DNA Nanotechnology

Volume 749 of the series Methods in Molecular Biology pp 235-254


DNA Contour Length Measurements as a Tool for the Structural Analysis of DNA and Nucleoprotein Complexes

  • Claudio RivettiAffiliated withDepartment of Biochemistry and Molecular Biology, University of Parma Email author 

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The atomic force microscope (AFM) is a widely used tool to image DNA and nucleoprotein complexes at the molecular level. This is because the AFM is relatively easy to operate, has the capability to image biomolecules under aqueous solutions, and, most importantly, can image mesoscopic macromolecular structures that are too complex to be studied by X-ray or NMR and too small to be visualized with the optical microscope. Although there are many AFM studies about the structure and the physical properties of DNA, only in few cases a rigorous method has been applied to analyze AFM images. This chapter describes procedures to prepare DNA and nucleoprotein complexes for AFM imaging and methods used to carry out simple image measurements to obtain structural data. In particular, methods to measure DNA contour length and the volume of free or DNA-bound proteins are presented and discussed.

Key words

Atomic force microscopy Image analysis Contour length Volume DNA Nucleoprotein complex