ArticleBiophysical journal2014
Modeling DNA thermodynamics under torsional stress.
Article in Biophysical journal, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Correlating fluorescence microscopy, optical and magnetic tweezers to study single chiral biopolymers such as DNA.Nature communications · 2024Article
- Coarse-Grained Simulations of DNA Reveal Angular Dependence of Sticky-End Binding.The journal of physical chemistry. B · 2021Article
- Nonequilibrium dynamics and action at a distance in transcriptionally driven DNA supercoiling.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results.Frontiers in molecular biosciences · 2021Review
- Effects of Model Shape, Volume, and Softness of the Capsid for DNA Packaging of phi29.The journal of physical chemistry. B · 2020Article
- Influence of DNA sequence on the structure of minicircles under torsional stress.Nucleic acids research · 2017Article
- Sequence Affects the Cyclization of DNA Minicircles.The journal of physical chemistry letters · 2016Article
- Twist-induced defects of the P-SSP7 genome revealed by modeling the cryo-EM density.The journal of physical chemistry. B · 2015Article
- Modelling toehold-mediated RNA strand displacement.Biophysical journal · 2015Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Negatively twisted DNA is essential to many biological functions. Due to torsional stress, duplex DNA can have local, sequence-dependent structural defects. In this work, a thermodynamic model of DNA was built to qualitatively predict the local sequence-dependent mechanical instabilities under torsional stress. The results were compared to both simulation of a coarse-grained model and experiment results. By using the Kirkwood superposition approximation, we built an analytical model to represent the free energy difference ΔW of a hydrogen-bonded basepair between the B-form helical state and the basepair opened (or locally melted) state, within a given sequence under torsional stress. We showed that ΔW can be well approximated by two-body interactions with its nearest-sequence-neighbor basepairs plus a free energy correction due to long-range correlations. This model is capable of rapidly predicting the position and thermodynamics of local defects in a given sequence. The result qualitatively matches with an in vitro experiment for a long DNA sequence (>4000 basepairs). The 12 parameters used in this model can be further quantitatively refined when more experimental data are available.
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Registered trials
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