3D reconstruction and comparison of shapes of DNA minicircles observed by cryo-electron microscopy.
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.
Amzallag
Arnaud
A
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
Vaillant
Cédric
C
Jacob
Mathews
M
Unser
Michael
M
Bednar
Jan
J
Kahn
Jason D
JD
Dubochet
Jacques
J
Stasiak
Andrzej
A
Maddocks
John H
JH
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
D002373:Cyclic AMP Receptor Protein; D004270:DNA, Circular