2 Topology in Biology: From DNA Mechanics to Enzymology 5Fig. 2.1.Canonical structures of DNA generated according to sequence-averaged
values of helical parameters in the corresponding geometries
B form in which the centers of the base pairs are nearly coincident with the
helix axis, the base pairs in A-form DNA are displaced from the central axis.
This feature, along with the strong inclination of A-form base pairs relative
to the helix axis, imparts radically different geometries to the B and A forms.
The Z form of DNA is a structure that is particular to alternating purine–
pyrimidine sequences such as GC and is present only under conditions of high
ionic strength in vitro or when DNA is negatively supercoiled (underwound).
It is a left-handed helical structure with 12.0 base pairs per turn and a pitch
of 4.5 nm. The biological significance of Z-form DNA has been a matter of
significant controversy [2, 3].
Subtle details of local DNA structure and/or the juxtaposition of these
different structural forms along the same DNA molecule can direct the global
structure of a particular DNA sequence [4, 5]. This is largely because the
thermodynamic stability of DNA structures depends on the favorable stacking
of base pairs in the interior of the double helix and attendant exclusion of water
from the hydrophobic interior of the helical structure. Because individual base
pairs can vary substantially in terms of their inclination relative to the helix
axis, the tendency of base pairs to stack generates local deflections in the
DNA-helix axis. An example of this phenomenon is shown in Fig. 2.2, in which
alternating helical structures generate a series of small bends in the double
helix. When repeated periodically in phase with the helix screw, such patterns
can generate large-scale intrinsic bends in DNA [6].
2.1.3 DNA Flexibility
For DNA molecules in solution (and presumably also in the cell), the in-
fluence of local DNA structure is attenuated by thermal Brownian motion.