  The macroscopic curvature induced in the double helical B-DNA by regularly
repeated adenine tracts (A-tracts) is a long known, but still unexplained
phenomenon. This effect plays a key role in DNA studies because it is unique in
the amount and the variety of the available experimental information and,
therefore, is likely to serve as a gate to the unknown general mechanisms of
recognition and regulation of genome sequences. We report the results of
molecular dynamics simulations of a 25-mer B-DNA fragment with a sequence
including three A-tract phased with the helical screw. It represents the first
model system where properly directed static curvature emerges spontaneously in
conditions excluding any initial bias except the base pair sequence. The effect
has been reproduced in three independent MD trajectories of 10-20 ns with
important qualitative details suggesting that the final bent state is a strong
attractor of trajectories form a broad domain of the conformational space. The
ensemble of curved conformations, however, reveals significant microscopic
heterogeneity in contradiction to all existing theoretical models of bending.
Analysis of these unexpected observations leads to a new, significantly
different hypothesis of the possible mechanism of intrinsic bends in the double
helical DNA.
