Several recent experiments have suggested that sharply bent DNA has a surprisingly high bending flexibility, but the cause  is poorly understood. It has been demonstrated that excitation of flexible defects can explain the results; while whether such defects can be excited under the level of DNA bending in those experiments has remained unclearand been debated. Interestingly, due to experimental design DNA contained pre-existing nicks in nearly all those experiments, while the potential effect of nicks have never been considered  . Here, using full-atom molecular dynamics (MD) simulations, we show that nicks promote DNA basepair disruption at the nicked sites which drastically reduced DNA bending energy. In the absence of nicks, basepair disruption can also occur , but it requires a higher level of DNA bending.  Overall, our results challenge the interpretations of previous sharp DNA bending experiments and highlight that the micromechanics of sharply bent DNA still remains an open question.
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.
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have suggested
suggest
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of this flexibility
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It has been demonstrated that
Although
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the results; while whether such defects can be excited under
these results, whether such excitation can occur with
R
those experiments has remained unclearand been debated. Interestingly, due to experimental design DNA contained pre-existing nicks in nearly all those experiments, while the potential effect of nicks have
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
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in the interpretation of experimental results
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(MD)
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which drastically reduced
, which drastically reduces
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the
addition, lower temperatures suppress the nick-dependent basepair disruption. In the
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, but it
but
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Therefore, basepair disruption inside B-form DNA can be suppressed if the DNA contains preexisting nicks.
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challenge the interpretations of previous sharp DNA bending experiments and highlight that the micromechanics
suggest that the reported mechanical anomaly of sharply bent DNA is likely dependent on preexisting nicks, therefore the intrinsic mechanisms
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DNA still remains
nick-free DNA remain