Physical properties of nucleosomes and DNA

on a length scale beyond some tens of base pairs, can be described as a stiff polymer chain with an electrostatic charge. In the most basic view, four parameters are sufficient to describe this chain with sufficient precision the diameter, the elastic constants for bending and torsion and the electrostatic potential. 

The average DNA helix diameter used in modeling applications such as the ones described here includes the diameter of the atomic-scale B-DNA structure and— approximately—the thickness of the hydration shell and ion layer closest to the double helix [18]. Both for the calculation of the electrostatic potential and the hydrodynamic properties of DNA (i.e., the friction coefficient of the helix for viscous drag) a helix diameter of 2.4 nm describes the chain best [19-22]. The choice of this parameter was supported by the results of chain knotting [23] or catenation [24], as well as light scattering [25] and neutron scattering [26] experiments. 

The interaction between nucleosomes plays an important role for the stability of the 30 nm fiber recent experiments on liquid crystals of mononucleosomes [44-47] and also less concentrated mononucleosome solutions [48,49] show an attractive interaction that can be parameterized by an anisotropic Leonard-Jones type potential [50]. Also, an electrostatic interaction potential has been computed using the crystallographic structure of the nucleosome [51]. The influence of these potentials on the structure of the fiber is discussed below together with the corresponding models. 

The computational description of a large biomolecular complex such as the chromatin fiber requires techniques that are difierent from the widely applied molecular dynamics methods used to simulate biopolymers at atomic resolution. 

For coarse-grained models of linear biopolymers—such as DNA or chromatin— two types of interactions play a role. The connectivity of the chain implies stretching, bending, and torsional potentials, which exist only between directly adjacent subunits and are harmonic for small deviations from equilibrium. As mentioned above, these potentials can be directly derived from the experimentally known persistence length or by directly measuring bulk elastic properties of the chain. 

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