Osmotic compaction of supercoiled DNA into a bacterial nucleoid.

A theory is presented of the phase separation of supercoiled DNA into a nucleoid in a bacterial cell. The suspension consists of DNA interacting with globular proteins in excess salt. A cross virial between DNA and a protein is computed as well as the DNA self-energy arising from excluded volume. The cellular parameters of Escherichia coli would appear to be compatible with the thermodynamic equilibrium derived theoretically. The state of superhelical DNA in the nucleoid could be liquid crystalline and rippled.

[1]  A. Minton,et al.  Macromolecular crowding: biochemical, biophysical, and physiological consequences. , 1993, Annual review of biophysics and biomolecular structure.

[2]  I. Sanchez,et al.  Monte Carlo simulation of polymer chain collapse in athermal solvents , 1996 .

[3]  D. Brooks,et al.  Phase separation in cytoplasm, due to macromolecular crowding, is the basis for microcompartmentation , 1995, FEBS letters.

[4]  Theo Odijk,et al.  Structure of DNA within the Bacterial Cell: Physics and Physiology , 1999 .

[5]  F. J. de Bruijn,et al.  Bacterial genomes : physical structure and analysis , 1998 .

[6]  R. Rill,et al.  DNA length and concentration dependencies of anisotropic phase transitions of DNA solutions. , 1997, Biophysical journal.

[7]  T. Odijk.  DNA in a liquid‐crystalline environment: Tight bends, rings, supercoils , 1996 .

[8]  Luis F. Rull,et al.  Observation, prediction and simulation of phase transitions in complex fluids , 1995 .

[9]  H V Westerhoff,et al.  Structure and partitioning of bacterial DNA: determined by a balance of compaction and expansion forces? , 1995, FEMS microbiology letters.

[10]  T. Odijk.  Theory of lyotropic polymer liquid crystals , 1986 .

[11]  N R Cozzarelli,et al.  Structure of plectonemically supercoiled DNA. , 1990, Journal of molecular biology.

[12]  D. Pettijohn.  Bacterial Chromosome Structure , 1990 .

[13]  S. Zimmerman,et al.  Condensation and cohesion of lambda DNA in cell extracts and other media: implications for the structure and function of DNA in prokaryotes. , 1995, Biophysical chemistry.

[14]  D. Stigter,et al.  Interactions of highly charged colloidal cylinders with applications to double‐stranded DNA , 1977 .

[15]  M. Gellert,et al.  Regulation of the genes for E. coli DNA gyrase: Homeostatic control of DNA supercoiling , 1983, Cell.

[16]  N. Cozzarelli,et al.  Use of site-specific recombination as a probe of DNA structure and metabolism in vivo. , 1987, Journal of molecular biology.

[17]  J. Ubbink,et al.  Dimensions of a plectonemic DNA supercoil under fairly general perturbations , 1998 .

[18]  E. Kellenberger,et al.  Concentration evaluation of chromatin in unstained resin-embedded sections by means of low-dose ratio-contrast imaging in STEM. , 1993, Ultramicroscopy.

[19]  K. Adolph.  Chromosomes : eukaryotic, prokaryotic, and viral , 1990 .

[20]  N. Nanninga.  Molecular cytology of Escherichia coli , 1985 .

[21]  S. Zimmerman,et al.  Stabilization of compact spermidine nucleoids from Escherichia coli under crowded conditions: implications for in vivo nucleoid structure. , 1997, Journal of structural biology.

[22]  Shaw,et al.  Free polymer in a colloidal solution. , 1991, Physical review. A, Atomic, molecular, and optical physics.

[23]  P. Schoot.  Protein-induced collapse of polymer chains. , 1998 .

[24]  A. Khokhlov,et al.  Liquid-crystalline ordering in the solution of long persistent chains , 1981 .