ArticleBiophysical journal2012
Probing the elasticity of DNA on short length scales by modeling supercoiling under tension.
Article in Biophysical journal, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 46 citations in OpenAlex.
- The effects of DMSO on DNA conformations and mechanics.Biophysical journal · 2025Article
- Exploring protein-mediated compaction of DNA by coarse-grained simulations and unsupervised learning.Biophysical journal · 2024Article
- Dynamic interplay between target search and recognition for a Type I CRISPR-Cas system.Nature communications · 2023Article
- DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling.Frontiers in microbiology · 2023Review
- A quantitative model for the dynamics of target recognition and off-target rejection by the CRISPR-Cas Cascade complex.Nature communications · 2022Article
- Probing the stability of the SpCas9-DNA complex after cleavage.Nucleic acids research · 2021Article
- Dynamics of the Buckling Transition in Double-Stranded DNA and RNA.Biophysical journal · 2020Article
- The temperature dependence of the helical twist of DNA.Nucleic acids research · 2018Article
- Probing the salt dependence of the torsional stiffness of DNA by multiplexed magnetic torque tweezers.Nucleic acids research · 2017Article
- Simulation of DNA Supercoil Relaxation.Biophysical journal · 2016Article
- Sequence Affects the Cyclization of DNA Minicircles.The journal of physical chemistry letters · 2016Article
- TrmBL2 from Pyrococcus furiosus Interacts Both with Double-Stranded and Single-Stranded DNA.PloS one · 2016Article
- Thermodynamics of long supercoiled molecules: insights from highly efficient Monte Carlo simulations.Biophysical journal · 2015Article
- Plectoneme tip bubbles: coupled denaturation and writhing in supercoiled DNA.Scientific reports · 2015Article
- Atomic force microscopy study of DNA flexibility on short length scales: smooth bending versus kinking.Nucleic acids research · 2014Article
- Double-stranded RNA under force and torque: similarities to and striking differences from double-stranded DNA.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- The structural code of cyanobacterial genomes.Nucleic acids research · 2014Article
- DNA, flexibly flexible.Biophysical journal · 2014Article
- Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Probing the elastic limit of DNA bending.Nucleic acids research · 2014Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
The wormlike-chain (WLC) model is widely used to describe the energetics of DNA bending. Motivated by recent experiments, alternative, so-called subelastic chain models were proposed that predict a lower elastic energy of highly bent DNA conformations. Until now, no unambiguous verification of these models has been obtained because probing the elasticity of DNA on short length scales remains challenging. Here we investigate the limits of the WLC model using coarse-grained Monte Carlo simulations to model the supercoiling of linear DNA molecules under tension. At a critical supercoiling density, the DNA extension decreases abruptly due to the sudden formation of a plectonemic structure. This buckling transition is caused by the large energy required to form the tightly bent end-loop of the plectoneme and should therefore provide a sensitive benchmark for model evaluation. Although simulations based on the WLC energetics could quantitatively reproduce the buckling measured in magnetic tweezers experiments, the buckling almost disappears for the tested linear subelastic chain model. Thus, our data support the validity of a harmonic bending potential even for small bending radii down to 3.5 nm.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.