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

Nucleic Acids Res. 2006;34(18):e125. doi: 10.1093/nar/gkl675. Epub 2006 Sep 29.


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.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Base Sequence
  • Binding Sites
  • Cluster Analysis
  • Cryoelectron Microscopy*
  • Cyclic AMP Receptor Protein / metabolism
  • DNA, Circular / chemistry*
  • DNA, Circular / metabolism
  • DNA, Circular / ultrastructure*
  • Imaging, Three-Dimensional*
  • Molecular Sequence Data
  • Motion
  • Nucleic Acid Conformation
  • Software
  • TATA Box


  • Cyclic AMP Receptor Protein
  • DNA, Circular