B-II conformer substate population increases with decreasing wateractivity. 1. A molecular dynamics study of d(CGCGAATTCGCG)(2)

The Bn substate of the biologically active B-DNA family is characterized by a different phosphate backbone geometry. In contrast to the current belief , the Bn substate of the d(CGCGAATTCGCG)(2) dodecamer is shown-both experim entally and by molecular dynamics simulations-to be significantly populated at water activities in the range of those in the cell nucleus. Three syste ms with different water contents show an increase in B-I reversible arrow B -II transitions as the water activity decreases. In addition, the transitio n mechanism is investigated and the sequence dependence of these interconve rsion processes in the form of pyrimidine-purine interconversion dominance is demonstrated.