  The recently proposed compressed backbone theory suggested that the intrinsic
curvature in DNA can result from a geometric mismatch between the specific
backbone length and optimal base stacking orientations. It predicted that the
curvature in A-tract repeats can be relaxed by introducing single stranded
breaks (nicks). This effect has not been tested earlier and it would not be
accounted for by alternative models of DNA bending. Here the curvature in a
specifically designed series of nicked DNA fragments is tested experimentally
by gel mobility assays and, simultaneously, by free molecular dynamics
simulations. Single stranded breaks produce virtually no effect upon the gel
mobility of the random sequence DNA. In contrast, nicked A-tract fragments
reveal a regular modulation of curvature depending upon the position of the
strand break with respect to the overall bend. Maximal relaxation is observed
when nicks occur inside A-tracts. The results are partially reproduced in
simulations. Analysis of computed curved DNA conformations reveals a group of
sugar atoms that exhibit reduced backbone length within A-tracts, which can
correspond to the compression hypothesis.
