ArticleNucleic acids research2017
Influence of DNA sequence on the structure of minicircles under torsional stress.
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 23 papers.
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Who cites it
23 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
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- DNA supercoiling-induced shapes alter minicircle hydrodynamic properties.Nucleic acids research · 2023Article
- DNA supercoiling-induced shapes alter minicircle hydrodynamic properties.bioRxiv : the preprint server for biology · 2023Article
- Revisiting DNA Sequence-Dependent Deformability in High-Resolution Structures: Effects of Flanking Base Pairs on Dinucleotide Morphology and Global Chain Configuration.Life (Basel, Switzerland) · 2022Article
- Structural interplay between DNA-shape protein recognition and supercoiling: The case of IHF.Computational and structural biotechnology journal · 2022Article
- Supercoiling and looping promote DNA base accessibility and coordination among distant sites.Nature communications · 2021Article
- Structural Landscape of the Transition from an ssDNA Dumbbell Plus Its Complementary Hairpin to a dsDNA Microcircle Via a Kissing Loop Intermediate.Molecules (Basel, Switzerland) · 2021Article
- Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field.Annual review of biophysics · 2021Article
- WASP: a software package for correctly characterizing the topological development of ribbon structures.Scientific reports · 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
- Improving therapeutic potential of non-viral minimized DNA vectors.Cell & gene therapy insights · 2020Article
- Chromosomal Organization and Regulation of Genetic Function inEcoSal Plus · 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
- BIOPHYSICS MEETS GENE THERAPY: HOW EXPLORING SUPERCOILING-DEPENDENT STRUCTURAL CHANGES IN DNA LED TO THE DEVELOPMENT OF MINIVECTOR DNA.Technology and innovation · 2019Article
- Small DNA circles as bacterial topoisomerase I inhibitors.RSC advances · 2019Article
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Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
The sequence dependence of the conformational distribution of DNA under various levels of torsional stress is an important unsolved problem. Combining theory and coarse-grained simulations shows that the DNA sequence and a structural correlation due to topology constraints of a circle are the main factors that dictate the 3D structure of a 336 bp DNA minicircle under torsional stress. We found that DNA minicircle topoisomers can have multiple bend locations under high torsional stress and that the positions of these sharp bends are determined by the sequence, and by a positive mechanical correlation along the sequence. We showed that simulations and theory are able to provide sequence-specific information about individual DNA minicircles observed by cryo-electron tomography (cryo-ET). We provided a sequence-specific cryo-ET tomogram fitting of DNA minicircles, registering the sequence within the geometric features. Our results indicate that the conformational distribution of minicircles under torsional stress can be designed, which has important implications for using minicircle DNA for gene therapy.
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