title: Structural diversity of supercoiled DNA.
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.
authors.affiliation: Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030 USA.|Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030 USA.
authors.forename: Rossitza N
authors.initials: RN
authors.lastname: Irobalieva
authors.affiliation: Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030 USA.|Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030 USA.|Department of Pharmacology, Baylor College of Medicine, Houston, Texas 77030 USA.
authors.forename: Jonathan M
authors.initials: JM
authors.lastname: Fogg
authors.affiliation: Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030 USA.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Catanese
authors.affiliation: Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030 USA.|Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030 USA.|Department of Pharmacology, Baylor College of Medicine, Houston, Texas 77030 USA.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Catanese
authors.affiliation: School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK.
authors.forename: Thana
authors.initials: T
authors.lastname: Sutthibutpong
authors.affiliation: Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030 USA.|Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030 USA.
authors.forename: Muyuan
authors.initials: M
authors.lastname: Chen
authors.affiliation: Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030 USA.
authors.forename: Anna K
authors.initials: AK
authors.lastname: Barker
authors.affiliation: Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030 USA.|Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030 USA.
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Ludtke
authors.affiliation: School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK.
authors.forename: Sarah A
authors.initials: SA
authors.lastname: Harris
authors.affiliation: Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030 USA.|Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030 USA.
authors.forename: Michael F
authors.initials: MF
authors.lastname: Schmid
authors.affiliation: Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030 USA.|Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030 USA.|Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030 USA.
authors.forename: Wah
authors.initials: W
authors.lastname: Chiu
authors.affiliation: Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030 USA.|Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030 USA.|Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030 USA.|Department of Pharmacology, Baylor College of Medicine, Houston, Texas 77030 USA.
authors.forename: Lynn
authors.initials: L
authors.lastname: Zechiedrich
mesh_terms: D004278:DNA, Superhelical; D056004:Molecular Dynamics Simulation
chemical_list: D004278:DNA, Superhelical