Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles.
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.
Demurtas
Davide
D
Faculty of Biology and Medicine, Center for Integrative Genomics, University of Lausanne, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
Amzallag
Arnaud
A
Rawdon
Eric J
EJ
Maddocks
John H
JH
Dubochet
Jacques
J
Stasiak
Andrzej
A
D000465:Algorithms; D020285:Cryoelectron Microscopy; D003500:Cyclization; D004270:DNA, Circular / Q000737:chemistry / Q000378:metabolism / Q000648:ultrastructure*; D004706:Endodeoxyribonucleases / Q000378:metabolism; D009690:Nucleic Acid Conformation
D004270:DNA, Circular; D004706:Endodeoxyribonucleases; C038407:exonuclease Bal 31