DOI: 10.1038/ncomms9440. Structural diversity of supercoiled DNA

10.1038/ncomms9440

Crossref journal-article

Springer Science and Business Media LLC

Nature Communications (297)

Abstract

AbstractBy regulating access to the genetic code, DNA supercoiling strongly affects DNA metabolism. Despite its importance, however, much about supercoiled DNA (positively supercoiled DNA, in particular) remains unknown. Here we use electron cryo-tomography together with biochemical analyses to investigate structures of individual purified DNA minicircle topoisomers with defined degrees of supercoiling. Our results reveal that each topoisomer, negative or positive, adopts a unique and surprisingly wide distribution of three-dimensional conformations. Moreover, we uncover striking differences in how the topoisomers handle torsional stress. As negative supercoiling increases, bases are increasingly exposed. Beyond a sharp supercoiling threshold, we also detect exposed bases in positively supercoiled DNA. Molecular dynamics simulations independently confirm the conformational heterogeneity and provide atomistic insight into the flexibility of supercoiled DNA. Our integrated approach reveals the three-dimensional structures of DNA that are essential for its function.

Bibliography

Irobalieva, R. N., Fogg, J. M., Catanese, D. J., Sutthibutpong, T., Chen, M., Barker, A. K., Ludtke, S. J., Harris, S. A., Schmid, M. F., Chiu, W., & Zechiedrich, L. (2015). Structural diversity of supercoiled DNA. Nature Communications, 6(1).

Authors 11

Rossitza N. Irobalieva (first)
Jonathan M. Fogg (additional)
Daniel J. Catanese (additional)
Thana Sutthibutpong (additional)
Muyuan Chen (additional)
Anna K. Barker (additional)
Steven J. Ludtke (additional)
Sarah A. Harris (additional)
Michael F. Schmid (additional)
Wah Chiu (additional)
Lynn Zechiedrich (additional)

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Dates

Type	When
Created	9 years, 10 months ago (Oct. 12, 2015, 5:41 a.m.)
Deposited	2 years, 7 months ago (Jan. 5, 2023, 5:40 a.m.)
Indexed	2 days, 14 hours ago (Aug. 21, 2025, 1:38 p.m.)
Issued	9 years, 10 months ago (Oct. 12, 2015)
Published	9 years, 10 months ago (Oct. 12, 2015)
Published Online	9 years, 10 months ago (Oct. 12, 2015)

Funders 0

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BibTeX

@article{Irobalieva_2015, title={Structural diversity of supercoiled DNA}, volume={6}, ISSN={2041-1723}, url={http://dx.doi.org/10.1038/ncomms9440}, DOI={10.1038/ncomms9440}, number={1}, journal={Nature Communications}, publisher={Springer Science and Business Media LLC}, author={Irobalieva, Rossitza N. and Fogg, Jonathan M. and Catanese, Daniel J. and Sutthibutpong, Thana and Chen, Muyuan and Barker, Anna K. and Ludtke, Steven J. and Harris, Sarah A. and Schmid, Michael F. and Chiu, Wah and Zechiedrich, Lynn}, year={2015}, month=oct }

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