ArticleBiophysical journal2015
Revisiting the Anomalous Bending Elasticity of Sharply Bent DNA.
Article in Biophysical journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Decoding force-transmission linkages for therapeutic targeting and engineering.APL bioengineering · 2025Review
- Understanding the Mechanism of Bent DNA Amplifying Sensors Using All-Atom Molecular Dynamics Simulations.Biosensors · 2025Article
- Catch bond models may explain how force amplifies TCR signaling and antigen discrimination.Nature communications · 2023Article
- Cytosine methylation regulates DNA bendability depending on the curvature.Chemical science · 2022Article
- Structures of artificially designed discrete RNA nanoarchitectures at near-atomic resolution.Science advances · 2021Article
- Bent DNA Bows as Sensing Amplifiers for Detecting DNA-Interacting Salts and Molecules.Sensors (Basel, Switzerland) · 2020Article
- Determinants of cyclization-decyclization kinetics of short DNA with sticky ends.Nucleic acids research · 2020Article
- Strongly Bent Double-Stranded DNA: Reconciling Theory and Experiment.Frontiers in physics · 2019Article
- Identifying Physical Causes of Apparent Enhanced Cyclization of Short DNA Molecules with a Coarse-Grained Model.Journal of chemical theory and computation · 2019Article
- Structural Flexibility of DNA-RNA Hybrid Duplex: Stretching and Twist-Stretch Coupling.Biophysical journal · 2019Article
- Structural-elastic determination of the force-dependent transition rate of biomolecules.Chemical science · 2018Article
- How Well Can DNA Rupture DNA? Shearing and Unzipping Forces inside DNA Nanostructures.ACS omega · 2018Article
- Sequence-Dependent Persistence Length of Long DNA.Physical review letters · 2017Article
- Understanding the Relative Flexibility of RNA and DNA Duplexes: Stretching and Twist-Stretch Coupling.Biophysical journal · 2017Article
- Single-molecule fluorescence studies on DNA looping.Methods (San Diego, Calif.) · 2016Article
- Simulation of DNA Supercoil Relaxation.Biophysical journal · 2016Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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