ArticleNucleic acids research2017
Analyzing DNA curvature and its impact on the ionic environment: application to molecular dynamics simulations of minicircles.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Cryo-EM structure of a 95-base-pair double-stranded DNA minicircle at 5.3 Å resolution.Nucleic acids research · 2026Article
- MDNA : a software module for DNA structure generation and analysis.Nucleic acids research · 2026Article
- cgNA+min: computation of sequence-dependent dsDNA energy-minimizing minicircles.Nucleic acids research · 2026Article
- A perspective on the molecular simulation of DNA from structural and functional aspects.Chemical science · 2021Review
- Atomistic insight into sequence-directed DNA bending and minicircle formation propensity in the absence and presence of phased A-tracts.Journal of computer-aided molecular design · 2020Article
- Chromatin Compaction Multiscale Modeling: A Complex Synergy Between Theory, Simulation, and Experiment.Frontiers in molecular biosciences · 2020Review
- Sequence-dependent response of DNA to torsional stress: a potential biological regulation mechanism.Nucleic acids research · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
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Abstract
We propose a method for analyzing the magnitude and direction of curvature within nucleic acids, based on the curvilinear helical axis calculated by Curves+. The method is applied to analyzing curvature within minicircles constructed with varying degrees of over- or under-twisting. Using the molecular dynamics trajectories of three different minicircles, we are able to quantify how curvature varies locally both in space and in time. We also analyze how curvature influences the local environment of the minicircles, notably via increased heterogeneity in the ionic distributions surrounding the double helix. The approach we propose has been integrated into Curves+ and the utilities Canal (time trajectory analysis) and Canion (environmental analysis) and can be used to study a wide variety of static and dynamic structural data on nucleic acids.
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