Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2003 Sep;85(3):1968-73.
doi: 10.1016/S0006-3495(03)74624-4.

Identification of binding mechanisms in single molecule-DNA complexes

Rainer Eckel  1 , Robert Ros, Alexandra Ros, Sven David Wilking, Norbert Sewald, Dario Anselmetti
Affiliations

Identification of binding mechanisms in single molecule-DNA complexes

Rainer Eckel et al. Biophys J. 2003 Sep.

Abstract

Changes in the elastic properties of single deoxyribonucleic acid (DNA) molecules in the presence of different DNA-binding agents are identified using atomic force microscope single molecule force spectroscopy. We investigated the binding of poly(dG-dC) dsDNA with the minor groove binder distamycin A, two supposed major groove binders, an alpha-helical and a 3(10)-helical peptide, the intercalants daunomycin, ethidium bromide and YO, and the bis-intercalant YOYO. Characteristic mechanical fingerprints in the overstretching behavior of the studied single DNA-ligand complexes were observed allowing the distinction between different binding modes. Docking of ligands to the minor or major groove of DNA has the effect that the intramolecular B-S transition remains visible as a distinct plateau in the force-extension trace. By contrast, intercalation of small molecules into the double helix is characterized by the vanishing of the B-S plateau. These findings lead to the conclusion that atomic force microscope force spectroscopy can be regarded as a single molecule biosensor and is a potent tool for the characterization of binding motives of small ligands to DNA.

PubMed Disclaimer

Figures

FIGURE 1
FIGURE 1
(A) Experimental setup; (B) Force-extension trace for free poly(dG-dC) dsDNA.
FIGURE 2
FIGURE 2
Force-extension traces for (A) the DNA-distamycin A complex; (B) the DNA complex with the α-helical peptide Ac-(Leu-Ala-Arg-Leu)3-NH-linker; (C) the complex of DNA with the 310-helical peptide Ac-(Aib-Leu-Arg)4-NH-linker.
FIGURE 3
FIGURE 3
Force-extension traces for the complexes of poly(dG-dC) dsDNA with the intercalants (A) daunomycin; (B) ethidium bromide; (C) YO; (D) YOYO.
See this image and copyright information in PMC

References

    1. Anselmetti, D., J. Fritz, B. Smith, and X. Fernandez-Busquets. 2000. Single molecule DNA biophysics with atomic force microscopy. Single Molecules. 1:17–23.
    1. Aubel-Sadron, G., and D. Londos-Gagliardi. 1984. Daunorubicin and doxorubicin, anthracycline antibiotics, a physicochemical and biological review. Biochimie. 66:333–352. - PubMed
    1. Baguley, B. C. 1982. Nonintercalative DNA-binding antitumour compounds. Mol. Cell. Biochem. 43:167–181. - PubMed
    1. Bailly, C., and J. B. Chaires. 1998. Sequence-specific DNA minor groove binders. Design and synthesis of netropsin and distamycin analogues. Bioconjug. Chem. 9:513–538. - PubMed
    1. Clausen-Schaumann, H., M. Rief, C. Tolksdorf, and H. E. Gaub. 2000. Mechanical stability of single DNA molecules. Biophys. J. 78:1997–2007. - PMC - PubMed

Publication types

MeSH terms