and it is longer and thinner than B-DNA.
The Z form
Major
groove
Minor
groove
Minor
groove
(a) B-DNA (b) Z-DNA
FIGURE 18-5 Alternative Forms of DNA. (a) In the normal B
form of DNA, the sugar-phosphate backbone forms a smooth right-
handed double helix. (b) In Z-DNA, the backbone forms a zigzag
left-handed helix. Color is used to highlight the backbones.
Another important feature is the antiparallel orienta-
tion of the two DNA strands, illustrated in Figure 18-4b.
This diagram shows that the phosphodiester bonds, which
join the 5¿ carbon of one nucleotide to the 3¿ carbon of
the adjacent nucleotide, are oriented in opposite directions
in the two DNA strands. Starting at the top of the
diagram, the strand on the left is said to exhibit a 5¿ : 3¿
orientation because its first nucleotide has a free 5¿ end
and its final nucleotide has a free 3¿ end. Conversely, the
strand on the right exhibits a 3¿ : 5¿ orientation starting
from the top because its first nucleotide has a free 3¿ end
and its final nucleotide has a free 5¿ end. The opposite ori-
entation of the two strands has important implications for
both DNA replication and DNA transcription, as we will
see in Chapters 19 and 21.
The right-handed Watson–Crick helix is an ideal-
ized version of what is called B-DNA (Figure 18-5a).
Naturally occurring B-DNA double helices are flexible
molecules whose exact shapes and dimensions depend
on the local nucleotide sequence. Although B-DNA is
the main form of DNA in cells (and in test tube solutions
of DNA), other forms may also exist, perhaps in short
segments interspersed in molecules that are mostly
B-DNA. The most important of these alternative forms
are Z-DNA and A-DNA. As shown in Figure 18-5b,
Z-DNA is a left-handed double helix. Its name derives
from the zigzag pattern of its sugar-phosphate backbone,
514 Chapter 18 The Structural Basis of Cellular Information: DNA, Chromosomes, and the Nucleus
arises most readily in DNA regions that contain either alter-
nating purines and pyrimidines or have cytosines with
extra methyl groups (which do occur in chromosomal
DNA; see Chapter 23). Although the biological signifi-
cance of Z-DNA is not well understood, some evidence
suggests that short stretches of DNA transiently flip into
the Z configuration as part of the process that activates
the expression of certain genes.
A-DNA is a right-handed helix, shorter and thicker
than B-DNA, and can be created artificially by dehy-
drating B-DNA. Although A-DNA does not exist in
significant amounts under normal cellular condition,
most RNA double helices are of the A type. A-type helices
have a wider minor groove and a narrower major groove
than B-type helices, so A-RNA is not well suited for base
recognition by RNA-binding proteins from the major
groove. To recognize specific base sequences in A-RNA,
regulatory proteins generally need to unwind the duplex.
DNA Can Be Interconverted Between Relaxed
and Supercoiled Forms
In many situations, the DNA double helix can be twisted
upon itself to form supercoiled DNA. Although now
known to be a widespread property of DNA, supercoiling
was first identified in the DNA of certain small viruses
containing circular DNA molecules that exist as closed
loops. Circular DNA molecules are also found in bacteria,
mitochondria, and chloroplasts. Although supercoiling is
not restricted to circular DNA, it is easiest to study in such
molecules.
A DNA molecule can go back and forth between the
supercoiled state and the nonsupercoiled, or relaxed, state.
To understand the basic idea, you might perform the fol-
lowing exercise. Start with a length of rope consisting of
two strands twisted together into a right-handed coil; this
is the equivalent of a relaxed, linear DNA molecule. Just
joining the ends of the rope together changes nothing; the
rope is now circular but still in a relaxed state. But before
sealing the ends, if you first give the rope an extra twist in
the direction in which the strands are already entwined
around each other, the rope is thrown into a positive super-
coil. Conversely, if before sealing, you give the rope an
extra twist in the opposite direction, the rope is thrown
into a negative supercoil. Like the rope in this example, a
relaxed DNA molecule can be converted to a positive
supercoil by twisting in the same direction as the double
helix is wound and into a negative supercoil by twisting in
the opposite direction (Figure 18-6). Circular DNA mol-
ecules found in nature, including those of bacteria,
viruses, and eukaryotic organelles, are invariably nega-
tively supercoiled.
Supercoiling also occurs in linear DNA molecules
when regions of the molecule are anchored to some cell
structure and so cannot freely rotate. At any given time,