DNA supercoiling-induced shapes alter minicircle hydrodynamic properties

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dc.citation.firstpage4027
dc.citation.issueNumber8
dc.citation.journalTitleNucleic Acids Research
dc.citation.lastpage4042
dc.citation.volumeNumber51
dc.contributor.authorWaszkiewicz, Radost
dc.contributor.authorRanasinghe, Maduni
dc.contributor.authorFogg, Jonathan M
dc.contributor.authorCatanese, Daniel J, Jr.
dc.contributor.authorEkiel-Jeżewska, Maria L
dc.contributor.authorLisicki, Maciej
dc.contributor.authorDemeler, Borries
dc.contributor.authorZechiedrich, Lynn
dc.contributor.authorSzymczak, Piotr
dc.date.accessioned2023-07-21T16:13:54Z
dc.date.available2023-07-21T16:13:54Z
dc.date.issued2023
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.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.
dc.identifier.digitalgkad183
dc.identifier.doihttps://doi.org/10.1093/nar/gkad183
dc.identifier.urihttps://hdl.handle.net/1911/114998
dc.language.isoeng
dc.publisherOxford University Press
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.
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.titleDNA supercoiling-induced shapes alter minicircle hydrodynamic properties
dc.typeJournal article
dc.type.dcmiText
dc.type.publicationpublisher version
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