title: Revisiting the Anomalous Bending Elasticity of Sharply Bent DNA.
abstract: 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.
authors.affiliation: Mechanobiology Institute, National University of Singapore, Singapore; Singapore-MIT Alliance, National University of Singapore, Singapore; Department of Physics, National University of Singapore, Singapore.
authors.forename: Peiwen
authors.initials: P
authors.lastname: Cong
authors.affiliation: BioSystems and Micromechanics IRG, Singapore-MIT Alliance for Research and Technology Centre, Singapore.
authors.forename: Liang
authors.initials: L
authors.lastname: Dai
authors.affiliation: Department of Physics, Xiamen University, Xiamen, Fujian, China.
authors.forename: Hu
authors.initials: H
authors.lastname: Chen
authors.affiliation: Department of Physics, National University of Singapore, Singapore.
authors.forename: Johan R C
authors.initials: JR
authors.lastname: van der Maarel
authors.affiliation: BioSystems and Micromechanics IRG, Singapore-MIT Alliance for Research and Technology Centre, Singapore; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts.
authors.forename: Patrick S
authors.initials: PS
authors.lastname: Doyle
authors.affiliation: Mechanobiology Institute, National University of Singapore, Singapore; Department of Physics, National University of Singapore, Singapore; BioSystems and Micromechanics IRG, Singapore-MIT Alliance for Research and Technology Centre, Singapore; Centre for BioImaging Sciences, National University of Singapore, Singapore. Electronic address: phyyj@nus.edu.sg.
authors.forename: Jie
authors.initials: J
authors.lastname: Yan
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D004548:Elasticity; D056004:Molecular Dynamics Simulation; D013696:Temperature
chemical_list: D004247:DNA