DNA, persistence length

Fig. 53. a DNA molecules of 5994 bp deposited on mica from a physiological solution, b Mean-square end-to-end distance, , as a function of the DNA contour length measured in different buffer solutions [493], The continuous line represents the evaluated from Eq. (10) for a DNA persistent length of 53 nm... 

Lu Y, Weers B, Stellwagen NC (2002) DNA persistence length revisited. Biopolymers 61 261-275... 

Geggier S, Kotlyar A, Vologodskii A (2011) Temperature dependence of DNA persistence length. Nucleic Acids Res 39 1419-1426... 

Figure 25 Dependence of the DNA persistence length on the solution ionic strength / obtained by Hagerman for short fragments of DNA (587 and 434 bp). Solid line is the best fit eqn [120], Reproduced with permission from Dobrynin, A. V. Carrillo, M. Y. J. Phys. Condens. Matter 2009, 21, 424112. Copyright 2009, Institute of Physics.

Fig. 1. The DNA persistence length a vs. ionic strength indicated by the concentration of NaCl [NaCl] from two measurements [81H2].

J. Bednar, P. Furrer, V. Katritch, A. Z. Stasiak, J. Dubochet, and A. Stasiak, /. Molec. Biol., 254, 579 (1995). Determination of DNA Persistence Length by Cryo-Electron Microscopy. Separation of the Static and Dynamic Contributions to the Apparent Persistence Length of DNA. 

The (bending) persistence length of DNA, which is proportional to its bending rigidity, has been extensively studied for well over two decades, usually via its effect on the overall dimensions of the DNA coil. This work... 

The persistence length of poly(dG-dC) was determined to be 800 A,(148) about 1.6 times the value characteristic of native DNAs. Possible long-term changes in these light scattering samples were not investigated. 

A prerequisite to these calculations is the knowledge of bending and torsional rigidity coefficients (A and C, respectively) of the naked DNA. A was calculated from a persistence length a = A/kT = 50 nm [58], and C through the following equation, valid only for a naked DNA minicircle near relaxation [59]... 

All this leads to the question of how DNA affects nucleosomal stability at the molecular level. DNA bendability has been repeatedly put forward as a candidate to play an important role [280-282]. This property is related to the persistence length of DNA [283]. A study on the characterization of nucleosomes reconstituted onto methylated DNA [poly(dG-m dC) poly (dG-m dC)] [284] provides support to this hypothesis. Poly(dG-m dC) poly (dG-m dQ DNA can be induced to change from its B to its Z conformation in the presence of millimolar amounts of divalent ions [285] such as MgCl2. The persistence length of poly(dG-m dC) poly (dG-m dC) in the Z form in high salt was found to be 208 nm (ca. 612 bp) [286], a value much lower than that of the same polymer in the B form (93.8 nm, 276 bp) at... 

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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