DNA supercoiling-induced shapes alter minicircle hydrodynamic properties.

Authors

Radost Waszkiewicz
Maduni Ranasinghe
Jonathan M Fogg
Daniel J Catanese
Maria L Ekiel-Jeżewska
Maciej Lisicki
Borries Demeler
Lynn Zechiedrich
Piotr Szymczak

Publication Date

5-8-2023

Journal

Nucleic Acids Research

DOI

10.1093/nar/gkad183

PMID

36971110

PMCID

MC10164573

PubMedCentral® Posted Date

3-27-2023

PubMedCentral® Full Text Version

Post-print

Published Open-Access

yes

Keywords

DNA, Superhelical, Hydrodynamics, DNA, Nucleic Acid Conformation

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.

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