Identification of binding mechanisms in single molecule-DNA complexes.
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.
Eckel
Rainer
R
Experimental Biophysics and Applied Nanosciences, Faculty of Physics, Bielefeld University, 33615 Bielefeld, Germany.
Ros
Robert
R
Ros
Alexandra
A
Wilking
Sven David
SD
Sewald
Norbert
N
Anselmetti
Dario
D
D020816:Amino Acid Motifs; D000903:Antibiotics, Antineoplastic / Q000494:pharmacology; D000998:Antiviral Agents / Q000494:pharmacology; D001583:Benzoxazoles / Q000494:pharmacology; D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry; D003630:Daunorubicin / Q000494:pharmacology; D004214:Distamycins / Q000494:pharmacology; D004996:Ethidium / Q000494:pharmacology; D007364:Intercalating Agents / Q000494:pharmacology; D008024:Ligands; D018625:Microscopy, Atomic Force / Q000379:methods; D010455:Peptides / Q000737:chemistry; D011485:Protein Binding; D017433:Protein Structure, Secondary; D011806:Quinolinium Compounds / Q000494:pharmacology
D000903:Antibiotics, Antineoplastic; D000998:Antiviral Agents; D001583:Benzoxazoles; D004268:DNA-Binding Proteins; D004214:Distamycins; D007364:Intercalating Agents; D008024:Ligands; D010455:Peptides; D011806:Quinolinium Compounds; C075296:1,1'-((4,4,7,7-tetramethyl)-4,7-diazaundecamethylene)bis-4-(3-methyl-2,3-dihydro(benzo-1,3-oxazole)-2-methylidene)quinolinium; C030000:stallimycin; D004247:DNA; D004996:Ethidium; D003630:Daunorubicin