Structure of DNA

AMAZING DNA
Your DNA contains enough information as
1000 page text books worth of
information.
You are made of 75 trillion cells containing 3
billion base pairs.
Your DNA is 99.9% similar to the person next
to you.
90% similar to a mouse, 60% similar to a
fruit fly,40% similar to a fish, 50% similar
to a banana.
 FACTS cont…

FACTS cont…
⚫ Although environment has some impact on
the traits of an organism, DNA has the final
word.

⚫ DNA achieves control because it determines

the structure of proteins.

⚫ All living things contain proteins and all the

actions of living things depend on proteins
called enzymes.
 Discovery of DNA

Discovery of DNA
⚫ 1950-Protein believed to be genetic material
because of the varying structures

⚫ 1952- Alfred Hershey and Martha Chase

performed experiments with radioactively
labeled viruses that infect bacteria

⚫ 1952-Rosalind Franklin X-ray diffraction of DNA

⚫ 1952-1953 Watson and Crick develop double

helix model of DNA
 Central Dogma
DNA ---------→ RNA---------→Protein.
⚫ This unidirectional flow equation represents the
Central Dogma (fundamental law) of molecular
biology.
⚫ This is the mechanism whereby inherited
information is used to create actual objects, namely
enzymes and structural proteins.

⚫ An exception to the central dogma is that certain

viruses (retroviruses) make DNA from RNA using the
enzyme reverse transcriptase.
 Gene
⚫ Genes are DNA sequences that encode some
functional product.

⚫ Gene expression refers to the process

whereby the information contained in genes
begins to have effects in the cell.

⚫ DNA encodes and transmits the genetic

information passed down from parents to
offspring.
 DNA
Gene

Gene
Protein

Trait
 Nucleic acids

Nucleic acids
⚫ Principle information molecule in the
cell.

⚫ All the genetic codes are carried out on

the nucleic acids.

⚫ Nucleic acid is a linear polymer of

nucleotides
 Nucleotides
⚫ Nucleotides are the unit structure of
nucleic acids.
⚫ Nucleotides composed of 3
components:
⚫ Nitrogenous base (A, C, G, T or U)
⚫ Pentose sugar
⚫ Phosphate
 Nucleotides

Phosphat
e
Nitrogenous
Base

Pentos
e
Sugar
The Sugars

THE SUGARS
 Nitrogenous bases

Nitrogenous bases
⚫ There are 2 types:
⚫ Purines:
⚫ Two ring structure
⚫ Adenine (A) and Guanine (G)

⚫ Pyrimidines:
⚫ Single ring structure
⚫ Cytosine (C) and Thymine (T) or
Uracil (U).
 The Bases

PYRIMIDINES

PURINES
 Nucleotides

A T

Adenine Thymine

C G

Cytosine Guanine
 Nucleotides
⚫ Each base will only bond with one other
specific base.

⚫ Adenine(A)
Form a base pair.
⚫ Thymine (T)

⚫ Cytosine(C)
Form a base pair.
⚫ Guanine (G)
 Types of Nucleic acids
There are 2 types of nucleic acids:
1. Deoxy-ribonucleic acid (DNA)
⚫ Pentose Sugar is deoxyribose (no OH
at 2’ position)
⚫ Bases are Purines (A, G) and
Pyrimidine (C, T).
2. Ribonucleic acid (RNA)
⚫ Pentose Sugar is Ribose.
⚫ Bases are Purines (A, G) and
Pyrimidines (C, U).
Linear Polymerization of Nucleotides

Linear Polymerization of Nucleotides

⚫ Nucleic acids are
formed of nucleotide
polymers.

⚫ Nucleotides
polymerize together by
phospho-diester
bonds via
condensation reaction.

⚫ The phospho-diester
bond is formed
between:
⚫ Hydroxyl (OH) group
of the sugar of one
nucleotide.
⚫ Phosphate group of
other nucleotide
Polymerization of Nucleotides

Polymerization of Nucleotides
⚫ The formed polynucleotide
chain is formed of:
⚫ Negative (-ve) charged
Sugar-Phosphate
backbone.
⚫ Free 5’ phosphate on
one end (5’ end)
⚫ Free 3’ hydroxyl on
other end (3’ end)
⚫ Nitrogenous bases are
not in the backbone
⚫ Attached to the
backbone
⚫ Free to pair with
nitrogenous bases of
other polynucleotide
chain
⚫ The polymerization of nucleotides to form
nucleic acids occur by condensation
reaction by making phospho-diester bond
between 5’ phosphate group of one
nucleotide and 3’ hydroxyl group of another
nucleotide.

⚫ Polynucleotide chains are always

synthesized in the 5’ to 3’ direction, with a
free nucleotide being added to the 3’ OH
group of a growing chain.
 Polymerization of Nucleotides

Polymerization of Nucleotides
⚫ Nucleic acids are polymers of nucleotides.
⚫ The nucleotides formed of purine or
pyrimedine bases linked to phosphorylated
sugars (nucleotide back bone).
⚫ The bases are linked to the pentose sugar to
form Nucleoside.
⚫ The nucleotides contain one phosphate
group linked to the 5’ carbon of the
nucleoside.
Nucleotide = Nucleoside + Phosphate
group
Nucleotides and Nucleosides
 Complementary base pairing
⚫ It is the most important structural feature of
nucleic acids
⚫ It connects bases of one polynucleotide
chain (nucleotide polymer) with
complementary bases of other chain
⚫ Complementary bases are bonded together
via:
⚫ Double hydrogen bond between A and T (DNA), A
and U (RNA) (A═T or A═U)
⚫ Triple H-bond between G and C in both DNA or
RNA (G≡C)
Complementary Base Pairing
 Significance of complementary
base pairing
⚫ The importance of such complementary base
pairing is that each strand of DNA can act as
template to direct the synthesis of other
strand similar to its complementary one.

⚫ Thus nucleic acids are uniquely capable of

directing their own self replication.

⚫ The information carried by DNA and RNA

direct the synthesis of specific proteins
which control most cellular activities.
DNA structure
DNA Structure

DNA STRUCTURE
In 1953, Watson and Crick postulated a
three dimensional model of DNA structure that
accounted for both the X-ray data and the
characteristic base pairing in DNA.

 It consist of two helical polynucleotide chains.

 Two polynucleotide chains coil around the same
axis to form a right –handed double helix.

 In the helix, the two chains or strands are anti

parallel i.e. have an opposite polarity.

 Backbone of each chain which consist of

alternate sugar-phosphate residues, (hydrophilic)
are on the out side of the double helix, facing the
surrounding.
 The purine and pyrimidine bases of each strand
face inward towards each other.
 The bases are stacked perpendicular to the long
axis of the double helix.
 The base pair are 0.34 nm apart in DNA helix. A
complete turn of helix takes 3.4 nm, therefore in
each helical turn, 10 bases are present. The
external diameter of helix is 2 nm.
 The helix has two external grooves, the narrow
groove is called as minor groove while the wide
groove is called as major groove . The major
groove is the site for DNA binding proteins. The
minor grooves often are the site for binding
small molecules.
 The pairs of bases are always between a purine and pyrimidine,
specifically the pairs A-T and G-C, which are the base pairs
found by Chargarff.
 There is hydrogen bonding between the bases. 2H-bonds
between A & T and 3H-bonds between G & C
 Two chains do not have the same base composition (not
identical), but two chains are complementary to each other.
Such chains are called as complementary chains.
1st chain ---- ATACGCAC---3A, 1T, 3C, 1G
2nd chain ---- TATGCGTG---1A, 3T, 1C, 3G
DNA IS A DOUBLE HELIX

DNA IS A DOUBLE HELIX

A sugar and phosphate P
“backbone” connects 3’
5’ A
nucleotides in a chain.
P C

P
Hydrogen bonds between G
paired bases hold the two
DNA strands together. P T

P C
DNA strands are antiparallel.
P
G 5’
3’
FORMS OF DNA
A-DNA

A-DNA

 A-DNA is one of the many possible

double helical structures of DNA.
 It is most active along with other forms.
 Helix has right-handed sense,

shorter more compact helical

structure.
 It occurs only in dehydrated samples of
DNA, such as those used in crystallographic
experiments.
 Structure:
 A-DNA is fairly similar to B-DNA.

 Slight increase in the number of bp/ rotation

(resulting in a tighter rotation angle), and smaller
rise/turn.
 deep major groove and a shallow minor groove.

 Favoured conformation at low water

concentrations.
 In a solution with higher salt concentrations or with
alcohol
added, the DNA structure may change to an A form,
which is still right-handed, but every 2.3 nm makes
a turn and there are 11 base pairs per turn.
B-DNA

B-DNA
 Most common DNA conformation
in vivo.
 Favoured conformation at high

water concentrations.
 Also known as Watson & Crick

model of DNA.
 First identified in fibre at 92%

relative humidity.
 Structure:

 Narrower, more elongated helix than A.

 Wide major groove easily accessible to proteins
& Narrow minor groove.
 Base pairs nearly perpendicular to helix axis
One spiral is 3.4nm or 34Ǻ.
 Distance between two H-bonds is 0.34nm or
3.4Ǻ.
Z-DNA

Z-DNA
 Z-DNA is one of the many possible
double helical structures of DNA.
 Helix has left-handed sense.
 It is most active double helical

structure.
 Can be formed in vivo, given proper

sequence and super helical tension, but

function remains obscure.
Denaturing and Annealing of DNA
⚫ The DNA double strands can denatured if
heated (95ºC) or treated with chemicals.
⚫ AT regions denature first (2 H bonds)
⚫ GC regions denature last (3 H bonds)

⚫ DNA denaturation is a reversible process, as

denatured strands can re-annealed again if
cooled.

⚫ This process can be monitored using the

hyperchromicity (melting profile).
 Denaturation of DNA

The Temp at which ½ the DNA sample is denatured is

called the melting temperature (Tm)
 Hyperchromicity (melting profile)
⚫ It is used to monitor the DNA denaturation and
annealing.

⚫ It is based on the fact that single stranded (SS)

DNA gives higher absorbtion reading than
double stranded (DS) at wavelength 260º.

⚫ Using melting profile we can differentiate

between single stranded and double stranded
DNA.
Hyperchromicity (melting profile)

Hyperchromicity (melting profile)

Using melting profile we can differentiate between SS DNA and DS
DNA

SS

SS
Ab260

DS

Tm
Temperature

Tm (melting temp.): temp. at which 50% of DS DNA denatured to SS

• Heating of SS DNA: little rise of Ab reading
• Heating of DS DNA: high rise of Ab reading
 Melting profile continue…..
⚫ Melting profile can be also used to give
an idea about the type of base pair rich
areas using the fact that:
⚫ A═T rich regions: denatured first (low melting point)
⚫ G≡C rich regions: denatured last (higher melting
point)
SS
AT rich DNA
Tm1: Small melting temp. of AT rich
GC/AT DNA
DNA
GC rich DNA
Tm2: higher melting temp. of AT/GC
equal DNA

Tm3: Highest melting temp. of GC rich DS

DNA

Tm1 Tm2 Tm3

 Importance of Tm
⚫ Critical importance in any technique that
relies on complementary base pairing
⚫ Designing PCR primers
⚫ Southern blots
⚫ Northern blots
⚫ Colony hybridization
 Factors Affecting Tm
⚫ G-C content of sample
⚫ Presence of intercalating agents (anything
that disrupts H-bonds or base stacking)
⚫ Salt concentration
⚫ pH
⚫ Length
 Renaturation
⚫ Strands can be induced to renature
(anneal) under proper conditions. Factors
to consider:
⚫ Temperature
⚫ Saltconcentration
⚫ DNA concentration
⚫ Time
Conclusion

CONCLUSION
 The secondary structure of DNA is important in
many events in cellular life. Replication,
transcription and regulation of expression of many
genes depends on local differences or changes in
DNA structure. Recombination which leads to
rearrangement of genes takes advantage of the
ability to form an unusual structure called a
Holliday’s structure. Also different kinds of
mutations occur as a result of specific DNA
structure.