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