  Dynamics of the polymorphic A<->B transitions in DNA is compared for two
polypurine sequences, poly(dA).poly(dT) and poly(dG).poly(dC), long known to
exhibit contrasting properties in experiments. In free molecular dynamics
simulations reversible transitions are induced by changing the size of a water
drop around DNA neutralized by Na ions. In poly(dG).poly(dC) the B<->A
transitions are easy, smooth and perfectly reversible. In contrast, a B->A
transition in poly(dA).poly(dT) dodecamer fragment could not be obtained even
though its A-form is stable under low hydration. Normal B->A transitions are
observed, however, in long poly(dA).poly(dT) stretches flanked by GC pairs. An
intermediate range of hydration numbers is identified where opposite
transitions are observed in the two dodecamer fragments, namely, A->B in
poly(dA).poly(dT) and B->A in poly(dG).poly(dC). With hydration numbers close
to the stability limit of the B-form, the two sequences exhibit qualitatively
different counterion distributions, with a characteristic accumulation of Na
ions next to the opening of the minor groove in poly(dA).poly(dT). This
difference can explain an increased persistence of poly(dA).poly(dT) DNA
towards A-form in crystalline and amorphous fibers as compared to solution
conditions. The good overall agreement with experimental data corroborates the
general role of the electrostatic condensation mechanism in the A/B
polymorphism in DNA.
