DNA supercoiling-induced shapes alter minicircle hydrodynamic properties

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dc.contributor.authorWaszkiewicz, Radost
dc.contributor.authorRanashinghe, Maduni
dc.contributor.authorFogg, Jonathan M.
dc.contributor.authorCatanese, Daniel J.
dc.contributor.authorEkiel-Jezewska, Maria L.
dc.contributor.authorLisicki, Maciej
dc.contributor.authorDemeler, Borries
dc.contributor.authorZechiedrich, Lynn
dc.contributor.authorSzymczak, Piotr
dc.date.accessioned2024-08-27T20:30:01Z
dc.date.available2024-08-27T20:30:01Z
dc.date.issued2023
dc.descriptionOpen access article. Creative Commons Attribution 4.0 International license (CC BY 4.0) applies
dc.description.abstractDNA in cells is organized in negatively supercoiled loops. The resulting torsional and bending strain allows DNA to adopt a surprisingly wide variety of 3-D shapes. This interplay between negative supercoiling, looping, and shape influences how DNA is stored, replicated, transcribed, repaired, and likely every other aspect of DNA activity. To understand the consequences of negative supercoiling and curvature on the hydrodynamic properties of DNA, we submitted 336 bp and 672 bp DNA minicircles to analytical ultracentrifugation (AUC). We found that the diffusion coefficient, sedimentation coefficient, and the DNA hydrodynamic radius strongly depended on circularity, loop length, and degree of negative supercoiling. Because AUC cannot ascertain shape beyond degree of non-globularity, we applied linear elasticity theory to predict DNA shapes, and combined these with hydrodynamic calculations to interpret the AUC data, with reasonable agreement between theory and experiment. These complementary approaches, together with earlier electron cryotomography data, provide a framework for understanding and predicting the effects of supercoiling on the shape and hydrodynamic properties of DNA.
dc.description.peer-reviewYes
dc.identifier.citationWaszkiewicz, R., Ranasinghe, M., Fogg, J. M., Catanese, D. J., Ekiel-Jezewska, M. L., Lisicki, M., Demeler, B., Zechiedrich, L., & Szymczak, P. (2023). DNA supercoiling-induced shapes alter minicircle hydrodynamic properties. Nucleic Acids Research, 51(8), 4027-4042. https://doi.org/10.1093/nar/gkad183
dc.identifier.urihttps://hdl.handle.net/10133/6890
dc.language.isoen
dc.publisherOxford University Press
dc.publisher.departmentDepartment Chemistry and Biochemistry
dc.publisher.facultyArts and Science
dc.publisher.institutionUniversity of Warsaw
dc.publisher.institutionUniversity of Lethbridge
dc.publisher.institutionBaylor College of Medicine
dc.publisher.institutionRice University
dc.publisher.institutionPolish Academy of Sciences
dc.publisher.institutionUniversity of Montana
dc.publisher.urlhttps://doi.org/10.1093/nar/gkad183
dc.subjectSupercoiling
dc.subjectDNA shapes
dc.subjectHydrodynamic properties
dc.subjectAnalytical ultracentrifugation
dc.subject.lcshDNA--Research
dc.titleDNA supercoiling-induced shapes alter minicircle hydrodynamic properties
dc.typeArticle
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