title: Compaction of isolated Escherichia coli nucleoids: Polymer and H-NS protein synergetics.
abstract: Escherichia coli nucleoids were compacted by the inert polymer polyethylene glycol (PEG) in the presence of the H-NS protein. The protein by itself appears to have little impact on the size of the nucleoids as determined by fluorescent microscopy. However, it has a significant impact on the nucleoidal collapse by PEG. This is quantitatively explained by assuming the H-NS protein enhances the effective diameter of the DNA helix leading to an increase in the depletion forces induced by the PEG. Ultimately, however, the free energy of the nucleoid itself turns out to be independent of the H-NS concentration. This is because the enhancement of the supercoil excluded volume is negligible. The experiments on the nucleoids are corroborated by dynamic light scattering and EMSA analyses performed on DNA plasmids in the presence of PEG and H-NS.
authors: Complex Fluids Theory, Kluyver Institute for Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands; Swammerdam Institute for Life Sciences, BioCentrum Amsterdam, University of Amsterdam, Kruislaan 316, 1098 SM Amsterdam, The Netherlands.
authors: Anna S
authors: AS
authors: Wegner
authors: Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703HB Wageningen, The Netherlands.
authors: Kathelijne
authors: K
authors: Wintraecken
authors: University of Camerino, School of Biosciences and Veterinary Medicine, 62032 Camerino, MC, Italy.
authors: Roberto
authors: R
authors: Spurio
authors: Swammerdam Institute for Life Sciences, BioCentrum Amsterdam, University of Amsterdam, Kruislaan 316, 1098 SM Amsterdam, The Netherlands.
authors: Conrad L
authors: CL
authors: Woldringh
authors: Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703HB Wageningen, The Netherlands.
authors: Renko
authors: R
authors: de Vries
authors: Complex Fluids Theory, Kluyver Institute for Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands; Lorentz Institute for Theoretical Physics, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands. Electronic address: odijktcf@online.nl.
authors: Theo
authors: T
authors: Odijk
mesh_terms: D000465:Algorithms; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D004926:Escherichia coli / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D036781:Fimbriae Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D007700:Kinetics; D008856:Microscopy, Fluorescence; D010957:Plasmids / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011092:Polyethylene Glycols / Q000737:chemistry / Q000378:metabolism; D011108:Polymers / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding
chemical_list: D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; C529458:FimG protein, E coli; D011108:Polymers; D036781:Fimbriae Proteins; D011092:Polyethylene Glycols
keywords: Dynamic light scattering; EMSA; Escherichia coli; H-NS protein; Nucleoid; Polyethylene glycol; Polymer physics; Supercoiling