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.

Download
OA
Zeitschriftenaufsatz | Veröffentlicht | Englisch
Volltext vorhanden für diesen Nachweis
Autor
; ; ; ; ;
Abstract / Bemerkung
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.
Erscheinungsjahr
Zeitschriftentitel
Biophysical journal
Band
85
Ausgabe
3
Seite(n)
1968-1973
ISSN
PUB-ID

Zitieren

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. doi:10.1016/S0006-3495(03)74624-4
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.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Copyright Statement:
This Item is protected by copyright and/or related rights. [...]
Volltext(e)
Access Level
OA Open Access
Zuletzt Hochgeladen
2017-02-21T16:07:45Z

34 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

The role of nonfat ingredients on confectionery fat crystallization.
West R, Rousseau D., Crit Rev Food Sci Nutr 58(11), 2018
PMID: 28362112
ZYH005, a novel DNA intercalator, overcomes all-trans retinoic acid resistance in acute promyelocytic leukemia.
Tong Q, You H, Chen X, Wang K, Sun W, Pei Y, Zhao X, Yuan M, Zhu H, Luo Z, Zhang Y., Nucleic Acids Res 46(7), 2018
PMID: 29554366
Mechanisms of small molecule-DNA interactions probed by single-molecule force spectroscopy.
Almaqwashi AA, Paramanathan T, Rouzina I, Williams MC., Nucleic Acids Res 44(9), 2016
PMID: 27085806
Investigation of the binding modes between AIE-active molecules and dsDNA by single molecule force spectroscopy.
Chen Y, Ma K, Hu T, Jiang B, Xu B, Tian W, Sun JZ, Zhang W., Nanoscale 7(19), 2015
PMID: 25920935
Single molecule DNA intercalation in continuous homogenous elongational flow.
Griffis JW, Safranovitch MM, Vyas SP, Gerrin S, Protozanova E, Malkin G, Meltzer RH., Lab Chip 14(19), 2014
PMID: 25133764
Analysis of DNA interactions using single-molecule force spectroscopy.
Ritzefeld M, Walhorn V, Anselmetti D, Sewald N., Amino Acids 44(6), 2013
PMID: 23468137
Direct force measurement of single DNA-peptide interactions using atomic force microscopy.
Chung JW, Shin D, Kwak JM, Seog J., J Mol Recognit 26(6), 2013
PMID: 23595808
Non-covalent duplex to duplex crosslinking of DNA in solution revealed by single molecule force spectroscopy.
Rackham BD, Howell LA, Round AN, Searcey M., Org Biomol Chem 11(48), 2013
PMID: 24158749
An improved measurement of dsDNA elasticity using AFM.
Nguyen TH, Lee SM, Na K, Yang S, Kim J, Yoon ES., Nanotechnology 21(7), 2010
PMID: 20090198
Biophysical characterization of DNA binding from single molecule force measurements.
Chaurasiya KR, Paramanathan T, McCauley MJ, Williams MC., Phys Life Rev 7(3), 2010
PMID: 20576476
Torsional sensing of small-molecule binding using magnetic tweezers.
Lipfert J, Klijnhout S, Dekker NH., Nucleic Acids Res 38(20), 2010
PMID: 20624816
Interaction of oxazole yellow dyes with DNA studied with hybrid optical tweezers and fluorescence microscopy.
Murade CU, Subramaniam V, Otto C, Bennink ML., Biophys J 97(3), 2009
PMID: 19651041
Single-molecule atomic force spectroscopy reveals that DnaD forms scaffolds and enhances duplex melting.
Zhang W, Machón C, Orta A, Phillips N, Roberts CJ, Allen S, Soultanas P., J Mol Biol 377(3), 2008
PMID: 18291414
Hydration and conformational mechanics of single, end-tethered elastin-like polypeptides.
Valiaev A, Lim DW, Schmidler S, Clark RL, Chilkoti A, Zauscher S., J Am Chem Soc 130(33), 2008
PMID: 18646848
Interaction of malachite green with guanine-rich single-stranded DNA: preferential binding to a G-quadruplex.
Bhasikuttan AC, Mohanty J, Pal H., Angew Chem Int Ed Engl 46(48), 2007
PMID: 17966964
Exploring the interaction of ruthenium(II) polypyridyl complexes with DNA using single-molecule techniques.
Mihailovic A, Vladescu I, McCauley M, Ly E, Williams MC, Spain EM, Nuñez ME., Langmuir 22(10), 2006
PMID: 16649785
Parallel manipulation of bifunctional DNA molecules on structured surfaces using kinesin-driven microtubules.
Dinu CZ, Opitz J, Pompe W, Howard J, Mertig M, Diez S., Small 2(8-9), 2006
PMID: 17193173
Probing DNA-peptide interaction forces at the single-molecule level.
Sewald N, Wilking SD, Eckel R, Albu S, Wollschläger K, Gaus K, Becker A, Bartels FW, Ros R, Anselmetti D., J Pept Sci 12(12), 2006
PMID: 17131299
Molecular mechanisms and kinetics between DNA and DNA binding ligands.
Sischka A, Toensing K, Eckel R, Wilking SD, Sewald N, Ros R, Anselmetti D., Biophys J 88(1), 2005
PMID: 15516529
Progressing single biomolecule force spectroscopy measurements for the screening of DNA binding agents.
Zhang W, Barbagallo R, Madden C, Roberts CJ, Woolford A, Allen S., Nanotechnology 16(10), 2005
PMID: 20818013
Single-molecule studies on DNA and RNA.
Greulich KO., Chemphyschem 6(12), 2005
PMID: 16331734
Single molecule force spectroscopy on ligand-DNA complexes: from molecular binding mechanisms to biosensor applications.
Ros R, Eckel R, Bartels F, Sischka A, Baumgarth B, Wilking SD, Pühler A, Sewald N, Becker A, Anselmetti D., J Biotechnol 112(1-2), 2004
PMID: 15288936

35 References

Daten bereitgestellt von Europe PubMed Central.


AUTHOR UNKNOWN, 2000
Nonintercalative DNA-binding antitumour compounds.
Baguley BC., Mol. Cell. Biochem. 43(3), 1982
PMID: 6283334
Mechanical stability of single DNA molecules.
Clausen-Schaumann H, Rief M, Tolksdorf C, Gaub HE., Biophys. J. 78(4), 2000
PMID: 10733978
DNA: an extensible molecule.
Cluzel P, Lebrun A, Heller C, Lavery R, Viovy JL, Chatenay D, Caron F., Science 271(5250), 1996
PMID: 8628993
Specific antigen/antibody interactions measured by force microscopy.
Dammer U, Hegner M, Anselmetti D, Wagner P, Dreier M, Huber W, Guntherodt HJ., Biophys. J. 70(5), 1996
PMID: 9172770
Binding strength between cell adhesion proteoglycans measured by atomic force microscopy.
Dammer U, Popescu O, Wagner P, Anselmetti D, Guntherodt HJ, Misevic GN., Science 267(5201), 1995
PMID: 7855599
Adhesion forces between individual ligand-receptor pairs.
Florin EL, Moy VT, Gaub HE., Science 264(5157), 1994
PMID: 8153628

AUTHOR UNKNOWN, 1995
Force-mediated kinetics of single P-selectin/ligand complexes observed by atomic force microscopy.
Fritz J, Katopodis AG, Kolbinger F, Anselmetti D., Proc. Natl. Acad. Sci. U.S.A. 95(21), 1998
PMID: 9770478
Detection and localization of individual antibody-antigen recognition events by atomic force microscopy.
Hinterdorfer P, Baumgartner W, Gruber HJ, Schilcher K, Schindler H., Proc. Natl. Acad. Sci. U.S.A. 93(8), 1996
PMID: 8622961

AUTHOR UNKNOWN, 1997

AUTHOR UNKNOWN, 1993

AUTHOR UNKNOWN, 2002
Discriminating small molecule DNA binding modes by single molecule force spectroscopy.
Krautbauer R, Pope LH, Schrader TE, Allen S, Gaub HE., FEBS Lett. 510(3), 2002
PMID: 11801245

AUTHOR UNKNOWN, 1994
Direct measurement of the forces between complementary strands of DNA.
Lee GU, Chrisey LA, Colton RJ., Science 266(5186), 1994
PMID: 7973628

AUTHOR UNKNOWN, 1994

AUTHOR UNKNOWN, 1979
Intermolecular forces and energies between ligands and receptors.
Moy VT, Florin EL, Gaub HE., Science 266(5183), 1994
PMID: 7939660

AUTHOR UNKNOWN, 1996
Sequence-dependent mechanics of single DNA molecules.
Rief M, Clausen-Schaumann H, Gaub HE., Nat. Struct. Biol. 6(4), 1999
PMID: 10201403
Reversible unfolding of individual titin immunoglobulin domains by AFM.
Rief M, Gautel M, Oesterhelt F, Fernandez JM, Gaub HE., Science 276(5315), 1997
PMID: 9148804
Single Molecule Force Spectroscopy on Polysaccharides by Atomic Force Microscopy
Rief M, Oesterhelt F, Heymann B, Gaub HE., Science 275(5304), 1997
PMID: 9036852
Antigen binding forces of individually addressed single-chain Fv antibody molecules.
Ros R, Schwesinger F, Anselmetti D, Kubon M, Schafer R, Pluckthun A, Tiefenauer L., Proc. Natl. Acad. Sci. U.S.A. 95(13), 1998
PMID: 9636161
Force-induced melting of the DNA double helix 1. Thermodynamic analysis.
Rouzina I, Bloomfield VA., Biophys. J. 80(2), 2001
PMID: 11159455
Force-induced melting of the DNA double helix. 2. Effect of solution conditions.
Rouzina I, Bloomfield VA., Biophys. J. 80(2), 2001
PMID: 11159456
Behavior of supercoiled DNA.
Strick TR, Allemand JF, Bensimon D, Croquette V., Biophys. J. 74(4), 1998
PMID: 9545060
Dynamic force spectroscopy of single DNA molecules.
Strunz T, Oroszlan K, Schafer R, Guntherodt HJ., Proc. Natl. Acad. Sci. U.S.A. 96(20), 1999
PMID: 10500167
The mutagenic properties of DNA minor-groove binding ligands.
Turner PR, Denny WA., Mutat. Res. 355(1-2), 1996
PMID: 8781582
Salt dependence of the elasticity and overstretching transition of single DNA molecules.
Wenner JR, Williams MC, Rouzina I, Bloomfield VA., Biophys. J. 82(6), 2002
PMID: 12023240

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 12944309
PubMed | Europe PMC

Suchen in

Google Scholar