title: Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles.
abstract: We use cryo-electron microscopy (cryo-EM) to study the 3D shapes of 94-bp-long DNA minicircles and address the question of whether cyclization of such short DNA molecules necessitates the formation of sharp, localized kinks in DNA or whether the necessary bending can be redistributed and accomplished within the limits of the elastic, standard model of DNA flexibility. By comparing the shapes of covalently closed, nicked and gapped DNA minicircles, we conclude that 94-bp-long covalently closed and nicked DNA minicircles do not show sharp kinks while gapped DNA molecules, containing very flexible single-stranded regions, do show sharp kinks. We corroborate the results of cryo-EM studies by using Bal31 nuclease to probe for the existence of kinks in 94-bp-long minicircles.
authors.affiliation: Faculty of Biology and Medicine, Center for Integrative Genomics, University of Lausanne, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
authors.forename: Davide
authors.initials: D
authors.lastname: Demurtas
authors.forename: Arnaud
authors.initials: A
authors.lastname: Amzallag
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Rawdon
authors.forename: John H
authors.initials: JH
authors.lastname: Maddocks
authors.forename: Jacques
authors.initials: J
authors.lastname: Dubochet
authors.forename: Andrzej
authors.initials: A
authors.lastname: Stasiak
mesh_terms: D000465:Algorithms; D020285:Cryoelectron Microscopy; D003500:Cyclization; D004270:DNA, Circular / Q000737:chemistry / Q000378:metabolism / Q000648:ultrastructure*; D004706:Endodeoxyribonucleases / Q000378:metabolism; D009690:Nucleic Acid Conformation
chemical_list: D004270:DNA, Circular; D004706:Endodeoxyribonucleases; C038407:exonuclease Bal 31