Structure of DNA

Structure of Nucleic acid

 Two types of nucleic acid are found
 Deoxyribonucleic acid (DNA)
 Ribonucleic acid (RNA)
• DNA or deoxyribonucleic acid
• present in chromosomes
• polymeric nucleotides

• RNA or ribonucleic acid

• NOT found in chromosomes
• 6 types of RNA
• polymeric nucleotides

The distribution of nucleic acids in the

Eukaryotic cell
DNA is found in the nucleus with small amounts in
mitochondria and chloroplasts

RNA is found throughout the cell

 DNA
•DNA - a polymer of deoxyribo nucleotides

•It founds in chromosomes, mitochondria and chloroplasts

• It carries the genetic information

Prokaryotic Cells
• Prokaryotic cells have a single circular DNA molecule that contains nearly all of its
genetic information
• Located in the cytoplasm

Eukaryotic Cells
Much more complex
1000 times the amount of DNA as prokaryotes
DNA is located in the nucleus in the form of chromosomes
 Deoxyribonucleic acid (DNA)

DNA responsible for preserving, copying and transmitting

information within cells and from generation to generation.

DNA is a nucleic acid that contains the genetic instructions used in

the development and functioning of all known living organisms
and some viruses.

DNA is a set of blueprints needed to construct other components

of cells, such as proteins and RNA molecules.

The amount of DNA in somatic cells (body cells) of any given

species is constant (like the number of chromosomes)
The DNA content of gametes (sex cells) is half that of somatic cells.
In cases of polyploidy (multiple sets of chromosomes) the DNA content
increases by a proportional factor.

A human cell contains about 2 meters of DNA, Each person has

around 60 trillion feet or around 10 billion miles of DNA inside of them.
The Earth is about 93 million miles away from the sun. So your DNA
could stretch to the sun and back 61 times! (That is one person’s DNA).
So it is tightly packed.

Arranged in 22 chromosomes, plus two sex chromosomes. Two copies

of each.

99.9% identical to other humans, 98% to chimp!

NUCLEIC ACID STRUCTURE
 Nucleic acids are polynucleotides
 Nucleotides are composed of
NUCLEOTIDE STRUCTURE

PHOSPATE SUGAR BASE

Ribose or PURINES PYRIMIDINES
Deoxyribose
Adenine (A) Cytocine (C)
Guanine(G) Thymine (T)
Uracil (U)

 DNA = A, G, C, T
 RNA = A, G, C, U
NUCLEOTIDE
Components of Nucleotide

Found in RNA Found in DNA

 NUCLEIC ACID STRUCTURE

Base

Phosphate
Sugar
X=H: DNA
X=OH: RNA
Nucleoside
Nucleotide
 Nomenclature of Nucleic Acid Components

Base Nucleoside Nucleotide Nucleic acid

Purines

Adenine Adenosine Adenylate RNA

Deoxyadenosine Deoxyadenylate DNA

Guanine Guanosine Guanylate RNA

Deoxy guanosine Deoxyguanylate DNA
Pyrimidines

Cytosine Cytidine Cytidylate RNA

Deoxycytidine Deoxycytidylate DNA

Thymine Thymidine Thymidylate DNA

(deoxythymidine) (deoxythymidylate)

Uracil Uridine Uridylate RNA

 Nucleosides
Base + Sugar = Nucleoside

• Adenine Adenosine
• Guanine Guanosine
• Thymine Thymidine
• Cytosine Cytidine
• Uracil Uridine

Nucleotides
Nucleoside + PO43- = Nucleotide

 Adenosine Deoxyadenosine 5’-monophosphate (dAMP)

 Cytidine Deoxycytidine 5’-monophosphate (dCMP)

 Uridine (in RNA) Uridine 5’-monophosphate (UMP)

 Thymidine (+2 PO43-) Deoxythymidine 5’-diphosphate (dTDP)

 Guanosine (+3 PO43-) Deoxyguanosine 5’-triphosphate (dGTP)

 NH2 NH2 NH2

N N N
N N N

N N N N N N
O O O O O O
O- P O CH2 O- P O P O CH2 O- P O P O P O CH2
O O O
O- O- O- O- O- O-

OH OH OH OH OH OH

adenosine monophosphate adenosine diphosphate adenosine triphosphate

AMP ADP ATP
 DNA - Primary Structure
The primary structure is based on the sequence
of nuclotides
• 1) The Backbone is made from Ribose (sugar) and Phosphate
• PO43- connected at Ribose 3’ and 5’
• 2) The Bases (AGTC, AGUC) are side-chains and are what makes each
monomer unit different. Bases connected at Ribose 1’
In DNA the reaction catalyzed by DNA polymerase enzyme
In RNA by RNA polymerase
 The primary structure of
DNA is the sequence 5’
P

5’ end

5’
P

P
3’

Phosphodiester P
linkage

P
3’
THE SUGAR-PHOSPHATE BACKBONE 3’ end
Nucleotides are linked by phosphodiester bonds to form polynucleotides.

Phosphodiester bond

Covalent bond between the phosphate group (attached to 5’ carbon) of

one nucleotide and the 3’ carbon of the sugar of another nucleotide.

This bond is very strong, and for this reason DNA is remarkably stable.
DNA can be boiled and even autoclaved without degrading!

5’ and 3’

The ends of the DNA or RNA chain are not the same. One end of the
chain has a 5’ carbon and the other end has a 3’ carbon.
 5’ P

G
ADDING IN THE BASES
P
• The bases are attached to the 1st Carbon
of the sugar C

• Their order is important

It determines the genetic information of P
the molecule
C
• The order of the bases (-GCCATT-)
provides the primary structure of DNA.
P
• The backbone of both DNA and RNA
consists of alternating sugar and A
phosphate groups
• There is a 5’ end and a 3’ end P
• The backbone adds stability to the T
structure

P
3’ T
 DNA - Primary Structure
•
 The secondary & Tertiary structure
of DNA (Double helix)

Circular ladder
Secondary Structure of DNA

It is the set of interactions between bases,

i.e., which parts of strands are bound to each
other. In DNA double helix, the two strands of
DNA are held together by hydrogen bonds.
The nucleotides on one strand base pairs
with the nucleotide on the other strand.

Tertiary Structure of DNA

Nucleic acid tertiary structure is the three-
dimensional shape of a nucleic acid polymer.

A pseudoknot is a nucleic acid secondary

structure containing at least two stem-loop
structures in which half of one stem is
intercalated between the two halves of another
stem. The pseudoknot was first recognized in
the turnip yellow mosaic virus in 1982
 DNA – Secondary Structure
• James Watson (1928- ) and
Francis Crick (1916-2004 )
• Established 3-D structure of DNA
• Bases on adjacent strands PAIRED so that
Hydrogen bonds formed:
Complementary Base Pairing
DNA IS MADE OF TWO STRANDS OF
POLYNUCLEOTIDE
• Two long strands makes the shape of a double helix.

• The sister strands of the DNA molecule run in opposite directions

(antiparallel)

• They are joined by the bases

• Each base is paired with a specific partner:

A is always paired with T
G is always paired with C
Purine with Pyrimidine

• This the sister strands are complementary but not identical

• The bases are joined by hydrogen bonds, individually weak but

collectively strong

DNA double helix

 Hydrogen bond
A chemical bond in which a hydrogen atom of one
molecule is attracted to an electronegative atom,
especially a nitrogen, oxygen, or fluorine atom,
usually of another molecule.

Complementary Base Pairing

Watson & Crick Base pairing

Position of H bonds and distance match

 Hydrogen bond formations

Alternative forms of base pairing

7 28 possible pairs of nitrogenous bases

8
5 4 6 5
9
3 1 4 10 possible base pair purine-pyrimidine
6 2 3 2 Watson-Crick pairs
1 T A
2 31 2 Reverse Watson Crick
4 6 2 Hoogsteen pairs
2 Reverse Hoogsteen
1 pair oscillating
1 pairs oscillating back
7 8
5 4 6 5 9 7 pairs homo purine-purine
3 1 4 (A = A, G = G)
6 2 3
1
2
4 pairs hetero purine –purine
C G A = G and
22
31 7 pyrimidine-pyrimidine pairs
4 6
Two hydrogen bonds between A:T pairs
Three hydrogen bonds between C:G pairs
 2 12
23
6 3
1
Reverse
Watson & Crick Base pairing Watson-Crick G-C
DNA - Tertiary Structure
 Major groove and Minor groove
The double helix is a quite rigid and viscous molecule of
an immense length and a small diameter. It presents a
major groove and a minor groove. The major groove is
deep and wide, the minor groove is narrow and
shallow.

DNA-protein interactions are major/essential processes in

the cell life (transcription activation or repression, DNA
replication and repair).

Proteins bind at the floor of the DNA grooves, using

specific binding: hydrogen bounds, and non specific
binding: van der Waals interactions, generalized
electrostatic interactions.

Proteins recognize H-bond donors, H-bond acceptors,

metyl groups (hydrophobic), the later being exclusively in
the major groove; there are 4 possible patterns of
recognition with the major groove, and only 2 with the
minor groove.

Some proteins bind DNA in its major groove, some other

in the minor groove, and some need to bind to both.
 Different forms of DNA
The double helical structure of DNA exists in at least 6 different
forms A to E and Z.

Among these A,B and Z forms are important.

At high humidity (and low salt) the dominant structure is called B-
DNA. It is most commonly found in vivo.

At low humidity (and high salt) the favoured form is A-DNA. It is not
found in vivo.

In 1979 a quite different structure was discovered namely a left

handed helix formed by a synthetic hexamer d(CGCGCG), now
known as a Z-DNA
 Normally hydrated DNA: B-form DNA

Helical sense: Right handed

Base pairs: almost perpendicular to the helix axis; 3.4 Å apart
One turn of the helix: 34 Å; ~10.4 base pairs
Minor groove: 12 Å across Major groove: 22 Å across
 B – DNA (Wet form exist in cells)

In B-DNA, the most common double helical structure, the double helix is right-
handed with about 10–10.5 nucleotides per turn.

The helix makes a turn every 3.4 nm, and the distance between two neighboring base
pairs is 0.34 nm.

The double helix structure of DNA contains a major groove and minor groove, the
major groove being wider than the minor groove.

Given the difference in widths of the major groove and minor groove, many proteins
which bind to DNA do so through the wider major groove.

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.
 A – DNA (Dry form)

A-DNA is one of the many possible double helical structures of DNA. A-

DNA is thought to be one of three biologically active double helical
structures along with B-and Z-DNA.

It is a right-handed double helix fairly similar to the more common and

well-known B-DNA form, but with a shorter more compact helical
structure. It appears likely that it occurs only in dehydrated samples of
DNA, such as those used in crystallographic experiments.

Gram positive bacteria undergoing sporulation contain a high proportion

of (20%) small acid-soluble spore proteins (SASPs), Some of which
induce a B-DNA to assume the A form.

The DNA in bacterial spores exhibits a resistance to UV-induced damage

that is abolished in mutant that lack these SASPs. This is because the
BA conformation change inhibits the UV-induced covalent cross-
linking of pyrimidine bases by increasing the distance between successive
pyrimidines. A form we can able to see in both DNA & RNA.
 Z - DNA

Z form is a left handed double helix with a zig-zag conformation of the

backbone (less smooth than B-DNA). Only one groove is observed,
resembling the minor groove, the base pairs (which form the major groove -
close to the axis- in B-DNA) being set off to the side, at the outer surface, far
from the axis. Phosphates are closer together than in B-DNA.

Z-DNA is thought to be one of three biologically active double helical

structures along with A- and B-DNA.

A high G-C content favours Z conformation. Cytosine methylation, and

molecules which can be present in vivo such as spermine and spermidine
can stabilize Z conformation. DNA sequences can flip from a B form to a Z
form and vice versa: Z-DNA is a transient form in vivo.

Z-DNA formation occurs during transcription of genes, at transription start

sites near promoters of actively transcribed genes. During transcription, the
movement of RNA polymerase induces negative supercoiling upstream
and positive supercoiling downstream the site of transcription The negative
supercoiling upstream favours Z-DNA formation; a Z-DNA function would
be to absorb negative supercoiling. At the end of transcription,
topoisomerase relaxes DNA back to B conformation.
 Comparison of different DNA Forms

Structural features A – DNA B – DNA Z – DNA

Helical sense Right – handled Right – handled Left - handled
Diameter 23 Å (2.3 nm) 20 Å (2.0 nm) 18 Å (1.8 nm)
Base pairs per helical turn 11 10.4 12
Helical twist per base pair 32.7° 35.9° 60°/2
Helical pitch (rise per turn) 28.2 Å 33.2 Å 45.6 Å
Helix rise per base pair 2.3 Å 3.32 Å 3.8 Å
Mean propeller twist +18° +16° 0°
Glycosyl angle anti anti C-anti, G: syn
C-C2'-endo
Sugar pucker C3'-endo C2'-endo
G- C2'-exo
Major groove Narrow and deep Wide and deep Flat
Minor groove Wide and shallow Narrow and deep Narrow and deep
 Sugar Pucker
The sugar pucker determines the shape of the a-helix, whether the helix will exist in the
A-form or in the B-form.

B DNA A DNA
Z DNA
C Base

Z DNA
G Base
Sugar Puckering
DNA Quaternary Structure
Six successive levels of the hierarchical
organization of DNA packing in a
metaphase chromosome.
• 2 main groups of proteins involved in folding/packaging
eukaryotic chromosomes

• Histones = positively charged proteins filled with amino acids

lysine and arginine that bond
• Nonhistones = less positive

20 to 30% of the amino acids in Histone are

Lysine and Arginine. Positively charged bind
to the negatively charged phosphate groups
in the sugar phosphate backbone of DNA.

Determining gene sequence: Treated with a

salt solution uncoils chromatin beccause of
Na+ attaches to the phosphate groups,
displaces the Histone Octamers.
 Histone Proteins

14 kDa 14 kDa 15 kDa 11 kDa

 d
1.67 times
14 kDa 14 kDa

15 kDa
11 kDa

DNA wrapped around its histone core. One

strand of DNA is shown in green, the other
in brown. The histones are shown in
different colors.
Model for Chromatin Structure
• Chromatin is linked together every 200 bps (nuclease digestion)
• Chromatin arranged like “beads on a string” (electron microscope)
• 8 histones in each nucleosome
• 147 bps per nucleosome core particle with 53 bps for linker DNA (H1)
A nucleosome consists of a core of eight histone molecules (octamer), two copies each
of H2 A, H2 B, H3, and H4, and about 150 bp DNA wrapped around it.

The total protein content is 108 kDa (28 kDa each for H2 A and H2 B, 30 kDa for H3, and
22 kDa for H4). The histone octamer forms a disc-shaped core.

About 140–150 (147 bp in humans) base pairs of DNA are wrapped 1.67 times in left-
handed turns around the histone core to form a nucleosome about 11 nm in diameter
and 6 nm high.

The DNA enters and leaves the nucleosome at points close to each other.

A fifth type of histone, H1, is located here and attaches to the DNA between two
nucleosomes. Each nucleosome is separated from the other by 50–70 bp of linkerDNA.

For transcription and repair the tight association of histones and DNA has to be
loosened.
Nucleosomes connected together by linker DNA and H1 histone to produce the
“beads-on-a-string” extended form of chromatin.

Histone octomer
H1

Linker DNA (50-70 bp)

10 nm chromatin is produced in the first level of packaging.
Histone proteins DNA is further compacted when the DNA nucleosomes
associate with one another to produce 30 nm chromatin.

Mechanism of compaction is not understood, but H1 plays a role (if H1 is

absent, then chromatin cannot be converted from 10 to 30 nm).

DNA is condensed to 1/6th its unfolded size

• Compaction continues by forming looped domains from the 30 nm chromatin, which seems
to compact the DNA to 300 nm chromatin
• Human chromosomes contain about 2000 looped domains
• 30 nm chromatin is looped and attached to a nonhistone protein scaffolding
• DNA in looped domains are attached to the nuclear matrix via DNA sequences called MARs
{matrix attachment regions or scaffold attachment region (SAR)}
• MARs are known to be near regions of the DNA that are actively expressed
• Loops are arranged so that the DNA condensation can be independently controlled for gene
expression
 Supercoil = coil over coil

Supercoiling:
If the two ends of a DNA molecule are fixed, the double helix can be wound
around itself in space.
Measured linearly, the Escherichia coli genome (4.6 Mb) would be 1,000
times longer than the E. coli cell.

The human genome (3.4 Gb) would be 2.3 m long if stretched linearly.

Chromosome released
from lysed E. coli cell
If DNA is in the form of a circular molecule, or if the ends are rigidly held so that it forms a
loop, then over twisting or under twisting leads to the supercoiled state. Supercoiling occurs
when the molecule relieves the helical stress by twisting around itself. Overtwisting leads to
postive supercoiling, while undertwisting leads to negative supercoiling.

Think of positive supercoiling as twisting the loop clockwise from the top, while think of
negative supercoiling as twisting the loop counterclockwise from the top.
 Proteins Involved in Supercoiling
The 1.6 mm long DNA molecule of the E. coli chromosome . E. coli cell size: 2 µm long
and 0.5-1 µm wide.

During the 1980s and 1990s, researchers discovered that multiple proteins act together to fold
and condense prokaryotic DNA.

They are (HU, H-NS,and IHF) associated with chromosomal DNA.

These proteins are necessary for packaging large, circular prokaryotic chromosomes into
small volumes is the twisting of the DNA molecules (Supercoiling).

These proteins are often called the ‘histone-like’ proteins, not because of any sequence
similarity to the eukaryotic histone proteins, but because, like the histones, they are small,
basic (and therefore positively charged) DNA-binding proteins.

In E. coli, once the prokaryotic genome has been condensed, DNA topoisomerase I,
DNA gyrase, help maintain the supercoils.

Genomes can be negatively supercoiled, meaning that the DNA is twisted in the opposite
direction of the double helix, or positively supercoiled, meaning that the DNA is twisted in the
same direction as the double helix. Most bacterial genomes are negatively supercoiled during
normal growth.
(Most abundant E coli protein associated with nucleoid {60,000/cell})
The HU, H-NS and IHF proteins all function as dimers. The HU and H-NS proteins both
interact with chromosomal DNA non-specifically and serve to stabilise negative
supercoils in the DNA. Whilst they do not bind DNA in a sequence-specific manner,
both these proteins show some preference for binding DNA that has a ‘bendable’ structure.

Escherichia coli HU, a small, basic, heat-stable DNA binding protein, is one of the most
abundant proteins associated with the E.coli nucleoid.

It works with an enzyme called topoisomerase I to bind DNA and introduce sharp bends in
the chromosome, generating the tension necessary for negative supercoiling.

There are some 60 000 HU proteins per E. coli cell, enough to cover about one-fifth of the
DNA molecule.

In E. coli, HU (18 kDa) is a hetero dimer composed of two highly homologous subunits
This heterotypic dimmer protein is composed of two subunits; HUa and HUb, which weigh
9kDa each
whereas in many other bacteria HU is present as a homo dimer.

The folded DNA is then organized into a variety of conformations that are supercoiled
and wound around tetramers of the HU protein, much like eukaryotic chromosomes are
wrapped around histones.
 Histone-like nucleoid-structuring (H-NS) protein

C
15.6 kDa dimeric protein
20,000/cells
Binds once every 300-400bp
N

A DNA-binding protein implicated in transcriptional repression (silencing) as well as in bacterial

chromosome organization. H-NS binds tightly to AT-rich dsDNA, increases its thermal stability and
inhibits transcription. Also binds to ssDNA and RNA but with a much lower affinity. H-NS has
possible histone-like function. May be a global transcriptional regulator through its ability to bind
to curved DNA sequences, which are found in regions upstream of a certain subset of promoters.
HU and H-NS help compact the DNA strand, but each also plays supporting roles in
replication and transcription by establishing or maintaining appropriate structure.
H-NS (histone-like nucleoid-structuring (H-NS) protein)binds DNA in a non-
sequence-specific manner but with a preference for intrinsically curved AT-rich
regions.

H-NS consists of an N-terminal dimerization domain and a C-terminal DNA-

binding domain that are separated by a linker domain.

H-NS which is a dimer of a 15.6 kDa polypeptide. The H-NS protein is not only
capable of interacting with DNA but also with itself and other proteins.

An E. coli contains approximately 20 000 molecules of the H-NS protein, which binds
approximately once every 300–400 bp along the chromosome.