  Several recent experiments suggest that sharply bent DNA has a surprisingly
high bending flexibility, but the cause of this flexibility is poorly
understood. Although excitation of flexible defects can explain these results,
whether such excitation can occur with the level of DNA bending in these
experiments remains unclear. Intriguingly, the DNA contained preexisting nicks
in most of these experiments but whether nicks might play a role in flexibility
has never been considered in the interpretation of experimental results. Here,
using full-atom molecular dynamics simulations, we show that nicks promote DNA
basepair disruption at the nicked sites, which drastically reduces DNA bending
energy. In addition, lower temperatures suppress the nick-dependent basepair
disruption. In the absence of nicks, basepair disruption can also occur but
requires a higher level of DNA bending. Therefore, basepair disruption inside
B-form DNA can be suppressed if the DNA contains preexisting nicks. Overall,
our results suggest that the reported mechanical anomaly of sharply bent DNA is
likely dependent on preexisting nicks, therefore the intrinsic mechanisms of
sharply bent nick-free DNA remain an open question.
