8 S.D. Levene
Fig. 2.3.Several conformations of an intrinsically straight wormlike chain with
contour length,L, equal to the persistence length,P. Conformations were simulated
by a Monte Carlo computer algorithm; each chain consisted of 150 rigid segments
connected to its neighbors by a semiflexible joint. Chains were fixed at a common
origin and assigned identical initial directions of propagation
wherePis the physical length of a segment in the wormlike chain model,Tis
the absolute temperature, and kBis Boltzmann’s constant. We assume here
thatPdis independent of the DNA sequence and that bending flexibility is
isotropic; however, more sophisticated treatments that relax these conditions
are sometimes warranted.
Many techniques have been used to measure the persistence length of
DNA and other nucleic-acid structures, including rotational and translational
diffusion [8, 9], ligase ring-closure kinetics [10, 11], and electron and atomic-
force microscopy [12, 13]. Discussion of these methods is beyond the scope
of this contribution; the reader may wish to consult a recent review [14] or
any of the above citations for details. Despite disagreements on the value of
P in the early literature, recent measurements have converged on a value
of about 50 nm at moderate ionic strength. As discussed above, this value
superposes the effects of intrinsic flexibility, as manifested in the dynamic
persistence length, and nonuniformity of DNA structure, characterized by the