Three helical forms of DNA are recognized to exist: A, B,
and Z (27). The B conformation is the dominate form under
physiological conditions. In B DNA, the basepairs are stacked
0.34 nm apart, with 10 basepairs per turn of the right-handed
double helix and a diameter of approx 2 nm. Like B DNA, the
A conformer is also a right-handed helix. However, A DNA
exhibits a larger diameter (2.6 nm), with 11 bases per turn of
the helix, and the bases are stacked closer together in the helix
(0.25 nm apart). Careful examination of space-filling models of
A and B DNA conformers reveals the presence of a major
groove and a minor grove (27). These grooves (particularly the
minor groove) contain many water molecules that interact
favorably with the amino and keto groups of the bases. In these
grooves, DNA-binding proteins can interact with specific DNA
sequences without disrupting the base-pairing of the molecule.
In contrast to the A and B conformers of DNA, Z DNA is a lefthanded
helix. This form of DNA has been observed primarily
in synthetic double-stranded oligonucleotides, especially those
with purine and pyrimidines alternating in the polynucleotide
strands. In addition, high salt concentrations are required for
the maintenance of the Z DNA conformer. Z DNA possesses a
minor groove but no major groove, and the minor groove is sufficiently
deep that it reaches the axis of the DNA helix.