St. George College of Management and Science
STRUCTURE OF DNA,
DNA POLYMORPHISM [A, B, Z
DNA is composed of two polynucleotide
chains twisted around each other in the
form of double helix.
The double helix looks superficially same
because of the complimentary nature of
the two DNA strands.
The nucleotide consists of phosphate
joined to a sugar known as
2’deoxyribose to which a base is
The sugar is called 2’deoxyribose because there
is no hydroxyl at position 2’.
The sugar and base alone are called
nucleoside. Adding a phosphate to a
nucleoside creates a nucleotide.
Nucleotides are joined to each other in
polynucleotide chains through 3’hydroxyl of
2’deoxyribose of one nucleotide and the
phosphate attached to 5’hydroxyl of another
This is phophodiester linkage in which the
phosphoryl group between two nucleotides has
one sugar esterified.
The phosphodiester linkages impart an
inherent polarity to DNA chain. This polarity
is defined by the asymmetry of the
nucleotides and the way they are joined.
EACH BASE HAS ITS PREFERRED
The bases in DNA are flat heterocyclic rings
consisting of carbon and nitrogen atoms.
They fall into 2 classes purines and
pyrimidines i.e adenine, guanine, cytosine,
Each of the bases exist in two alternative
tautomeric state states which are in
equillibrium with each other.
THE TWO STRANDS OF THE DOUBLE HELIX
ARE WOUND AROUND EACH OTHER IN AN
The two chains have the same helical geometry
but have opposite 5’ to 3’ orientation.
Adenine in one chain pair with thymine of other
chain likewise guanine pairing with cytosine.
THE TWO CHAINS OF DOUBLE HELIX HAVE
Pairing between adenine and thymine and
between guanine and cytosine reults in
complementary relationship between the base
sequence on to interwined chains and gives
DNA itself encoding character.
THE DOUBLE HELIX IS STABILIZED BY BASE
PAIRING AND BASE STACKING:
The hydrogen bonds between contribute to
thermodynamic stability and specificity of base
Base stacking also contributes to the stability by
The hydrophobic surfaces are buried by base
stacking thus minimising the exposure of base
surfaces to water molecules and hence lowering
the free energy.
BASE CAN FLIP OUT FROM DOUBLE HELIX:
Individual bases can protrude from double helix by
phenomenon called base flipping.
Certain enzymes that remove damaged bases do so
with the base in an extrahelical configuration in
which it is flipped out enabling the base to sit
in catalytic cavity of the enzyme.
THE DOUBLE HELIX HAS MAJOR AND
The narrow angle between the sugars on
one edge of the base pair generates minor
groove and large angle on the other hand
generates major groove.
The major groove is rich in chemical
DNA STRANDS CAN SEPARATE (DENATURE)
The complementary strands of double helix can be
made to come apart by process called
denaturation. But this is reversible.
However when the heated solutions of denatured
dna cools single strands often meet there
The capacity to renature denatured DNA molecules
permits artificial hybrid dna molecules to be
The ability to form hybrids between two single
stranded nucleic acids is called hybridization
THE DOUBLE HELIX EXISTS IN MULTIPLE
X-ray diffractions revealed thet there are A,
B, Z forms of DNA.
The B form of DNA represents the ideal
structure and forms right handed helix.
The Z DNA forms a left handed helix .
• Refined resolution of DNA structure ,based
on X-ray crystallography of short synthetic
pieces of DNA has shown that there is
considerable variance of helical structure of
o There are three families of DNA helices:
o A- DNA : Which can readily form within
certain stretches of purines (eg: GAGGGA)
B DNA: Which is favoured by mixed
sequences( although the exact conformation
depends on the particular nucleotide
Z-DNA: Which is favoured by alternating
pyrimidine –purine steps (EG: CGCGCG).
The A and B DNA families are right handed
helices, while Z DNA family has a left handed
orientation of helix.
The different conformations of DNA helix
have important biological functions.
A-DNA is one of the possible double helical
structure which DNA can adopt along with
other two biologically active helix
Right handed double helix
Short and thick compared to B-DNA.
Occur only in dehydrated sample of DNA, like
those used in crystallography experiments.
A-DNA was originally identified by X-ray
diffraction analysis of DNA fibres at
The grooves are not deep as in B-DNA
Bases are more tilted.
Base pair turn is 11.
Rise per base pair is 2.3 angstorm.
Discovered by Watson and Crick .
Most common form of DNA.
DNA molecule consists of 2 helical
polynucleotide chains coiled around common
Two helices are coiled in such a way so as to
produce 2 interchain spacing or groove.
Major/wide groove, Minor/ narrow groove.
.These grooves provides surface with which
proteins ,chemicals, drugs interact.
Discovered by Rich, Nordheim and Wang in
One of the many possible DNA double helix
Left handed double helix structure in zig zag
manner so termed as Z-DNA
Has anti parallel strand ass in B-DNA.
Long and thin in comparison to B-DNA.
Adjacent sugar have alternating orientation.
In Z-DNA : a. purines: syn conformation
(bases and sugar are near and on same side).
b. pyrimidines : anti (bases and sugar are
distant , on opposite sides.)
Only one deep helical groove.
12 base pairs per turn with axial rise 3.8
angstorm. & angle twist of 60 degree
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