Journal of Biological Physics

, Volume 37, Issue 1, pp 117–131 | Cite as

DNA condensation by TmHU studied by optical tweezers, AFM and molecular dynamics simulations

  • Carolin WagnerEmail author
  • Carsten Olbrich
  • Hergen Brutzer
  • Mathias Salomo
  • Ulrich Kleinekathöfer
  • Ulrich F. Keyser
  • Friedrich Kremer
Original Paper


The compaction of DNA by the HU protein from Thermotoga maritima (TmHU) is analysed on a single-molecule level by the usage of an optical tweezers-assisted force clamp. The condensation reaction is investigated at forces between 2 and 40 pN applied to the ends of the DNA as well as in dependence on the TmHU concentration. At 2 and 5 pN, the DNA compaction down to 30% of the initial end-to-end distance takes place in two regimes. Increasing the force changes the progression of the reaction until almost nothing is observed at 40 pN. Based on the results of steered molecular dynamics simulations, the first regime of the length reduction is assigned to a primary level of DNA compaction by TmHU. The second one is supposed to correspond to the formation of higher levels of structural organisation. These findings are supported by results obtained by atomic force microscopy.


Optical tweezers Single-molecule study Protein–DNA interaction Thermotoga maritima Force clamp Steered molecular dynamics 



histone-like protein from Thermotoga maritima;







We thank G. Stober, C. Gutsche and K. Kegler for useful discussions. W. Skokow and J. Reinmuth are acknowledged for their help with the setup. The TmHU protein was kindly provided by C. Immisch from the ACGT-Progenomics AG.


  1. 1.
    Dame, R.T.: The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin. Mol. Microbiol. 56(4), 858–870 (2005)CrossRefGoogle Scholar
  2. 2.
    Nelson, K.E., Clayton, R.A., Gill, S.R., Gwinn, M.L., Dodson, R.J., Haft, D.H., Hickey, E.K., Peterson, J.D., Nelson, W.C., Ketchum, K.A., McDonald, L., Utterback, T.R., Malek, J.A., Linher, K.D., Garrett, M.M., Stewart, A.M., Cotton, M.D., Pratt, M.S., Phillips, C.A., Richardson, D., Heidelberg, J., Sutton, G.G., Fleischmann, R.D., Eisen, J.A., White, O., Salzberg, S.L., Smith, H.O., Venter, J.C., Fraser, C.M.: Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima. Nature 399, 323–329 (1999)CrossRefADSGoogle Scholar
  3. 3.
    Huber, R., Langworthy, T.A., König, H., Thomm, M., Woese, C.R., Sleytr, W., Stetter, K.O.: Thermotoga maritima sp. nov. represents a new genus of unique extremely thermophilic eubacteria growing up to 90°. Arch. Microbiol. 144, 324–333 (1986)CrossRefGoogle Scholar
  4. 4.
    Mukherjee, A., Sokunbi, A.O., Grove, A.: DNA protection by histone-like protein HU from the hyperthermophilic eubacterium Thermotoga maritima. Nucleic Acids Res. 36, 3956–3968 (2008)CrossRefGoogle Scholar
  5. 5.
    Esser, D., Rudolph, R., Jaenicke, R., Böhm, G.: The HU protein from Thermotoga maritima: recombinant expression, purification and physicochemical characterization of an extremely hyperthermophilic DNA-binding protein. J. Mol. Biol. 291, 1135–1146 (1999)CrossRefGoogle Scholar
  6. 6.
    Swinger, K.S., Lemberg, K.M., Zhang, Y., Rice, P.A.: Flexible DNA bending in HU–DNA cocrystal structures. EMBO J. 22, 3749–3760 (2003)CrossRefGoogle Scholar
  7. 7.
    van Noort, J., Verbrugge, S., Goosen, N., Dekker, C., Dame, R.T.: Dual architectural roles of HU: formation of flexible hinges and rigid filaments. Proc. Natl. Acad. Sci. USA 101, 6969–6974 (2004)CrossRefADSGoogle Scholar
  8. 8.
    Dame, R.T., Goosen, N.: HU: promoting or counteracting DNA compaction? FEBS Lett. 529, 151–156 (2002)CrossRefGoogle Scholar
  9. 9.
    Luijsterburg, M.S., Noom, C.N., Wuite, G.J.L., Dame, R.T.: The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: a molecular perspective. J. Struct. Biol. 156, 262–272 (2006)CrossRefGoogle Scholar
  10. 10.
    Grove, A., Lim, L.: High-affinity DNA binding of HU protein from the hyperthermophile Thermotoga maritima. J. Mol. Biol. 311, 491–502 (2001)CrossRefGoogle Scholar
  11. 11.
    Christodoulou, E., Rypniewski, W.R., Vorgias, C.R.: High-resolution X-ray structure of the DNA-binding protein HU from the hyperthermophilic Thermotoga maritima and the determinants of its thermostability. Extremophiles 7, 111–122 (2002)Google Scholar
  12. 12.
    Ashkin, A.: Acceleration and trapping of particles by radiation pressure. Phys. Rev. Lett. 24, 156–159 (1970)CrossRefADSGoogle Scholar
  13. 13.
    Marko, J.F., Siggia, E.D.: Stretching DNA. Macromolecules 28, 8759–8770 (1995)CrossRefADSGoogle Scholar
  14. 14.
    Smith, S.B., Cui, Y., Bustamante, C.: Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science 271, 795–799 (1996)CrossRefADSGoogle Scholar
  15. 15.
    Salomo, M., Kegler, K., Gutsche, C., Struhalla, M., Reinmuth, J., Skokow, W., Hahn, U., Kremer, F.: The elastic properties of single double-stranded DNA chains of different lengths as measured with optical tweezers. Colloid Polym. Sci. 284, 1325–1331 (2006)CrossRefGoogle Scholar
  16. 16.
    Baumann, C.G., Bloomfield, V.A., Smith, S.B., Bustamante, C., Wang, M.D., Block, S.M.: Stretching of single collapsed DNA molecules. Biophys. J. 78, 1965–1978 (2000)CrossRefGoogle Scholar
  17. 17.
    Tolic-Nørrelykke, S.F., Rasmussen, M.B., Pavone, F., Berg-Sørensen, K., Oddershede, L.B.: Stepwise bending of DNA by a single TATA-box binding protein. Biophys. J. 90, 3694–3703 (2006)CrossRefGoogle Scholar
  18. 18.
    Sischka, A., Toensing, K., Eckel, R., Wilking, S.D., Sewald, N., Ros, R., Anselmetti, D.: Molecular mechanisms and kinetics between DNA and DNA binding ligands. Biophys. J. 88, 404–411 (2005)CrossRefADSGoogle Scholar
  19. 19.
    Salomo, M., Keyser, U.F., Struhalla, M., Kremer, F.: Optical tweezers to study single protein A/immunoglobulin G interactions at varying conditions. Eur. Biophys. J. 37, 927–934 (2008)CrossRefGoogle Scholar
  20. 20.
    Li, P.T., Collin, D., Smith, S.B., Bustamante, C., Tinoco, I. Jr.: Probing the mechanical folding kinetics of TAR RNA by hopping, force-jump, and force-ramp methods. Biophys. J. 90, 250–260 (2006)CrossRefADSGoogle Scholar
  21. 21.
    Wen, J.D., Manosas, M., Li, P.T.X., Smith, S.B., Bustamante, C., Ritort, F., Tinoco, I. Jr.: Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results. Biophys. J. 92, 2996–3009 (2007)CrossRefADSGoogle Scholar
  22. 22.
    Block, S.M., Goldstein, L.S., Schnapp, B.J.: Bead movement by single kinesin molecules studied with optical tweezers. Nature 348, 348–352 (1990)CrossRefADSGoogle Scholar
  23. 23.
    Finer, J.T., Simmons, R.M., Spudich, J.A.: Single myosin molecule mechanics: piconewton forces and nanometre steps. Nature 368, 113–119 (1994)CrossRefADSGoogle Scholar
  24. 24.
    Wen, J.D., Lancaster, L., Hodges, C., Zeri, A.C., Yoshimura, S.H., Noller, H.F., Bustamante, C., Tinoco, I.: Following translation by single ribosomes one codon at a time. Nature 452, 598–603 (2008)CrossRefADSGoogle Scholar
  25. 25.
    Bennink, M.L., Leuba, S.H., Leno, G.H., Zlatanova, J., de Grooth, B.G., Greve, J.: Unfolding individual nucleosomes by stretching single chromatin fibers with optical tweezers. Nat. Struct. Biol. 8, 606–610 (2001)CrossRefGoogle Scholar
  26. 26.
    Pope, L.H., Bennink, M.L., van Leijenhorst-Groener, K.A., Nikova, D., Greve, J., Marko, J.F.: Single chromatin fiber stretching reveals physically distinct populations of disassembly events. Biophys. J. 88, 3572–3583 (2005)CrossRefGoogle Scholar
  27. 27.
    Brower-Toland, B.D., Smith, C.L., Yeh, R.C., Lis, J.T., Peterson, C.L., Wang, M.D.: Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA. Proc. Natl. Acad. Sci. USA 99, 1960–1965 (2002)CrossRefADSGoogle Scholar
  28. 28.
    Dame, R.T., Noom, M.C., Wuite, G.J.L.: Bacterial chromatin organization by H-NS protein unravelled using dual DNA manipulation. Nature 444, 387–390 (2006)CrossRefADSGoogle Scholar
  29. 29.
    Salomo, M., Kroy, K., Kegler, K., Gutsche, C., Struhalla, M., Reinmuth, J.,Skokov, W., Immisch, C., Hahn, U., Kremer, F.: Binding of TmHU to single dsDNA as observed by optical tweezers. J. Mol. Biol. 359, 769–776 (2006)CrossRefGoogle Scholar
  30. 30.
    Salomo, M., Keyser, U.F., Kegler, K., Gutsche, C., Struhalla, M., Immisch, C., Hahn, U., Kremer, F.: Kinetics of TmHU binding to DNA as observed by optical tweezers. Microsc. Res. Tech. 70, 938–943 (2007)CrossRefGoogle Scholar
  31. 31.
    Otto, O., Gutsche, C., Kremer, F., Keyser, U.: Optical tweezers with 2.5 kHz bandwidth video detection for single-colloid electrophoresis. Rev. Sci. Instrum. 79, 023710 (2008)CrossRefADSGoogle Scholar
  32. 32.
    Christodoulou, E., Vorgias, C.E.: Cloning, overproduction, purification and crystallization of the DNA binding protein HU from the hyperthermophilic eubacterium Thermotoga maritima. Acta Crystallogr. D 54, 1043–1045 (1998)CrossRefGoogle Scholar
  33. 33.
    Phillips, J.C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R.D., Kale, L., Schulten, K.: Scalable molecular dynamics with NAMD. J. Comput. Chem. 26, 1781–1802 (2005)CrossRefGoogle Scholar
  34. 34.
    MacKerell, A.D., Foloppe, N.: All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data. J. Comput. Chem. 21, 86–104 (2000)CrossRefGoogle Scholar
  35. 35.
    Morfill, J., Kühner, F., Blank, K., Lugmaier, R.A., Sedlmair, J., Gaub, H.E.: B-S transition in short oligonucleotides. Biophys. J. 60, 2400–2409 (2007)CrossRefGoogle Scholar
  36. 36.
    Strunz, T., Orosylan, K., Schäfer, R., Güntherodt, H.J.: Dynamic force spectroscopy of single DNA molecules. Proc. Natl. Acad. Sci. USA 96, 11277–11282 (1999)CrossRefADSGoogle Scholar
  37. 37.
    Evans, E., Ritchie, K.: Strength of a weak bond connecting flexible polymer chains. Biophys. J. 76, 2439–2447 (1999)CrossRefGoogle Scholar
  38. 38.
    Lee, E.H., Hsin, J., Sotomayor, M., Cornellas, G., Schulten, K.: Discovery through the computational microscope. Structure 17, 1295–1306 (2009)CrossRefGoogle Scholar
  39. 39.
    Lu, H., Isralewitz, B., Krammer, A., Vogel, V., Schulten, K.: Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation. Biophys. J. 75, 662–671 (1998)CrossRefADSGoogle Scholar
  40. 40.
    Gräter, F., Shen, J., Jiang, H., Gautel, M., Grubmüller, H.: Mechanically induced titin kinase activation studied by force-probe molecular dynamics simulations. Biophys. J. 88, 790–804 (2005)CrossRefGoogle Scholar
  41. 41.
    Lankaš, F., Šponer, J., Hobza, P., Langowski, J.: Sequence-dependent elastic properties of DNA. J. Mol. Biol. 299(3), 695–709 (2000)CrossRefGoogle Scholar
  42. 42.
    Scipioni, A., Anselmi, C., Zuccheri, G., Samori, B., De Santis, P.: Sequence-dependent DNA curvature and flexibility from scanning force microscopy images. Biophys. J. 83(5), 2408–2418 (2002)CrossRefADSGoogle Scholar
  43. 43.
    Broyles, S.S., Pettijohn, D.E.: Interaction of the Escherichia coli HU protein with DNA. J. Mol. Biol. 187, 47–60 (1986)CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Carolin Wagner
    • 1
    • 6
    Email author
  • Carsten Olbrich
    • 2
  • Hergen Brutzer
    • 3
  • Mathias Salomo
    • 4
  • Ulrich Kleinekathöfer
    • 2
  • Ulrich F. Keyser
    • 5
  • Friedrich Kremer
    • 1
  1. 1.Experimental Physics 1University of LeipzigLeipzigGermany
  2. 2.School of Engineering and ScienceJacobs University BremenBremenGermany
  3. 3.Biotechnology CenterTU DresdenDresdenGermany
  4. 4.c-LEcta GmbH, LeipzigLeipzigGermany
  5. 5.Cavendish Laboratory, Biological and Soft SystemsUniversity of CambridgeCambridgeUK
  6. 6.Molecular Physics, Experimental Physics IUniversity of LeipzigLeipzigGermany

Personalised recommendations