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

Abstract

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.

Keywords

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

Abbreviations

TmHU

histone-like protein from Thermotoga maritima;

bp

basepairs;

Da

Dalton

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Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Carolin Wagner
    • 1
    • 6
  • 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

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