ArticleNucleic acids research2009
In the absence of writhe, DNA relieves torsional stress with localized, sequence-dependent structural failure to preserve B-form.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- Structural basis of DNA crossover capture byScience (New York, N.Y.) · 2024Article
- Correlating fluorescence microscopy, optical and magnetic tweezers to study single chiral biopolymers such as DNA.Nature communications · 2024Article
- DNA opening during transcription initiation by RNA polymerase II in atomic detail.Biophysical journal · 2022Article
- Supercoiling and looping promote DNA base accessibility and coordination among distant sites.Nature communications · 2021Article
- Effects of Model Shape, Volume, and Softness of the Capsid for DNA Packaging of phi29.The journal of physical chemistry. B · 2020Article
- Specifically bound BZIP transcription factors modulate DNA supercoiling transitions.Scientific reports · 2020Article
- The emergence of sequence-dependent structural motifs in stretched, torsionally constrained DNA.Nucleic acids research · 2020Article
- Article
- BIOPHYSICS MEETS GENE THERAPY: HOW EXPLORING SUPERCOILING-DEPENDENT STRUCTURAL CHANGES IN DNA LED TO THE DEVELOPMENT OF MINIVECTOR DNA.Technology and innovation · 2019Article
- Superstructure-Dependent Loading of DNA Origami Nanostructures with a Groove-Binding Drug.ACS omega · 2018Article
- Sequence-dependent response of DNA to torsional stress: a potential biological regulation mechanism.Nucleic acids research · 2018Article
- Probing hyper-negatively supercoiled mini-circles with nucleases and DNA binding proteins.PloS one · 2018Article
- Influence of DNA sequence on the structure of minicircles under torsional stress.Nucleic acids research · 2017Article
- Phage-like packing structures with mean field sequence dependence.Journal of computational chemistry · 2017Article
- Sequence Affects the Cyclization of DNA Minicircles.The journal of physical chemistry letters · 2016Article
- DNA Shape versus Sequence Variations in the Protein Binding Process.Biophysical journal · 2016Article
- Protein/DNA interactions in complex DNA topologies: expect the unexpected.Biophysical reviews · 2016Review
- Protein/DNA interactions in complex DNA topologies: expect the unexpected.Biophysical reviews · 2016Review
- Structural diversity of supercoiled DNA.Nature communications · 2015Article
- Twist-induced defects of the P-SSP7 genome revealed by modeling the cryo-EM density.The journal of physical chemistry. B · 2015Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
To understand how underwinding and overwinding the DNA helix affects its structure, we simulated 19 independent DNA systems with fixed degrees of twist using molecular dynamics in a system that does not allow writhe. Underwinding DNA induced spontaneous, sequence-dependent base flipping and local denaturation, while overwinding DNA induced the formation of Pauling-like DNA (P-DNA). The winding resulted in a bimodal state simultaneously including local structural failure and B-form DNA for both underwinding and extreme overwinding. Our simulations suggest that base flipping and local denaturation may provide a landscape influencing protein recognition of DNA sequence to affect, for examples, replication, transcription and recombination. Additionally, our findings help explain results from single-molecule experiments and demonstrate that elastic rod models are strictly valid on average only for unstressed or overwound DNA up to P-DNA formation. Finally, our data support a model in which base flipping can result from torsional stress.
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