Correction: Stokesian dynamics of sedimenting elastic rings

Gruziel-Słomka, Magdalena; Kondratiuk, Paweł; Szymczak, Piotr; Ekiel-Jeżewska, Maria L.

doi:10.1039/d2sm90079c

Cited by 2 publications

(1 citation statement)

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“…This finding provides an important input to future models of circularised polymers. Incorporating torsional interactions is more difficult than just bending interactions and is often neglected when constructing models of circularized molecules (68, 69, 70, 71). Since the torsional forces play a role even when Δ Lk is close to zero, additional care needs to be taken when generalising such models for the context of supercoiled DNA.…”

Section: Discussionmentioning

confidence: 99%

DNA supercoiling-induced shapes alter minicircle hydrodynamic properties

Waszkiewicz

Ranasinghe

Fogg

et al. 2023

Preprint

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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.

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