Torsional persistence length

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]... 

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. 

A theoretical analysis of the possible conformations of polylp-phenylene terephthalate) (PPTA) and polylp-phenylene isophthalate) (PPIA) is performed on the basis of molecular mechanics and molecular dynamics trajectories. The dependence of the persistence length on the fluctuations of the torsional angle around the ester bond is discussed for PPTA in the frame of the RIS model. Realistic parameters like bond length and bond angles are provided by computer simulations using MD. 

X) A. Recently, Erman, Flory, and Hummel carried out a detailed analysis of end-to-end vectors as a function of the chain length for />-phenylene polyamides and polyesters. The required geometrical parameters were obtained from the results for model compounds. Configurational averaging was performed on the basis of torsional potentials obtained by the same authors The value of persistence length depends on... 

The sensitivity of the helical preference of polyisocyanates to small chiral influences is also observed in chiral solvents. Poly(n-hexyl isocyanate) was found experimentally to have a persistence length of 20— 40 nm depending on the solvent in which the measurements were carried out.66 It was hypothesized that in more polar solvents a local interaction of the solvent would give rise to larger torsional oscillations around the backbone bonds. It was indeed observed that dissolution of poly(n-hexyl isocyanate) in non-racemic chiral solvents, e.g., (5)-l-chloro-2-methyl-butane, changed the persistence length and in addition also resulted in an excess of one helical sense.67 The chiral bias favoring one helical sense by itself is miniscule, but due to the cooperativity, a chiral preference is observed. More recently it was noted that the circular dichroism of these polymers decreases upon the addition of an achiral or racemic... 

Within the framework of this model, the DNA chain is characterized by three parameters the bending rigidity, measured in terms of the persistence length, a, or the Kuhn statistical length (6 = 2a) the torsional rigidity C the DNA effective diameter, d. Numerous properties of linear and circular DNA molecules can be quantitatively understood in terms of the elastic rod model and the same set, under given ambient conditions, of the above three parameters. 

The conformational properties of Novolac type resins prepared from p-cresol have been studied. The limited conformational flexibility of 4-phenylene polyamides and 4-phenylene polyesters causes them to have large persistent lengths. The existence of minima in the torsion potentials on each side of the planar conformation together with minor differences between the bond angles at... 

A chain with fixed bond angle and free internal rotation. The angle 0 between consecutive bonds is fixed for this model 0 - const the internal torsional rotation is completely free. In this case K(l) = cos 0,K n) = (cos 0)". The latter result can be obtained, for example, by calculating (m2), (m3), and so on for a fixed orientation of the first bond ntj. A strongly stretched chain adopts the trans-conformation with Tmax = L = IbN co for even N, that is, Z b = ZbCO. On using eqns [3], [4], and [8] one can find the persistence and the Kuhn lengths ... 

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