title: 3D reconstruction and comparison of shapes of DNA minicircles observed by cryo-electron microscopy.
abstract: 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.
authors.affiliation: Laboratory for Computation and Visualization in Mathematics and Mechanics, EPFL FSB IMB, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland. arnaud.amzallag@epfl.ch
authors.forename: Arnaud
authors.initials: A
authors.lastname: Amzallag
authors.forename: Cédric
authors.initials: C
authors.lastname: Vaillant
authors.forename: Mathews
authors.initials: M
authors.lastname: Jacob
authors.forename: Michael
authors.initials: M
authors.lastname: Unser
authors.forename: Jan
authors.initials: J
authors.lastname: Bednar
authors.forename: Jason D
authors.initials: JD
authors.lastname: Kahn
authors.forename: Jacques
authors.initials: J
authors.lastname: Dubochet
authors.forename: Andrzej
authors.initials: A
authors.lastname: Stasiak
authors.forename: John H
authors.initials: JH
authors.lastname: Maddocks
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D001665:Binding Sites; D016000:Cluster Analysis; D020285:Cryoelectron Microscopy; D002373:Cyclic AMP Receptor Protein / Q000378:metabolism; D004270:DNA, Circular / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure*; D021621:Imaging, Three-Dimensional; D008969:Molecular Sequence Data; D009038:Motion; D009690:Nucleic Acid Conformation; D012984:Software; D016385:TATA Box
chemical_list: D002373:Cyclic AMP Receptor Protein; D004270:DNA, Circular