One of the more interesting discoveries of the last decade was that segments of DNA that have

sequences in which purines and pyrimidines alternate along each strand can form left-handed
double helices. The Watson-Crick B-form of DNA is a right-handed double helix. The novel left-
handed double-helical form of DNA has been named Z-DNA for the zigzagged paths of the
sugar-phosphate backbones of the molecule (Fig. 5.10).

Normally, the Z-form of alternating purine and pyrimidine DNA sequences occurs only at high
salt concentrations. When some of the bases in the potential Z-form sequences are methylated
however, the Z-conformation is stable at lower salt concentrations.

Thus, Z- DNA composed of alternating purine-pyrimidine sequences containing methylated

bases may be stable in vivo. Moreover, its stability is enhanced by cations, including polyamines
such as spermine, by negative supercoiling and by DNA binding proteins specific for Z- DNA.

In fact, there is evidence that Z-DNA exists in the interband regions of the giant salivary gland
chromosomes of Drosophila melanogaster and in the transcriptionally active macronucleus of the
ciliated protozoan Stylonychia mytilus. A. Rich and colleagues have prepared antibodies specific
for Z-DNA, these antibodies do not react with B-form DNA.
Rich and coworkers have shown that the Z-DNA-specific antibodies bind to the interband
regions of the polytene chromosomes of D. melanogaster. It will be of great interest to determine
the sequences and methylation patterns of the DNA in the interband regions of these polytene
chromosomes. Do these interband sequences control the expression (puffing) of the genes
located in the adjacent bands? Or are these sequences merely structural or involved in synapsis?

Another hint of the possible involvement of Z-DNA in regulating gene expression is that the
structures of certain regulatory proteins suggest that they may bind in the major groove of left-
handed double helices, but not right-handed helices.

In fact, D. B. McKay and T. A. Steitz have proposed that the catabolite activator protein
stabilizes its CAP-binding sequence in a left-handed conformation. They further propose that this
right-handed to left- handed transition in the double helix unwinds the adjacent promoter or RNA
polymerase binding site and thus activates transcription of the adjacent structural genes.

Repressor proteins might act in the opposite direction, stabilizing regulatory sequences in the
right-handed B-form and preventing transcription. Although their functions are still unknown, Z-
DNA-specific binding proteins have been isolated from Drosophila.

When alternating purine-pyrimidine sequences are complexed with histones, these sequences do
not display B-DNA to Z-DNA transitions. This and other observations suggest that Z-DNA
sequences must be stabilized by Z-DNA-specific binding proteins, and that Z-DNA sequences
may not be found in nucleosomes.

Indications of nuclease sensitivity of B- DNA to Z-DNA junctions has led to speculation that
such junctions may be related to the nuclease-sensitive sites near the promoter regions of
transcriptionally active genes.

Clearly much more information is needed before the potential validity of these proposals can be
evaluated. Although transitions from sequences of DNA in the B-conformation to sequences in
the Z-conformation have been shown to occur within individual plasmids, the biological
significance of these transitions remains unknown.

Experiments designed to test the possibilities:

1. That B-form to Z-form transitions in DNA are involved in the regulation of gene expression.

2. Regulatory proteins may act by binding to and stabilizing one or the other of these
conformation may lead to some exciting developments during the next decades, hopefully.