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Nucleic Acids Research Advance Access originally published online on September 29, 2006
Nucleic Acids Research 2006 34(18):e125; doi:10.1093/nar/gkl675
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Nucleic Acids Research, 2006, Vol. 34, No. 18 e125
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

3D reconstruction and comparison of shapes of DNA minicircles observed by cryo-electron microscopy

Arnaud Amzallag*, Cédric Vaillant, Mathews Jacob1, Michael Unser1, Jan Bednar2, Jason D. Kahn3, Jacques Dubochet4, Andrzej Stasiak4 and John H. Maddocks*

Laboratory for Computation and Visualization in Mathematics and Mechanics, EPFL FSB IMB Ecole Polytechnique Fédérale de Lausanne CH-1015 Lausanne, Switzerland 1 Biomedical Imaging Group, EPFL LIB Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland 2 Laboratoire de Spectrometrie Physique, UMR 5588 CNRS, 140 Av. de la Physique, BP 87, 38402 St Martin d'Heres Cedex, France 3 Department of Chemistry and Biochemistry, University of Maryland College Park, MD 20742-2021, USA 4 Laboratory of Ultrastructural Analysis, University of Lausanne 1015 Lausanne, Switzerland

*To whom correspondence should be addressed. Tel: +41 21 693 2767; Fax: +41 21 693 5530; Email: arnaud.amzallag{at}epfl.ch

Received June 14, 2006. Revised August 19, 2006. Accepted August 30, 2006.

We use cryo-electron microscopy to compare 3D shapes of 158 bp long DNA minicircles that differ only in the sequence within an 18 bp block containing either a TATA box or a catabolite activator protein binding site. We present a sorting algorithm that correlates the reconstructed shapes and groups them into distinct categories. We conclude that the presence of the TATA box sequence, which is believed to be easily bent, does not significantly affect the observed shapes.

*Correspondence may also be addressed to John H. Maddocks. Tel: +41 21 693 2762; Fax: +41 21 693 5530; Email: john.maddocks{at}epfl.ch

Present addresses: Cédric Vaillant, Laboratoire Joliot Curie, Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France Mathews Jacob, Beckman Institute, University of Illinois at Urbana- Champaign, Urbana, IL 61801, USA


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