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Atomic force microscopy study of DNA conformation in the presence of drugs

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Abstract

Binding of ligands to DNA gives rise to several relevant biological and biomedical effects. Here, through the use of atomic force microscopy (AFM), we studied the consequences of drug binding on the morphology of single DNA molecules. In particular, we quantitatively analyzed the effects of three different DNA-binding molecules (doxorubicin, ethidium bromide, and netropsin) that exert various pharmacologic and therapeutic effects. The results of this study show the consequences of intercalation and groove molecular binding on DNA conformation. These single-molecule measurements demonstrate morphological features that reflect the specific modes of drug–DNA interaction. This experimental approach may have implications in the design of therapeutically effective agents.

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References

  • Abels JA, Moreno-Herrero F, van der Heijden T, Dekker C, Dekker NH (2005) Single-molecule measurements of the persistence length of double-stranded RNA. Biophys J 88:2737–2744

    Article  CAS  PubMed  Google Scholar 

  • Baumann CG, Smith SB, Bloomfield VA, Bustamante C (1997) Ionic effects on the elasticity of single DNA molecules. Proc Natl Acad Sci USA 94:6185–6190

    Article  CAS  PubMed  Google Scholar 

  • Baumann CG, Bloomfield VA, Smith SB, Bustamante C, Wang MD, Block SM (2000) Stretching of single collapsed DNA molecules. Biophys J 78:1965–1978

    Article  CAS  PubMed  Google Scholar 

  • Besteman K, Hage S, Dekker NH, Lemay SG (2007) Role of tension and twist in single-molecule DNA condensation. Phys Rev Lett 98:058103/1–4

    Google Scholar 

  • Bigioni M, Salvatore C, Bullo A, Bellarosa D, Iafrate E, Animati F, Capranico G, Goso C, Maggi CA, Pratesi G, Zunino F, Manzini S (2001) A comparative study of cellular and molecular pharmacology of doxorubicin and MEN 10755, a disaccharide analogue. Biochem Pharmacol 62:63–70

    Article  CAS  PubMed  Google Scholar 

  • Bornhop DJ, Latham JC, Kussrow A, Markov DA, Jones RD, Sorensen HS (2007) Free-solution, label-free molecular interactions studied by back-scattering interferometry. Science 317:1732–1736

    Article  CAS  PubMed  Google Scholar 

  • Bustamante C, Rivetti C (1996) Visualizing protein-nucleic acid interactions on a large scale with the scanning force microscope. Annu Rev Biophys Biomol Struct 25:395–429

    CAS  PubMed  Google Scholar 

  • Bustamante C, Bryant Z, Smith SB (2003) Ten years of tension: single-molecule DNA mechanics. Nature 421:423–427

    Article  PubMed  Google Scholar 

  • Coury JE, McFaillsom L, Williams LD, Bottomley LA (1996) A novel assay for drug–DNA binding mode, affinity, and exclusion number: scanning force microscopy. Proc Natl Acad Sci USA 93:12283–12286

    Article  CAS  PubMed  Google Scholar 

  • Dame RT, Wyman C, Goosen N (2000) H-NS mediated compaction of DNA visualised by atomic force microscopy. Nucleic Acids Res 28:3504–3510

    Article  CAS  PubMed  Google Scholar 

  • Gosse C, Croquette V (2002) Magnetic tweezers: micromanipulation and force measurements at the molecular level. Biophys J 82:3314–3329

    Article  CAS  PubMed  Google Scholar 

  • Hansma HG, Laney DE (1996) DNA binding to mica correlates with cationic radius: assay by Atomic Force Microscopy. Biophys J 70:1933–1939

    Article  CAS  PubMed  Google Scholar 

  • Hansma HG, Kim KJ, Laney DE, Garcia RA, Argaman M, Allen MJ, Parsons SM (1997) Properties of biomolecules measured from atomic force microscope images: a review. J Struct Biol 119:99–108

    Article  CAS  PubMed  Google Scholar 

  • Hayashi M, Harada Y (2007) Direct observation of the reversible unwinding of a single DNA molecule caused by the intercalation of ethidium bromide. Nucleic Acids Res 35:e125/1–7

    Google Scholar 

  • Hou XM, Zhang XH, Wei KJ, Ji C, Dou SX, Wang WC, Li M, Wang PY (2009) Cisplatin induces loop structures and condensation of single DNA molecules. Nucleic Acids Res 37:1400–1410

    Article  CAS  PubMed  Google Scholar 

  • Kopka ML, Yoon C, Goodsell D, Pjura P, Dickerson RE (1985) The molecular origin of DNA-drug specificity in netropsin and distamycin. Proc Natl Acad Sci USA 82:1376–1380

    Article  CAS  PubMed  Google Scholar 

  • Krautbauer R, Clausen-Schaumann H, Gaub HE (2000) Cisplatin changes the mechanics of single DNA molecules. Angew Chem 39:3912–3915

    Article  CAS  Google Scholar 

  • Krautbauer R, Pope LH, Schrader TE, Allen S, Gaub HE (2002) Discriminating small molecule DNA binding modes by single molecule force spectroscoy. FEBS Lett 510:154–158

    Article  CAS  PubMed  Google Scholar 

  • Langner KM, Kedzierski P, Sokalski WA, Leszczynski J (2006) Physical nature of ethidium and proflavine interactions with nucleic acid bases in the intercalation plane. J Phys Chem B 110:9720–9727

    Article  CAS  PubMed  Google Scholar 

  • Lerman LS (1964) Acridine mutagens and DNA structure. J Cell Comp Physiol 64:1–191

    Article  CAS  Google Scholar 

  • Lipfert J, Klijnhout S, Dekker NH (2010) Torsional sensing of small-molecule binding using magnetic tweezers. Nucleic Acids Res (in press)

  • Lysetska M, Knoll A, Boehringer D, Hey T, Krauss G, Krausch G (2002) UV light-damaged DNA and its interaction with human replication protein a: an atomic force microscopy study. Nucleic Acids Res 30:2686–2691

    Article  CAS  PubMed  Google Scholar 

  • Lyubchenko Y, Shlyakhtenko LS (1997) Visualization of supercoiled DNA with atomic force microscopy in situ. Proc Natl Acad Sci USA 94:496–501

    Article  CAS  PubMed  Google Scholar 

  • Lyubchenko Y, Gall AA, Shlyakhtenko LS, Harrington RE, Jacobs BL, Oden PI, Lindsay SM (1992) Atomic force microscopy imaging of double stranded DNA and RNA. J Biomol Struct Dyn 9:589–606

    Google Scholar 

  • MacKerell ADJ, Lee GU (1999) Structure, force, and energy of a double-stranded DNA oligonucleotide under tensile loads. Eur Biophys J 28:415–426

    Article  CAS  PubMed  Google Scholar 

  • McCauley M, Hardwidge PR, III LJM, Williams MC (2005) Dual binding modes for an HMG domain from human HMGB2 on DNA. Biophys J 89:353–364

    Article  CAS  PubMed  Google Scholar 

  • Mihailovic A, Vladescu I, McCauley M, Ly E, Williams MC, Spain EM, Nunez ME (2006) Exploring the interaction of ruthenium(II) polypyridyl complexes with DNA using single-molecule techniques. Langmuir 22:4699–4709

    Article  CAS  PubMed  Google Scholar 

  • Minotti G, Menna P, Salvatorelli E, Cairo G, Gianni L (2004) Anthracyclines: molecular advances and pharmacologic developments in antitumor activity and cardiotoxicity. Pharmacol Rev 56:185–229

    Article  CAS  PubMed  Google Scholar 

  • Moffitt JR, Chemla YR, Smith SB, Bustamante C (2008) Recent advances in optical tweezers. Annu Rev Biochem 77:205–228

    Article  CAS  PubMed  Google Scholar 

  • Moreno-Herrero F, Seidel R, Johnson SM, Fire A, Dekker NH (2006) Structural analysis of hyperperiodic DNA from Caenorhabditis elegans. Nucleic Acids Res 34:3057–3066

    Article  CAS  PubMed  Google Scholar 

  • Murayama Y, Sakamaki Y, Sano M (2003) Elastic response of single DNA molecules exhibits a reentrant collapsing transition. Phys Rev Lett 90:018102/1–4

    Google Scholar 

  • Neuman KC, Nagy A (2008) Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy. Nat Methods 5:491–505

    Article  CAS  PubMed  Google Scholar 

  • Noom MC, van den Broek B, van Mameren J, Wuite GJL (2007) Visualizing single DNA-bound proteins using DNA as a scanning probe. Nat Methods 4:1031–1036

    Article  CAS  PubMed  Google Scholar 

  • Podestá A, Indrieri M, Brogioli D, Manning GS, Milani P, Guerra R, Finzi L, Dunlap D (2005) Positively charged surfaces increase the flexibility of DNA. Biophys J 89:2558–2563

    Article  PubMed  Google Scholar 

  • Pope LH, Davies MC, Laughton CA, Roberts CJ, Tendler SJB, Williams PM (2000) Atomic force microscopy studies of intercalation-induced changes in plasmid DNA tertiary structure. J Microsc 199:68–78

    Article  CAS  PubMed  Google Scholar 

  • Rivetti C, Guthold M, Bustamante C (1996) Scanning force microscopy of DNA deposited onto mica: equilibration versus kinetic trapping studied by satistical polymer chain analysis. J Mol Biol 264:919–932

    Article  CAS  PubMed  Google Scholar 

  • Rocha MS, Ferreira MC, Mesquita ON (2007) Transition on the entropic elasticity of DNA induced by intercalating molecules. J Chem Phys 127:105108/1–7

    Google Scholar 

  • Rocha MS, Lucio AD, Alexandre SS, Nunes RW, Mesquita ON (2009) DNA-psoralen: single-molecule experiments and first principles calculations. Appl Phys Lett 95:253703

    Article  Google Scholar 

  • Ros A, Hellmich W, Duong T, Anselmetti D (2004) Towards single molecule analysis in PDMS microdevices: from the detection of ultra low dye concentrations to single DNA molecule studies. J Biotechnol 112:65–72

    Article  CAS  PubMed  Google Scholar 

  • Salerno D, Brogioli D, Cassina V, Turchi D, Beretta GL, Seruggia D, Ziano R, Zunino F, Mantegazza F (2010) Magnetic tweezers measurements of the nanomechanical properties of dna in the presence of drugs. Nucleic Acids Res (in press)

  • Smith SB, Finzi L, Bustamante C (1992) Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science 258:1122–1126

    Article  CAS  PubMed  Google Scholar 

  • Snounou G, Malcolm ADB (1983) Production of positively supercoiled DNA by netropsin. J Mol Biol 167:211–216

    Article  CAS  PubMed  Google Scholar 

  • Strick TR, Dessinges MN, Charvin G, Dekker NH, Allemand JF, Bensimon D, Croquette V (2003) Stretching of macromolecules and proteins. Rep Prog Phys 66:1–45

    Article  CAS  Google Scholar 

  • Triebel H, Bar H, Walter A, Burckhardt G, Zimmer C (1994) Modulation of DNA supercoiling by interaction with netropsin and other minor groove binders. J Biomol Struct Dyn 11:1085–1105

    CAS  PubMed  Google Scholar 

  • Triebel H, Bär H, Geuther R, Burckhardt G (1995) Netropsin-induced changes of DNA supercoiling; sedimentation studies. Progr Colloid Polym Sci 99:45–54

    Article  Google Scholar 

  • van Mameren J, Modesti M, Kanaar R, Wyman C, Wuite GJ, Peterman EJ (2006) Dissecting elastic heterogeneity along DNA molecules coated partly with Rad51 using concurrent fluorescence microscopy and optical tweezers. Biophys J 91:L78–L80

    Article  PubMed  Google Scholar 

  • Viglasky V, Valle F, Adamik J, Joab I, Podhradsky D, Dietler G (2003) Anthracycline-dependent heat-induced transition from positive to negative supercoiled DNA. Electrophoresis 24:1703–1711

    Article  CAS  PubMed  Google Scholar 

  • Vilfan ID, Lipfert J, Kostera DA, Lemay SG, Dekker NH (2009) Magnetic tweezers for single-molecule experiments. In: Hinterdorfer P, van Oijen A (eds) Handbook of single-molecule biophysics. Springer, New York, pp 371–395

    Chapter  Google Scholar 

  • Vladescu ID, McCauley MJ, Rouzina I, Williams MC (2005) Mapping the phase diagram of single DNA molecule force-induced melting in the presence of ethidium. Phys Rev Lett 95:158102

    Article  PubMed  Google Scholar 

  • Walter NG, Huang CY, Manzo AJ, Sobhy MA (2008) Do-it-yourself guide: how to use the modern single-molecule toolkit. Nat Methods 5:475–489

    Article  CAS  PubMed  Google Scholar 

  • Wang J (1974) The degree of unwinding of the DNA helix by ethidium: I. titration of twisted PM2 DNA molecules in alkaline cesium chloride density gradients. J Mol Biol 89:783–801

    Article  CAS  PubMed  Google Scholar 

  • Wiggins PA, van der Heijden T, Moreno-Herrero F, Spakowitz A, Phillips R, Widom J, Dekker C, Nelson PC (2006) High flexibility of DNA on short length scales probed by atomic force microscopy. Nat Nanotechnol 1:137–141

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

The authors thank D. Barisani and M. Parisotto for useful discussions and critical reading of the manuscript.

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Authors and Affiliations

  1. Department of Experimental Medicine, University of Milano–Bicocca, Via Cadore 48, 20052, Monza, Milan, Italy

    Valeria Cassina, Davide Seruggia, Domenico Salerno, Doriano Brogioli & Francesco Mantegazza

  2. Department of Experimental Oncology, Fondation IRCCS Istituto Nazionale Tumori, 20133, Milan, Italy

    Giovanni Luca Beretta & Franco Zunino

  3. Department of Surgical Sciences, University of Milano–Bicocca, Via Cadore 48, 20052, Monza, Milan, Italy

    Stefano Manzini

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  1. Valeria Cassina
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Correspondence to Valeria Cassina.

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Cassina, V., Seruggia, D., Beretta, G.L. et al. Atomic force microscopy study of DNA conformation in the presence of drugs. Eur Biophys J 40, 59–68 (2011). https://doi.org/10.1007/s00249-010-0627-6

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  • DOI: https://doi.org/10.1007/s00249-010-0627-6

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