6 S.D. Levene
Fig. 2.2.Structure of an intrinsically bent DNA sequence in which alternating tracts
of [dA:dT] 5 and random-sequence DNA are arranged in phase with the DNA helical
screw. There are ten [dA:dT] 5 , which each generate an average intrinsic bend of 18
degrees [45, 46]. Given the near-perfect phasing of these intrinsic bends, the overall
intrinsic bend generated over the entire 105 base-pair sequence is approximately 180
degrees
The polyelectrolyte nature of DNA molecules confers a high degree of bending
rigidity on the double helix; however, double-stranded molecules that are any
larger than about 30 base pairs deviate significantly from rigid-rod behavior.
It is more useful to consider the superposition of modes of thermal flexibility,
which may be isotropic or anisotropic, on the sequence-dependent intrinsic
structure of DNA molecules. The theoretical description of semiflexible poly-
mer chains according to the wormlike-chain model [7] provides a nearly ideal
framework for analyzing DNA tertiary structure.
The wormlike-chain model postulates a resistance to local bending that is
proportional to the angular deviation from the chain’s equilibrium conforma-
tion. The contribution to the total energy of a wormlike chain from a chain
segmenti,ui, is given by
ui=αi(
θi−θ^0 i) 2
, (2.1)
whereθiis the angular displacement of theith segment relative to segment
i−1,θ^0 iis the value ofθiin the chain’s minimum-energy conformation, andαi
is a bending energy constant for this displacement. This expression is recog-
nizable as a classical Hooke’s law potential for the local deformation of an
elastic rod.