STRUCTURE OF DEOXYRIBONUCLEIC ACID(DNA)
Presented by
Mr. Amol A. Shirsath

CONTENTS:
• Introduction
• Discovery of DNA
• Structure of DNA
• Salient Features of DNA Double Helix
• Helix Geometries
• Functions of DNA
• Summary

INTRODUCTION:
• In living organisms, DNA molecule is the blueprint for life. It is the
repository and carrier of genetic information and plays integral role in
its development, functioning and reproduction.
• Deoxyribonucleic acid is a molecule composed of two chains that coil
around each other to form a double helix.

DISCOVERY OF DNA:
• Exploration of DNA has involved the work of many scientists for many
years. The background for the discovery of DNA was however formed by
scientific advances made by four scientists, namely Maurice Wilkins,
Rosalind Franklin, Francis Crick and James Watson.
• Rosalind Franklin used X-Rays to be beamed through crystals of DNA
and recorded by using a photographic film The shadows on the film
would show where the dense molecules lie. Cross shaped shadows were
found on the X-Ray film, thereby confirming that the DNA molecule was
helical in shape.
• In 1953, James Watson and Francis Crick proposed a model for the
structure of DNA. This proposal was based on the previous assumptions
of Chargaff’s experimental finding(equal numbers of A and T bases and
of G and C bases in DNA) and X-Ray data obtained from Rosalind
Franklin.
• Watson and Crick outlined the theory that DNA molecule comprised of
two complementary polynucleotide strands, which wound around each
other to form a double helical structure.

STRUCTURE OF DNA:
• The structure of DNA is represented in the form of polynucleotide strands
of DNA coiled around each other to form a double helix. The backbone of
this helix is formed by sugar-phosphate and the bases lie towards the
interior of the helix, extended at right angles (at 90°) to the helix axis.
• Bases remain stacked over each other in the double helix. Hydrophobic
interactions between stacked bases lead to stabilization of the DNA
molecule.
• Overall the sugar phosphate backbone of each strand is negatively
charged due to phosphate group.

• Complementary bases from opposite helix pair with each other. Purines form
base pairs with pyrimidines, that is base A pairs with base T, and base C with
base G.
• The hydrogen bonding in the base pairs imparts stability to the helical structure
of DNA.
• The base-pairs G and C are bonded to each other by three H-bonds, while A and
C are bonded to each other by two H-bonds.
• Owing to larger number of H-bonds between the two, the G-C base-pairs are
therefore stronger than A-T base-pairs. Greater the number of GC base pairs in
a DNA molecule, greater will be the stability than a DNA molecule having
more AT base pairs.

SALIENT FEATURES OF DNA DOUBLE HELIX :
• The overall structure of DNA is a double helical structure composed of two
polynucleotide strands. Helix is right handed along the axis.
• The backbone of each polynucleotide is formed by alternate sugar and
phosphate, and the bases lie within the helix, arranged at right angles to the
helix axis.
• The phosphate group remains bonded to the 5' C of one sugar, and to the 3'
C of the next sugar.
• A common representation of polynucleotide is 5'pApTpGpC OH3'
• Two strands run antiparallel to each other: one in 5' ---> 3' direction and the
other in the 3' ---> 5' direction.
• Each base in the DNA double helix forms hydrogen bonds with
complementary bases directly opposite it, forming base pairs. A pairs with
T and G with C.

• The planes in which the adjacent base pairs are located are separated by 3.6 Å.
• There are 10 base pairs found per turn of the helix with a rise of 3.6 Å. One turn
of the helix measures 36 Å.
• Each turn of the double helix contains an average of 25 hydrogen bonds to
provides a strong stability.
• The diameter of DNA helix measures 20 Å.
• Two deep grooves are found on the surface of double helix which are the major
and minor grooves.
 Minor groove exposes edge from which C1’ atoms where Major groove
extend exposes opposite edge of base pair.
 Major group is wider than the minor group
 Protein binding to DNA molecule takes place through the major groove.

• The DNA molecule exhibits conformational flexibility, and could therefore exist
in alternative structural forms. There are three conformations of DNA named as
A-DNA, B-DNA and Z-DNA.
• Under physiological conditions, the B-DNA forms the most stable structure and
is therefore considered as a standard reference in any study.
• The Watson-Crick structure is also the B-form DNA or B-DNA.
• Apart from the B-DNA, A-DNA and Z-DNA are two other structural variants of
DNA.
• These have been well characterized in crystal structures. They also form helical
structures like the B-DNA, but differ in their geometry and dimensions from B-
DNA.
HELIX GEOMETRIES :

Property/Parameter A-DNA B-DNA Z-DNA
Shape of helix Broad Intermediate Narrow
Type of helix Right-Handed Right-Handed Left-Handed
Repeating units 1 base pair 1 base pair 2 base pair
Rotation per base pair (°) 33 34.3 30
Base pairs per turn of helix 11 10.5 12
Tilt of base pairs from normal to
the helix (°)
19 1 9
Vertical rise per base pair along
the axis (Å)
2.3 3.2 3.8
Pitch per turn of helix (Å) 25.3 35.4 45.6
Mean propeller twist (°) 18 16 0
Diameter of the helix (Å) 23 20 18
Major groove Narrow and deep Wide and deep Flat
Minor groove Broad and shallow Narrow and deep Very narrow and deep
Glycosyl bond formation Anti Anti Anti for pyrimidine,
syn for purine
Sugar pucker conformation C-3’ endo C-2’ endo C-2’ endo for pyrimidines,
C-3’ endo for purines
Comparative understanding of the three major forms of DNA

FUNCTIONS OF DNA:
• DNA is the storehouse of biological information. The two strands of DNA
provide a simple mechanism for copying the molecule. Upon separation, DNA
replication occurs and each strand acts a template for creating the other strand.
Thus two identical 'daughter' molecules are created.
• Some portions of DNA are non-coding, implying that these sections are not
engaged in coding for protein sequences.
• Within nucleus of cells, DNA is organized into chromosomes. During cell
division these chromosomes are duplicated in the process of DNA replication,
providing each daughter cell its own complete set of chromosomes.
• Eukaryotes store most of their DNA inside the nucleus and some of their DNA
in organelles like mitochondria or chloroplasts, prokaryotes store their DNA
only in the cytoplasm.
• Chromatin proteins (histones) play key role in compacting and organizing the
DNA within the chromosomes.

SUMMARY:
• DNA molecule serves as the molecular repository of genetic information in
living organisms.
• The background for the discovery of DNA was formed by several scientific
breakthroughs made by four scientists, namely Maurice Wilkins, Rosalind
Franklin, Francis Crick and James Watson.
• Watson and Crick proposed the three-dimensional structure of DNA for the first
time in 1953. They outlined the theory that DNA has a double helical structure
comprising of two complementary anti-parallel polynucleotide strands, wound
around each other in a rightward direction.
• The helix is right handed and runs antiparallel. The backbone of the helix is
sugar-phosphate and the bases in the interior extend perpendicular to the axis of
the helix.
• Complementary bases from opposite helix pair with each other.

• The planes in which the adjacent base pairs are located are separated by 3.6
Å. 10 base pairs are found per turn with rise of 3.6 Å and one turn of the
helix is 36 Å. The diameter of DNA helix is 20 Å.
• DNA exists in alternative structural forms, namely as A-DNA, B-DNA and
Z-DNA. B from is the most stable structure for a random sequence DNA
molecule.