DNA supercoiling-induced shapes alter minicircle hydrodynamic properties

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dc.citation.firstpage4027en_US
dc.citation.issueNumber8en_US
dc.citation.journalTitleNucleic Acids Researchen_US
dc.citation.lastpage4042en_US
dc.citation.volumeNumber51en_US
dc.contributor.authorWaszkiewicz, Radosten_US
dc.contributor.authorRanasinghe, Madunien_US
dc.contributor.authorFogg, Jonathan Men_US
dc.contributor.authorCatanese, Daniel J, Jr.en_US
dc.contributor.authorEkiel-Jeżewska, Maria Len_US
dc.contributor.authorLisicki, Maciejen_US
dc.contributor.authorDemeler, Borriesen_US
dc.contributor.authorZechiedrich, Lynnen_US
dc.contributor.authorSzymczak, Piotren_US
dc.date.accessioned2023-07-21T16:13:54Zen_US
dc.date.available2023-07-21T16:13:54Zen_US
dc.date.issued2023en_US
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.en_US
dc.identifier.citationWaszkiewicz, Radost, Ranasinghe, Maduni, Fogg, Jonathan M, et al.. "DNA supercoiling-induced shapes alter minicircle hydrodynamic properties." <i>Nucleic Acids Research,</i> 51, no. 8 (2023) Oxford University Press: 4027-4042. https://doi.org/10.1093/nar/gkad183.en_US
dc.identifier.digitalgkad183en_US
dc.identifier.doihttps://doi.org/10.1093/nar/gkad183en_US
dc.identifier.urihttps://hdl.handle.net/1911/114998en_US
dc.language.isoengen_US
dc.publisherOxford University Pressen_US
dc.rightsExcept where otherwise noted, this work is licensed under a Creative Commons Attribution (CC BY) license.  Permission to reuse, publish, or reproduce the work beyond the terms of the license or beyond the bounds of Fair Use or other exemptions to copyright law must be obtained from the copyright holder.en_US
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en_US
dc.titleDNA supercoiling-induced shapes alter minicircle hydrodynamic propertiesen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
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