Identification of binding mechanisms in single molecule-DNA complexes

Eckel R, Ros R, Ros A, Wilking SD, Sewald N, Anselmetti D (2003)
Biophysical journal 85(3): 1968-1973.

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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.
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Eckel R, Ros R, Ros A, Wilking SD, Sewald N, Anselmetti D. Identification of binding mechanisms in single molecule-DNA complexes. Biophysical journal. 2003;85(3):1968-1973.
Eckel, R., Ros, R., Ros, A., Wilking, S. D., Sewald, N., & Anselmetti, D. (2003). Identification of binding mechanisms in single molecule-DNA complexes. Biophysical journal, 85(3), 1968-1973.
Eckel, R., Ros, R., Ros, A., Wilking, S. D., Sewald, N., and Anselmetti, D. (2003). Identification of binding mechanisms in single molecule-DNA complexes. Biophysical journal 85, 1968-1973.
Eckel, R., et al., 2003. Identification of binding mechanisms in single molecule-DNA complexes. Biophysical journal, 85(3), p 1968-1973.
R. Eckel, et al., “Identification of binding mechanisms in single molecule-DNA complexes”, Biophysical journal, vol. 85, 2003, pp. 1968-1973.
Eckel, R., Ros, R., Ros, A., Wilking, S.D., Sewald, N., Anselmetti, D.: Identification of binding mechanisms in single molecule-DNA complexes. Biophysical journal. 85, 1968-1973 (2003).
Eckel, Rainer, Ros, Robert, Ros, Alexandra, Wilking, S.D., Sewald, Norbert, and Anselmetti, Dario. “Identification of binding mechanisms in single molecule-DNA complexes”. Biophysical journal 85.3 (2003): 1968-1973.
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Direct force measurement of single DNA-peptide interactions using atomic force microscopy.
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