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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.

SUBMITTER: Demurtas D 

PROVIDER: S-EPMC2685088 | biostudies-other | 2009 May

REPOSITORIES: biostudies-other

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Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles.

Demurtas Davide D   Amzallag Arnaud A   Rawdon Eric J EJ   Maddocks John H JH   Dubochet Jacques J   Stasiak Andrzej A  

Nucleic acids research 20090312 9

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 an  ...[more]