Molecular mechanisms and kinetics between DNA and DNA binding ligands

Sischka A, Tönsing K, Eckel R, Wilking SD, Sewald N, Ros R, Anselmetti D (2005)
Biophysical Journal 88(1): 404-411.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
Sischka, AndyUniBi; Tönsing, KatjaUniBi; Eckel, Rainer; Wilking, Sven David; Sewald, NorbertUniBi ; Ros, Robert; Anselmetti, DarioUniBi
Abstract / Bemerkung
Mechanical properties of single double-stranded DNA (dsDNA) in the presence of different binding ligands were analyzed in optical-tweezers experiments with subpiconewton force resolution. The binding of ligands to DNA changes the overall mechanic response of the dsDNA molecule. This fundamental property can be used for discrimination and identification of different binding modes and, furthermore, may be relevant for various processes like nucleosome packing or applications like cancer therapy. We compared the effects of the minor groove binder distamycin-A, a major groove binding [alpha]-helical peptide, the intercalators ethidium bromide, YO-1, and daunomycin as well as the bisintercalator YOYO-1 on [lambda]-DNA. Binding of molecules to the minor and major groove of dsDNA induces distinct changes in the molecular elasticity compared to the free dsDNA detectable as a shift of the overstretching transition to higher forces. Intercalating molecules affect the molecular mechanics by a complete disappearance of the B-S transition and an associated increase in molecular contour length. Significant force hysteresis effects occurring during stretching/relaxation cycles with velocities >10 nm/s for YOYO-1 and >1000 nm/s for daunomycin. These indicate structural changes in the timescale of minutes for the YOYO-DNA and of seconds for the daunomycin-DNA complexes, respectively.
Biophysical Journal
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Sischka A, Tönsing K, Eckel R, et al. Molecular mechanisms and kinetics between DNA and DNA binding ligands. Biophysical Journal. 2005;88(1):404-411.
Sischka, A., Tönsing, K., Eckel, R., Wilking, S. D., Sewald, N., Ros, R., & Anselmetti, D. (2005). Molecular mechanisms and kinetics between DNA and DNA binding ligands. Biophysical Journal, 88(1), 404-411.
Sischka, Andy, Tönsing, Katja, Eckel, Rainer, Wilking, Sven David, Sewald, Norbert, Ros, Robert, and Anselmetti, Dario. 2005. “Molecular mechanisms and kinetics between DNA and DNA binding ligands”. Biophysical Journal 88 (1): 404-411.
Sischka, A., Tönsing, K., Eckel, R., Wilking, S. D., Sewald, N., Ros, R., and Anselmetti, D. (2005). Molecular mechanisms and kinetics between DNA and DNA binding ligands. Biophysical Journal 88, 404-411.
Sischka, A., et al., 2005. Molecular mechanisms and kinetics between DNA and DNA binding ligands. Biophysical Journal, 88(1), p 404-411.
A. Sischka, et al., “Molecular mechanisms and kinetics between DNA and DNA binding ligands”, Biophysical Journal, vol. 88, 2005, pp. 404-411.
Sischka, A., Tönsing, K., Eckel, R., Wilking, S.D., Sewald, N., Ros, R., Anselmetti, D.: Molecular mechanisms and kinetics between DNA and DNA binding ligands. Biophysical Journal. 88, 404-411 (2005).
Sischka, Andy, Tönsing, Katja, Eckel, Rainer, Wilking, Sven David, Sewald, Norbert, Ros, Robert, and Anselmetti, Dario. “Molecular mechanisms and kinetics between DNA and DNA binding ligands”. Biophysical Journal 88.1 (2005): 404-411.
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76 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Determining if DNA Stained with a Cyanine Dye Can Be Digested with Restriction Enzymes.
Maschmann A, Masters C, Davison M, Lallman J, Thompson D, Kounovsky-Shafer KL., J Vis Exp (132), 2018
PMID: 29443093
Measuring the wall depletion length of nanoconfined DNA.
Bhandari AB, Reifenberger JG, Chuang HM, Cao H, Dorfman KD., J Chem Phys 149(10), 2018
PMID: 30219022
Study on the interaction of anthracenyl-methyl homospermidine conjugate (ANTMHspd) with DNA by spectroscopic methods.
Tian Z, Zhao L, Dong H, Zhang Y, Zhang Y, Ren Q, Shao S, Huang Y, Song L, Guo T, Xu X, Wang C., J Photochem Photobiol B 169(), 2017
PMID: 28258044
Determination of restriction enzyme activity when cutting DNA labeled with the TOTO dye family.
Maschmann A, Kounovsky-Shafer KL., Nucleosides Nucleotides Nucleic Acids 36(6), 2017
PMID: 28362164
Study on the interaction between the 1,4,5,8-naphthalene diimide-spermine conjugate (NDIS) and DNA using a spectroscopic approach and molecular docking.
Tian Z, Cui H, Liu H, Dong J, Dong H, Zhao L, Li X, Zhang Y, Huang Y, Song L, Bian L, Wang Y, Xu X, Wang C., Medchemcomm 8(11), 2017
PMID: 30108725
Transition state theory demonstrated at the micron scale with out-of-equilibrium transport in a confined environment.
Vestergaard CL, Mikkelsen MB, Reisner W, Kristensen A, Flyvbjerg H., Nat Commun 7(), 2016
PMID: 26732388
Depletion interactions and modulation of DNA-intercalators binding: Opposite behavior of the "neutral" polymer poly(ethylene-glycol).
Crisafuli FA, da Silva LH, Ferreira GM, Ramos EB, Rocha MS., Biopolymers 105(4), 2016
PMID: 26615825
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
Nanomechanics of Fluorescent DNA Dyes on DNA Investigated by Magnetic Tweezers.
Wang Y, Sischka A, Walhorn V, Tönsing K, Anselmetti D., Biophys J 111(8), 2016
PMID: 27760348
Synthesis and characterization of azo-guanidine based alcoholic media naked eye DNA sensor.
Altaf AA, Hashmat U, Yousaf M, Lal B, Ullah S, Holder AA, Badshah A., R Soc Open Sci 3(11), 2016
PMID: 28018613
Characterizing the interaction between DNA and GelRed fluorescent stain.
Crisafuli FA, Ramos EB, Rocha MS., Eur Biophys J 44(1-2), 2015
PMID: 25391339
Single-molecule kinetics and footprinting of DNA bis-intercalation: the paradigmatic case of Thiocoraline.
Camunas-Soler J, Manosas M, Frutos S, Tulla-Puche J, Albericio F, Ritort F., Nucleic Acids Res 43(5), 2015
PMID: 25690887
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
The impact of DNA intercalators on DNA and DNA-processing enzymes elucidated through force-dependent binding kinetics.
Biebricher AS, Heller I, Roijmans RF, Hoekstra TP, Peterman EJ, Wuite GJ., Nat Commun 6(), 2015
PMID: 26084388
Visualization of large elongated DNA molecules.
Lee J, Kim Y, Lee S, Jo K., Electrophoresis 36(17), 2015
PMID: 25994517
Collapse of DNA under alternating electric fields.
Zhou C, Riehn R., Phys Rev E Stat Nonlin Soft Matter Phys 92(1), 2015
PMID: 26274209
DNA visualization in single molecule studies carried out with optical tweezers: Covalent versus non-covalent attachment of fluorophores.
Suei S, Raudsepp A, Kent LM, Keen SA, Filichev VV, Williams MA., Biochem Biophys Res Commun 466(2), 2015
PMID: 26362181
Photobehaviour of methyl-pyridinium and quinolinium iodide derivatives, free and complexed with DNA. A case of bisintercalation.
Mazzoli A, Carlotti B, Consiglio G, Fortuna CG, Miolo G, Spalletti A., Photochem Photobiol Sci 13(6), 2014
PMID: 24740459
Effect of YOYO-1 on the mechanical properties of DNA.
Kundukad B, Yan J, Doyle PS., Soft Matter 10(48), 2014
PMID: 25366273
Naked Eye DNA detection: synthesis, characterization and DNA binding studies of a novel azo-guanidine.
Jamil M, Altaf AA, Badshah A, Shafiqullah, Ahmad I, Zubair M, Kemal S, Ali MI., Spectrochim Acta A Mol Biomol Spectrosc 105(), 2013
PMID: 23299023
DNA interaction with Actinomycin D: mechanical measurements reveal the details of the binding data.
Cesconetto EC, Junior FS, Crisafuli FA, Mesquita ON, Ramos EB, Rocha MS., Phys Chem Chem Phys 15(26), 2013
PMID: 23715013
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
Heterogeneous staining: a tool for studies of how fluorescent dyes affect the physical properties of DNA.
Nyberg L, Persson F, Akerman B, Westerlund F., Nucleic Acids Res 41(19), 2013
PMID: 23975199
Probing concentration-dependent behavior of DNA-binding proteins on a single-molecule level illustrated by Rad51.
Frykholm K, Freitag C, Persson F, Tegenfeldt JO, Granéli A., Anal Biochem 443(2), 2013
PMID: 23994563
Is DNA a Good Model Polymer?
Tree DR, Muralidhar A, Doyle PS, Dorfman KD., Macromolecules 46(20), 2013
PMID: 24347685
DNA condensation by TmHU studied by optical tweezers, AFM and molecular dynamics simulations.
Wagner C, Olbrich C, Brutzer H, Salomo M, Kleinekathöfer U, Keyser UF, Kremer F., J Biol Phys 37(1), 2011
PMID: 22210966
DNA condensation by TmHU studied by optical tweezers, AFM and molecular dynamics simulations
Wagner Carolin, Olbrich Carsten, Brutzer Hergen, Salomo Mathias, Kleinekathöfer Ulrich, Keyser UlrichF, Kremer Friedrich., J Biol Phys 37(1), 2011
PMID: IND44467793
Single-molecule studies of the stringency factors and rates governing the polymerization of RecA on double-stranded DNA.
Feinstein E, Danilowicz C, Conover A, Gunaratne R, Kleckner N, Prentiss M., Nucleic Acids Res 39(9), 2011
PMID: 21245047
Specific berenil-DNA interactions: an approach for separation of plasmid isoforms by pseudo-affinity chromatography.
Caramelo-Nunes C, Tente T, Almeida P, Marcos JC, Tomaz CT., Anal Biochem 412(2), 2011
PMID: 21284930
Nanochannel confinement: DNA stretch approaching full contour length.
Kim Y, Kim KS, Kounovsky KL, Chang R, Jung GY, dePablo JJ, Jo K, Schwartz DC., Lab Chip 11(10), 2011
PMID: 21431167
Analysis of the fluctuations of a single-tethered, quantum-dot labeled DNA molecule in shear flow.
Laube K, Günther K, Mertig M., J Phys Condens Matter 23(18), 2011
PMID: 21508487
Is photocleavage of DNA by YOYO-1 using a synchrotron radiation light source sequence dependent?
Gilroy EL, Hoffmann SV, Jones NC, Rodger A., Eur Biophys J 40(10), 2011
PMID: 21931957
DNA manipulation, sorting, and mapping in nanofluidic systems.
Levy SL, Craighead HG., Chem Soc Rev 39(3), 2010
PMID: 20179829
Mechanical and structural properties of YOYO-1 complexed DNA.
Günther K, Mertig M, Seidel R., Nucleic Acids Res 38(19), 2010
PMID: 20511588
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
The kinetics of YOYO-1 intercalation into single molecules of double-stranded DNA.
Reuter M, Dryden DT., Biochem Biophys Res Commun 403(2), 2010
PMID: 21073861
Cisplatin induces loop structures and condensation of single DNA molecules.
Hou XM, Zhang XH, Wei KJ, Ji C, Dou SX, Wang WC, Li M, Wang PY., Nucleic Acids Res 37(5), 2009
PMID: 19129234
Optical tweezers study of topoisomerase inhibition.
Pla D, Sischka A, Albericio F, Alvarez M, Fernàndez-Busquets X, Anselmetti D., Small 5(11), 2009
PMID: 19291733
Role of structure-proteins in the porphyrin-DNA interaction.
Csík G, Egyeki M, Herényi L, Majer Z, Tóth K., J Photochem Photobiol B 96(3), 2009
PMID: 19604705
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
Probing the dynamic differential stiffness of dsDNA interacting with RecA in the enthalpic regime.
Lien CH, Wei MT, Tseng TY, Lee CD, Wang C, Wang TF, Ou-Yang HD, Chiou A., Opt Express 17(22), 2009
PMID: 19997266
Binding kinetics of bisintercalator Triostin a with optical tweezers force mechanics.
Kleimann C, Sischka A, Spiering A, Tönsing K, Sewald N, Diederichsen U, Anselmetti D., Biophys J 97(10), 2009
PMID: 19917232
Interaction of cationic surfactants with DNA: a single-molecule study.
Husale S, Grange W, Karle M, Bürgi S, Hegner M., Nucleic Acids Res 36(5), 2008
PMID: 18203749
Effects of electrostatic screening on the conformation of single DNA molecules confined in a nanochannel.
Zhang C, Zhang F, van Kan JA, van der Maarel JR., J Chem Phys 128(22), 2008
PMID: 18554066
Single beam optical tweezers setup with backscattered light detection for three-dimensional measurements on DNA and nanopores.
Sischka A, Kleimann C, Hachmann W, Schäfer MM, Seuffert I, Tönsing K, Anselmetti D., Rev Sci Instrum 79(6), 2008
PMID: 18601408
The promotion of secondary structures in single-stranded DNA by drugs that bind to duplex DNA: an atomic force microscopy study.
Adamcik J, Valle F, Witz G, Rechendorff K, Dietler G., Nanotechnology 19(38), 2008
PMID: 21832575
Conformation and dynamics of DNA confined in slitlike nanofluidic channels.
Bonthuis DJ, Meyer C, Stein D, Dekker C., Phys Rev Lett 101(10), 2008
PMID: 18851263
Lgf-YL-9 induces apoptosis in human epidermoid carcinoma KB cells and multidrug resistant KBv200 cells via reactive oxygen species-independent mitochondrial pathway.
Wang XH, Jia DZ, Liang YJ, Yan SL, Ding Y, Chen LM, Shi Z, Zeng MS, Liu GF, Fu LW., Cancer Lett 249(2), 2007
PMID: 17055640
Molecular seismology: an inverse problem in nanobiology.
Hinow P, Boczko EM., J Theor Biol 246(1), 2007
PMID: 17275035
Rapid DNA mapping by fluorescent single molecule detection.
Xiao M, Phong A, Ha C, Chan TF, Cai D, Leung L, Wan E, Kistler AL, DeRisi JL, Selvin PR, Kwok PY., Nucleic Acids Res 35(3), 2007
PMID: 17175538
Mechanisms of DNA binding determined in optical tweezers experiments.
McCauley MJ, Williams MC., Biopolymers 85(2), 2007
PMID: 17080421
Transition on the entropic elasticity of DNA induced by intercalating molecules.
Rocha MS, Ferreira MC, Mesquita ON., J Chem Phys 127(10), 2007
PMID: 17867787
Fluorescence images of DNA-bound YOYO between coupled silver particles.
Zhang J, Fu Y, Lakowicz JR., Langmuir 23(23), 2007
PMID: 17914851
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
Conformational analysis of single DNA molecules undergoing entropically induced motion in nanochannels.
Mannion JT, Reccius CH, Cross JD, Craighead HG., Biophys J 90(12), 2006
PMID: 16732056
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
Mapping the phase diagram of single DNA molecule force-induced melting in the presence of ethidium.
Vladescu ID, McCauley MJ, Rouzina I, Williams MC., Phys Rev Lett 95(15), 2005
PMID: 16241765

44 References

Daten bereitgestellt von Europe PubMed Central.


Observation of a single-beam gradient force optical trap for dielectric particles.
Ashkin A, Dziedzic JM, Bjorkholm JE, Chu S., Opt Lett 11(5), 1986
PMID: 19730608
Optical trapping and manipulation of neutral particles using lasers.
Ashkin A., Proc. Natl. Acad. Sci. U.S.A. 94(10), 1997
PMID: 9144154
Single-molecule manipulation of double-stranded DNA using optical tweezers: interaction studies of DNA with RecA and YOYO-1.
Bennink ML, Scharer OD, Kanaar R, Sakata-Sogawa K, Schins JM, Kanger JS, de Grooth BG, Greve J., Cytometry 36(3), 1999
PMID: 10404969
DNA-binding properties and cytotoxicity of extended aromatic bisamidines in breast cancer MCF-7 cells.
Bielawski K, Wolczynski S, Bielawska A., Pol J Pharmacol 53(2), 2001
PMID: 11787954
Atomic force microscope.
Binnig G, Quate CF, Gerber C., Phys. Rev. Lett. 56(9), 1986
PMID: 10033323
Estimating the persistence length of a worm-like chain molecule from force-extension measurements.
Bouchiat C, Wang MD, Allemand J, Strick T, Block SM, Croquette V., Biophys. J. 76(1 Pt 1), 1999
PMID: 9876152
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
Crystal structure of a double-stranded DNA containing a cisplatin interstrand cross-link at 1.63 A resolution: hydration at the platinated site.
Coste F, Malinge JM, Serre L, Shepard W, Roth M, Leng M, Zelwer C., Nucleic Acids Res. 27(8), 1999
PMID: 10101191
A novel assay for drug-DNA binding mode, affinity, and exclusion number: scanning force microscopy.
Coury JE, McFail-Isom L, Williams LD, Bottomley LA., Proc. Natl. Acad. Sci. U.S.A. 93(22), 1996
PMID: 8901572
Identification of binding mechanisms in single molecule-DNA complexes.
Eckel R, Ros R, Ros A, Wilking SD, Sewald N, Anselmetti D., Biophys. J. 85(3), 2003
PMID: 12944309
Selective nucleosome disruption by drugs that bind in the minor groove of DNA.
Fitzgerald DJ, Anderson JN., J. Biol. Chem. 274(38), 1999
PMID: 10480928

DNA and its associated processes as targets for cancer therapy.
Hurley LH., Nat. Rev. Cancer 2(3), 2002
PMID: 11990855



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

Structure of DNA-porphyrin complex.
Lipscomb LA, Zhou FX, Presnell SR, Woo RJ, Peek ME, Plaskon RR, Williams LD., Biochemistry 35(9), 1996
PMID: 8608116

Binding of ethidium to the nucleosome core particle. 2. Internal and external binding modes.
McMurray CT, Small EW, van Holde KE., Biochemistry 30(23), 1991
PMID: 2043608

Determination of DNA minor groove width in distamycin-DNA complexes by solid-state NMR.
Olsen GL, Louie EA, Drobny GP, Sigurdsson ST., Nucleic Acids Res. 31(17), 2003
PMID: 12930959
Structural characterization of a 2:1 distamycin A.d(CGCAAATTGGC) complex by two-dimensional NMR.
Pelton JG, Wemmer DE., Proc. Natl. Acad. Sci. U.S.A. 86(15), 1989
PMID: 2762292
Recent developments in sequence selective minor groove DNA effectors.
Reddy BS, Sharma SK, Lown JW., Curr. Med. Chem. 8(5), 2001
PMID: 11281837

Sequence-dependent mechanics of single DNA molecules.
Rief M, Clausen-Schaumann H, Gaub HE., Nat. Struct. Biol. 6(4), 1999
PMID: 10201403

Biological applications of optical forces.
Svoboda K, Block SM., Annu Rev Biophys Biomol Struct 23(), 1994
PMID: 7919782

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
Effect of pH on the overstretching transition of double-stranded DNA: evidence of force-induced DNA melting.
Williams MC, Wenner JR, Rouzina I, Bloomfield VA., Biophys. J. 80(2), 2001
PMID: 11159454
Thermodynamics of DNA interactions from single molecule stretching experiments.
Williams MC, Rouzina I, Bloomfield VA., Acc. Chem. Res. 35(3), 2002
PMID: 11900519
An integrated laser trap/flow control video microscope for the study of single biomolecules.
Wuite GJ, Davenport RJ, Rappaport A, Bustamante C., Biophys. J. 79(2), 2000
PMID: 10920045

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