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. 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.

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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

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