DNA supercoiling-induced shapes alter minicircle hydrodynamic properties
Loading...
Date
2023
Authors
Waszkiewicz, Radost
Ranashinghe, Maduni
Fogg, Jonathan M.
Catanese, Daniel J.
Ekiel-Jezewska, Maria L.
Lisicki, Maciej
Demeler, Borries
Zechiedrich, Lynn
Szymczak, Piotr
Journal Title
Journal ISSN
Volume Title
Publisher
Oxford University Press
Abstract
DNA 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.
Description
Open access article. Creative Commons Attribution 4.0 International license (CC BY 4.0) applies
Keywords
Supercoiling , DNA shapes , Hydrodynamic properties , Analytical ultracentrifugation
Citation
Waszkiewicz, 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