chapter 23
Structure and Properties of DNA
space for other strands of nucleic acids and also for
binding of regulatory proteins.
Alternative DNA Structures
The W-C DNA structure is a right-handed helix as one
looks down either axis of the molecule and the helix ro-
tates in a clockwise direction. This conformation of DNA
is called
and is the form found in solution and
inside cells. The double helix is stabilized by a num-
ber of forces, including hydrophobic interactions and van
der Waals forces, which also help stabilize single polynu-
cleotide chains. Collectively, these two forces are known
stacking interactions
because of their contribution to
the stacked arrangement of the bases in DNA.
Other stabilizing forces in DNA are the hydrogen bonds
between the AT and GC base pairs. AT base pairs share
two hydrogen bonds and GC base pairs share three. These
hydrogen bonds are of sufficient strength to discriminate
between insertion of a correct and an incorrect base during
DNA replication.
Although B-DNA is the physiologically significant
form of DNA, two other conformations,
have been observed. When water is removed from
solutions of DNA (such as in DNA prepared for x-ray anal-
ysis), a structure referred to as A-DNA is observed. While
A-DNA is still a right-handed helix, the helix is wider
and more condensed than in B-DNA. Also, the bases are
tilted with respect to the helix axis and the minor groove
in the molecule almost disappears. A-DNA is not believed
to have any biological significance.
CGCGCGCGCG base pairs forms a structure in so-
lution that is a left-handed double helix with only one
major groove. Also, because the repeating units are
dinucleotide pairs, the phosphate groups in the backbone
are rearranged to form a zig-zag configuration; this
feature accounts for the term Z-DNA. While it is not
known what biological role, if any, Z-DNA plays in cells,
the fact that long CG tracts exist in DNA
in vivo
that segments of DNA may assume different structural
configurations and that DNA exists in a dynamic rather
than a static state in chromosomes.
Plasmid DNA
Circular DNA molecules that are of great significance in
nature as well as in numerous biotechnology applications
which are widespread among bacteria. Plas-
mids are small circular DNA molecules consisting of just
a few genes to more than a hundred. Among the important
genes carried in plasmids are those coding for resistance to
a wide range of antibiotics and genes that allow plasmids
to be transferred to other bacteria, even to other species
of bacteria. The process of transfer of plasmid and chro-
mosomal DNA from one bacterium to another is called
Transfer of antibiotic resistance genes among bacteria
in nature has created serious problems in the treatment of
many infectious diseases such as tuberculosis, gonorrhea,
pneumonia, staphylococcus, and others. The widespread
use of antibiotics in agriculture and in hospitals has re-
sulted in the selection and evolution of pathogenic mi-
croorganisms that are resistant to many, sometimes all, of
the antibiotics normally used to treat infections by these
Plasmids also have been genetically engineered in a
multitude of ways so that they can carry and express for-
eign genes in bacteria. For example, the genes coding for
human insulin and human growth hormone have been in-
serted into plasmids which are then reintroduced into bac-
teria such as
E. coli.
The genetically engineered bacteria
are then used as biological factories to produce the desired
Circular and Supercoiled DNA
Most DNA molecules isolated from prokaryotes and from
some virus particles are circular. A circular molecule may
be covalently closed, consisting of two unbroken com-
plementary single strands, or nicked, i.e., having one or
more interruptions (nicks) in one or both strands. With
few exceptions, covalently closed circles assume the form
(Figure 23-7).
The two ends of a linear DNA helix can be brought
together and joined in such a way that each strand is con-
tinuous. Consider a molecule in which one of the ends is
rotated 360 degrees with respect to the other in the unwind-
ing direction, and then the ends are joined. If the hydrogen
bonds re-form, the resulting covalent circle will twist in the
opposite sense to form a twisted circle, in order to relieve
the strain of underwinding. Such a molecule will resemble
a figure 8 and will have one crossover point. If it is un-
derwound by 720 degrees before the ends are joined, the
resulting superhelical molecule will have two crossover
points. In the case of a 720-degree unwinding of the helix,
20 base pairs must be broken (because the linear molecule
has 10 base pairs per turn of the helix). However, such a
DNA molecule tries to maintain a right-handed (positive)
helical structure with 10 base pairs per turn; it will deform
itself in such a way that the underwinding is compensated
for by negative (left-handed) twisting of the circle.
All naturally occurring, superhelical DNA molecules
are initially underwound and, hence, form negative
previous page 558 Bhagavan Medical Biochemistry 2001 read online next page 560 Bhagavan Medical Biochemistry 2001 read online Home Toggle text on/off