Explaining these forms of DNA

1. A, B, and Z forms of DNA
By: ZERAVAN ALI

2. Contents:
• Introduction.
• A-form DNA.
• B-form DNA.
• Z-form DNA.
• Comparisons of A, B, and Z form DNA.
• References.

3. Introduction:
• Pictures of the double helix of deoxyribonucleic acid (DNA) have become
so common that everyone is familiar with its overall shape and structure.
This structure is known as B-DNA, and represents an average
conformation of DNA, based on fibre diffraction studies.
• However, this average shape of DNA is very unlikely
to exist within the cells of living organisms, for several
reasons. First, there is simply not enough room for the
DNA to be stretched out in a perfect, linear B-DNA
conformation.

4. Introduction:
• Refined resolution of the structure of DNA, based on X-ray
crystallography of short synthetic pieces of DNA, has shown that there is
considerable variance of the helical structure of DNA, based on the
sequence.
• The double helix is not the same uniform structure. The structure (and
function) of DNA depends on the sequence of the DNA.
• There are three families of DNA helices: A-DNA, which can readily
form within certain stretches of purines (e.g. GAGGGA); B-DNA, which
is favored by mixed sequences (although the exact conformation depends
on the particular nucleotide sequence, as described below); and Z-DNA,
which is favored by alternating pyrimidine–purine steps (e.g. CGCGCG).

5. Different forms of DNA:
Q)Why do different forms of DNA
exist?
Ans) There is simply not enough room
for the DNA to be stretched out in a
perfect, linear B-DNA conformation. In
nearly all cells, from simple bacteria
through complex eukaryotes, the DNA
must be compacted by more than a
thousand-fold in order even to fit inside
the cell or nucleus.

6. A-form DNA:
• The right-handed A form is favored in nonaqueous
solutions.
• It is one of the biologically active double helical structure
along with B and Z DNA.
• Most DNA crystallize in this form due to dehydration from
crystallization methods.
• The helix is wider than the B form and has 11 base pairs
per helical turn (rather than 10.5).
• The plane of the base pairs is tilted about 20° with respect
to the helix axis.
 Deeper major groove.
 Shallower minor groove.

7. A-form DNA:
• It appears that at least four purines (or pyrimidines) in a row are enough to
set up a local A-DNA helix, although of course certain purine stretches are
more likely to form A-DNA than others. (For example, the sequence
AAAA crystallizes as B-DNA, not in the A helix.
• A-DNA helix is less stable than the B-DNA conformation.
• A-DNA is also more rigid than B-DNA, again because the off-centre
stacking of the bases makes them less flexible.
• The base-pair tilt is higher in A-DNA than in B-DNA.
• The right-handed A-helix is characterized by 11 base pairs per turn (111
symmetry), a rise per base pair along the helix axis of 2.55 Å.

8. B-form DNA:
• B-DNA is the Watson–Crick form of the double helix that most
people are familiar with the right-sided figure.
• They proposed two strands of DNA each in a right hand helix
wound around the same axis. The two strands are held together
by H bonding between the bases (in anti-conformation).
• The two strands of the duplex are antiparallel and
plectonemically coiled. The nucleotides arrayed in a 5′ to 3′
orientation on one strand align with complementary
nucleotides in the 3′ to 5′ orientation of the opposite strand.
• B-form is the most common form, present in most DNA at
neutral pH and physiological salt concentrations.

9. B-form DNA:
• This form is the most stable structure for a random-sequence DNA
molecule under physiological conditions.
• The two helices are wound in such a way so as to produce to interchain
spacing or groove.
• Major/wide groove (width 12 Å, depth 8.5 Å).
• Minor/narrow groove (width 6 Å, depth 7.5 Å).
• These grooves provide surface with which protein, chemicals, drugs can
interact.

10. Z-form DNA:
• The backbone of the left-handed helix takes on a zigzag
appearance and the structure is more slender and elongated.
• Z-DNA can form when the DNA is in an alternating purine-
pyrimidine sequence such as GCGCGC, and indeed the G and C
nucleotides are in different conformations, leading to the zig-zag
pattern.
• There are 12 base pairs per helical turn.
• Prominent form when pyrimidines alternate with purine,
especially alternating C and G.
• The purine adopts a syn conformation while the pyrimidine is in
the anti conformation.

11. Z-form DNA:
• The major groove is barely apparent but minor groove is deepen yet
narrow.
• It has antiparallel strands as B-DNA.
• It is long and thin compared to B-DNA.
• Does exist in vivo though not abundantly.

12. Comparisons of B-form, A-form and Z DNA:
Table 2.5.12.5.1 Comparisons of B-form, A-form and Z-DNA
B-Form A-Form Z-Form
helix sense Right-Handed Right-Handed Left-Handed
base pairs per turn 10 11 12
vertical rise per bp 3.4 Å 2.56 Å 19 Å
rotation per bp +36° +33° -30°
helical diameter 19 Å 19 Å 19 Å

13. References:
1. Ussery, D.W., 2001. DNA Structure: A‐, B‐and Z‐DNA Helix Families. e
LS.
2. Ghosh, A. and Bansal, M., 2003. A glossary of DNA structures from A to
Z. Acta Crystallographica Section D: Biological Crystallography, 59(4),
pp.620-626.
3. Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., & Walter, P.
(2002). Molecular biology of the cell. New York: Garland Science.