Structural diversity of supercoiled DNA

Rossitza N. Irobalieva, Jonathan M. Fogg, Daniel J. Catanese, Thana Sutthibutpong, Muyuan Chen, Anna K. Barker, Steven J. Ludtke, Sarah A. Harris, Michael F. Schmid, Wah Chiu () and Lynn Zechiedrich ()
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Rossitza N. Irobalieva: Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030 USA
Jonathan M. Fogg: Baylor College of Medicine, Houston, Texas 77030 USA
Daniel J. Catanese: Baylor College of Medicine, Houston, Texas 77030 USA
Thana Sutthibutpong: School of Physics and Astronomy, University of Leeds
Muyuan Chen: Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030 USA
Anna K. Barker: Baylor College of Medicine
Steven J. Ludtke: Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030 USA
Sarah A. Harris: School of Physics and Astronomy, University of Leeds
Michael F. Schmid: Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030 USA
Wah Chiu: Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030 USA
Lynn Zechiedrich: Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030 USA

Nature Communications, 2015, vol. 6, issue 1, 1-11

Abstract: Abstract By 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.

Date: 2015
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DOI: 10.1038/ncomms9440

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