  The macroscopic curvature induced in the double helical B-DNA by regularly
repeated adenine tracts (A-tracts) plays an exceptional role in structural
studies of DNA because this effect presents the most well-documented example of
sequence specific conformational modulations. Recently, a new hypothesis of its
physical origin has been put forward, based upon the results of molecular
dynamics simulations of a 25-mer fragment with three A-tracts phased with the
helical screw. Its sequence, however, had never been encountered in
experimental studies, but was constructed empirically so as to maximize the
magnitude of bending in specific computational conditions. Here we report the
results of a similar investigation of another 25-mer B-DNA fragment now with a
natural base pair sequence found in a bent locus of a minicircle DNA. It is
shown that the static curvature of a considerable magnitude and stable
direction towards the minor grooves of A-tracts emerges spontaneously in
conditions excluding any initial bias except the base pair sequence. Comparison
of the bending dynamics of these two DNA fragments reveals both qualitative
similarities and interesting differences. The results suggest that the A-tract
induced bending obtained in simulations reproduces the natural phenomenon and
validates the earlier conclusions concerning its possible mechanism.
