This document discusses three forms of DNA: A-DNA, B-DNA, and Z-DNA. A-DNA has a more compact helical structure than B-DNA, with the basepairs closer to the helix axis. It occurs under dehydrated conditions. Z-DNA has a left-handed helical structure and is formed by alternating purines and pyrimidines, especially GC stretches. The major differences between A, B, and Z-DNA involve the sugar conformation, placement of basepairs, and helical geometry.

1. Presented By: Sumeena Karki
Central Department of Biotechnology,
Kirtipur
Kathmandu, Nepal
FORMS OF DNA
Date: 11th June, 2015

2. A FORM OF
DNA
It is right handed double helix fairly similar
to B-DNA but with shorter ,more compact
helical structure whose basepairs are not
perpendicular to the helix axis as in B-DNA.
It is one of the biologically active double
helical structure along with B and Z DNA.
In A-DNA there is slight increase in number
of basepairs per rotation resulting in a
tighter rotation angle and smaller rise per
turn which results in deepening of major
groove and a shallowing of the minor.
It occurs in dehydrated conditions such as
in crystallographic experiments.

3. A form of DNA (3D)

4. Z FORM OF DNA
 Z-DNA is left handed and is
formed by stretches of
alternating purines and
pyrimidines e.g. GCGCGC
especially in negatively
supercoiled DNA which leads to
zigzag confirmation.
 This structure may be involved
in some way in regulation of
some cellular function such as
transcription or regulation.

5. Animated orbital of Z-DNA

6. How does confirmation change?
 The major difference between A-form
and B-form nucleic acid is in the
conformation of the deoxyribose sugar
ring. It is in the C2' endoconformation
for B-form, whereas it is in the C3'
endoconformation in A-form.
 The C2' atom is above the plane,
whereas the C3' atom is above the
plane in the C3' endoconformation. The
latter conformation brings the 5' and 3'
hydroxyls (both esterified to the
phosphates linking to the next
nucleotides) closer together than is
seen in the. C2' endoconfromation.
 Thus the distance between adjacent
nucleotides is reduced by about 1
Angstrom in A-form relative to B-form
nucleic acid.

7. Cont…
 Z-DNA has the sugar in the C3'
endoconformation (like A-form nucleic
acid, and in contrast to B-form DNA) and
the guanine base is in the
synconformation. This places the guanine
back over the sugar ring, in contrast to the
usual anticonformation seen in A- and B-
form nucleic acid.
 The duplex in Z-DNA has to accommodate
the distortion of this G nucleotide in the
synconformation. The cytosine in the
adjacent nucleotide of Z-DNA is in the
"normal" C2' endoanticonformation.
 So the base in the anticonformation
places it in the position where it can
readily form H-bonds with the
complementary base on the opposite
strand.

8. Contd…

9. Contd…
 A second major
difference between A-
form and B-form
nucleic acid is the
placement of base-
pairs within the
duplex. In B-form, the
base-pairs are almost
centered over the
helical axis but in A-
form, they are
displaced away from
the central axis and
closer to the major
groove. The result is
a ribbon-like helix
with a more open
cylindrical core in A-
form. Whereas in Z
form it is dispersed.

10. Geometric attribute A-form B-form Z-form
Helix sense Right
handed
Right
handed
Left handed
Repeating unit 1 bp 1 bp 2 bp
Rotation/bp 32.7
degree
34.3 degree 60 degree
Mean bp/turn 11 10.5 12
Inclination of bp to axis +19 degree -1.2 degree -9 degree
Glycosyl angle Anti Anti Py:anti
Pu:syn
Nucleotide phosphate to
phosphate distance
5.9
Angstroms
7.0 Ang C: 5.7 Ang
G: 6.1 Ang
Sugar pucker C3’-endo C2’-endo C:C2’-endo
G:C3’-endo
Helical diameter 23
angstroms
(2.3 nm)
20 A
(2.0nm)
18
Ang(1.8nm)