Structural diversity of supercoiled DNA
Rossitza N. Irobalieva, Jonathan M. Fogg, Daniel J. Catanese Jr, Thana Sutthibutpong, Muyuan Chen, Anna K. Barker, Steven J. Ludtke, Sarah A. Harris, Michael F. Schmid, Wah Chiu & Lynn Zechiedrich
Affiliations Contributions Corresponding authors
Nature Communications 6, Article number: 8440 doi:10.1038/ncomms9440
Received 31 January 2015 Accepted 21 August 2015 Published 12 October 2015 Updated online 29 October 2015
Erratum (October, 2015)
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.
Subject terms: Biological sciences Biochemistry Biophysics
