DNA

STRUCTURE
DNA-What is in the name?

Deoxyribo : the pentose does not have any oxygen in

D
position 2. Compare a deoxyribose with a ribose .

Nucleic: these molecules were first found in the nucleus

of the cell, before being found in mitochondria,
N
chloroplasts (of plant cells), and in the cytoplasm of
prokaryotes.

A Acid: phosphoric acid are used to form the DNA chain.

 DNA
• DNA is often called
the blueprint of life.

• In simple terms, DNA

contains the
instructions for
making proteins
within the cell.
Why do we study DNA?
We study DNA for
many reasons, e.g.,
its central
importance to all life
on Earth,
medical benefits such
as cures for diseases
better food crops.
Forensic Analysis
 First Structure
• By 1910 actual
components
known
(nucleotides)
– Phoebus Levene
proposed a
tetranucleotide
structure for DNA
• Tetranucleotide repeat of ATCG
• data showed nucleotides not in 1:1:1:1 ratio
 The Shape of the
Molecule
• DNA is a very
long polymer.
• The basic shape
is like a twisted
ladder or zipper.
• This is called a
double helix.
The Double Helix Molecule

The DNA double

helix has two
strands twisted
together.
 One Strand of DNA
• The backbone phosphate

of the molecule
is alternating
phosphate and deoxyribose
deoxyribose, a
sugar, parts.
• The teeth are
bases
nitrogenous
bases.
 Nucleotides
O
O -P
O One deoxyribose together
O
O with its phosphate and
O -P base make a nucleotide.
O
O O
O -P
O
O
O
C

Phosphate
C Nitrogenous
C

base
C C
Deoxyribose
O
 One Strand of DNA
• One strand of nucleotide
DNA is a polymer
of nucleotides.
• One strand of
DNA has many
millions of
nucleotides.
Four nitrogenous bases
DNA has four different bases:

• CytosineC
• Thymine T
• Adenine A
• Guanine G
 Two Kinds of Bases in DNA
• Pyrimidines are
CN
single ring bases. O C
N
C
C
N
• Purines are double
ring bases. N
N C
C C
N
C
N N C
 Thymine and Cytosine are
pyrimidines

• Thymine and cytosine each have one

ring of carbon and nitrogen atoms.

O N
C
N C N
O C C
O C C C
C
C N
N cytosine
thymine
 Adenine and Guanine are
purines
• Adenine and guanine each have two
rings of carbon and nitrogen atoms.

O
N
C C
N N
C C C C
N N
N
C C
N N C
Adenine C Guanine
N N
 Two Stranded DNA
• DNA has two
strands that fit
together
something like a
zipper.
• The teeth are the
nitrogenous bases
but why do they
stick together?
 Hydrogen Bonds
• The bases attract each

N
other because of
hydrogen bonds.

C
N

N
• Hydrogen bonds are

C
weak but there are

C
C
O

N
millions and millions of
them in a single

C
molecule of DNA.
N
C
• (The bonds between N
cytosine and guanine C C O
are shown here.)
C
N
 Hydrogen Bonds, cont.
• When making
O
hydrogen bonds,
N C
cytosine always pairs
up with guanine, O C C C
• And adenine always
N
pairs up with C
C N
thymine.
N
• (Adenine and thymine C N
are shown here.)
C
C C
N
N
 Important:
• Adenine and Thymine always join
together
A T
• Cytosine and Guanine always
join together
C G
 Erwin Chargaff
• 1949-1953
• Digested many DNAs and subjected
products to chromatographic separation
• Results
– A = T, C = G
– A + G = C + T (purine = pyrimidine)
– A + T does not equal C + G
• Members of a species similar but different species
vary in AT/CG ratio
What is DNA made of?
Nucleotide :
Phosphate
s
Sugar
Bas
e

Carbon atoms of sugar are numbered

 Double helix of DNA
• James Watson and Francis Crick proposed a model
for the structure of DNA.
– Utilizing X-ray diffraction data, obtained from crystals of
DNA)
• This model predicted that DNA
– as a helix of two complementary anti-parallel strands
that is, one strand runs 5′ to 3′ while the other runs 3′ to 5′.
– wound around each other in a rightward direction
– stabilized by H-bonding between bases in adjacent
strands.
– The bases are in the interior of the helix
• Purine bases form hydrogen bonds with pyrimidine.
 Double helix of DNA (contd.)
❖ The double helix of DNA has these features:
– Concentration of adenine (A) is equal to thymine (T)
– Concentration of cytosine (C) is equal to guanine (G).
– Watson-Crick base-pairing A will only base-pair with T,
and C with G
• base-pairs of G and C contain three H-bonds,
• Base-pairs of A and T contain two H-bonds.
• G-C base-pairs are more stable than
A-T base-pairs
– The backbone of each consists of alternating
deoxyribose and phosphate groups
 Double helix of DNA (contd.)
• The DNA strands are assembled in the 5' to 3'
direction
– by convention, we "read" them the same way.

• The phosphate group bonded to the 5' carbon atom

of one deoxyribose is covalently bonded to the 3'
carbon of the next.

• Human DNA consists of approximately 3 x 109 such

“base pairs”.
 Double-stranded DNA
5’ 3’

Major groove

Minor groove

“B” DNA
3’ 5’ 3’ 5’
 Double helix of DNA (contd.)
• DNA is a double-stranded molecule twisted into a helix
(like a spiral staircase).

• There is an average of 25 hydrogen bonds within each

complete turn of the double helix providing a stability of
binding about as strong as what a covalent bond would
provide.

• The diameter of the helix is 20 Å.

Nucleotides are linked in a chain through the sugars and
phosphates
 Double helix of DNA (contd.)
• 3.4 Å separate the planes in which adjacent base
pairs are located.

• The double helix makes a complete turn in just

over 10 nucleotide pairs, so each turn takes a little
more (35.7 Å to be exact) than the 34 Å shown in
the diagram.

• In 1962 Watson and Crick shared a Nobel Prize

with Wilkins (+ Franklin) For DNA structure..
SRUCTURE OF D.N.A.
Basic Structure

Phosphate
 O

O CH3 Sugar + Nitrogenous Base O

-O
H P
-O P O
Phosphate
C
O*
****** H N
NucleosideN CH
H O
groupC
HC
O T N H *** Nitrogen C
C
H C3 H
N
C
* * * * N
base A C N C1
H H
H 2C
C5 O Deoxyribose
Sugar +CNitrogenous Base + O H 2C
C5
C1 O N
H H sugar
Thymine Phosphate group
H C3 H H Adenine O
H -O
O H H O
P
-O N H* Nucleotide
P O C
C
****** O H O
2.90A N
O HC
C N C
C
CH H C3 H
N ******* H H
C H N
G C1
H 2C
C5
H
O
SRTUCTURE
H C1
* * *
Cytosine *** *
OF DNA O
3.00A

H N
C
N
C N O H 2C
C5

H C3 H 2.90A Guanine O
H -O
O H CH3 O
2.80A H P
O*
-O P O C ****** H N H O
C N
HC
O T N H 3.00A
*******
C
C
CH H
H
C3
H
H
N N
H 2C5
C O
C A C N C1
C
O H 2C
C5
C1 O N
H H
H C3 H
Thymine H Adenine O
-O
O H O
P
-O
O
P
Hydrogen bonds O

O
 Basic Structure Implications
• DNA is (-) charged due to phosphate

• H-bonds form between specific bases: C-G

bound tighter than A-T due to triple H-bond

• DNA-protein interactions (via major & minor grooves):

transcriptional regulation

• DNA polymerization:
5’ to 3’ – phosphodiester bond formed between 5’ phosphate
and 3’ OH
 DNA by the numbers
• Each cell has about 2 m of DNA.
• The average human has 75 trillion
cells.
• The average human has enough DNA
to go from the earth to the sun more
than 400 times (The earth is 150
billion m or 93 million miles from
the sun).
• DNA has a diameter of only
0.000000002 m.
 DNA STRUCTURE
• 1o Structure - Linear array of
nucleotides
• 2o Structure – double helix
• 3o Structure - Super-coiling,
stem-loop formation
• 4o Structure – Packaging into
chromatin
 Determination of the DNA 1o
Structure (DNA Sequencing)
• Can determine the sequence of DNA
base pairs in any DNA molecule
Chain-termination method developed
by Sanger
• Involves in-vitro replication of
target DNA
• Technology led to the sequencing of
the human genome
 Chain Termination Method
• Based on DNA polymerase reaction
• 4 separate rxns
• Each reaction mixture contains dATP, dGTP,
dCTP and dTTP
• Each reaction also contains a small amount of
one dideoxynucleotide (ddATP, ddGTP, ddCTP
and ddTTP).
• Each of the 4 dideoxynucleotides are labeled
with a different fluorescent dye.
• Dideoxynucleotides missing 3’-OH group. Once
incorporated into the DNA chain, chain
elongation stops)
 Chain Termination Method
• Most of the time, the polymerase uses
normal nucleotides and DNA molecules
grow normally
• Occasionally, the polymerase uses a
dideoxynucleotide, which adds to the
chain and then prevents further growth
in that molecule
• Random insertion of dd-nucleotides
leaves (optimally) at least a few chains
terminated at every occurrence of a
given nucleotide
 Chain Termination Method
• Run each reaction mixture on electrophoresis gel
• Short fragments go to bottom, long fragments
on top
• Read the "sequence" from bottom of gel to top
• Convert this "sequence" to the complementary
sequence
• Now read from the other end and you have the
sequence you wanted - read 5' to 3'
 DNA Secondary structure
• DNA is double stranded with
antiparallel strands
• Right hand double helix
• Three different helical forms (A, B
and Z DNA.
 o
DNA 3 Structure
• Super coiling
• Cruciform structures
 Supercoils
• In duplex DNA, ten bp per turn of helix (relaxed
form)
• DNA helix can be over-wound.
• Over winding of DNA helix can be done by
supercoiling.
• Supercoiling present in circular DNA molecules and
within local regions of long linear DNA strands
• Enzymes called topoisomerases or gyrases can
introduce or remove supercoils
• In-vivo most DNA is negatively supercoiled.
• Therefore, it is easy to unwind short regions of
the molecule to allow access for enzymes
Each super coil compensates for one + or – turn of
the double helix
 Curciform structures
• Cruciforms occur in palindromic
regions of DNA
• Can form intra-chain base pairing
• Negative supercoiling may promote
cruciforms
 o
DNA 4 Structure
• In chromosomes, DNA is tightly
associated with proteins
 DNA STRUCTURE

STRUCTURE, FORCES AND TOPOLOGY

 DNA GEOMETRY
• A polymer of deoxyribonucleotides
• Double-stranded
• INDIVIDUAL deoxynucleoside TRIPHOSPHATES ARE
COUPLED BY PHOSPHODIESTER BONDS
– Esterification
– Link 3’ carbon of one ribose with 5’ c of another
– Terminal ends : 5’ and 3’
• A “double helical” structure
– Common axis for both helices
– “Handedness” of helices
– Antiparallel relationship between 2 DNA strands
 DNA GEOMETRY
• PERIPHERY OF DNA
– SUGAR-PHOSPHATE CHAINS
• CORE OF DNA
– BASES ARE STACKED IN PARALLEL FASHION
– CHARGAFF’S RULES
• A=T
• G=C
– “COMPLEMENTARY” BASE-PAIRING
 TAUTOMERIC FORMS OF
BASES
• TWO POSSIBILITIES
– KETO (LACTAM)
– ENOL (LACTIM)
• PROTON SHIFTS BETWEEN TWO FORMS
• IMPORTANT IN ORDER TO SPECIFY HYDROGEN
BONDING RELATIONSHIPS
• THE KETO FORM PREDOMINATES
 MAJOR AND MINOR
GROOVES
• MINOR
– EXPOSES EDGE FROM WHICH C1’ ATOMS EXTEND
• MAJOR
– EXPOSES OPPOSITE EDGE OF BASE PAIR
• THE PATTERN OF H-BOND POSSIBILITIES IS MORE
SPECIFIC AND MORE DISCRIMINATING IN THE
MAJOR GROOVE
– STUDY QUESTION: LOCATE ALL OF THE POSSIBILITIES
FOR H-BONDING IN THE MAJOR AND MINOR GROOVES
FOR THE 4 POSSIBLE BASE-PAIRS
 Functions of DNA
• Genetic Information Storage- It contains instructions
for the development, growth, and functioning of all living
organisms.
• Replication DNA – During cell division, each daughter
cell receives an identical copy of the genetic information.
• Gene Expression - DNA carries the instructions for
synthesizing proteins and other molecules essential for
the structure and function of cells.
DNA to mRNA to proteins.
This protein synthesis is critical for the functioning and
development of organisms.
 Functions of DNA
• Mutation and Genetic Variation - which is the basis for
evolution.
• Information Transfer - DNA to RNA
These RNA molecules are involved in various cellular
processes, such as protein synthesis and regulation of
gene expression.
• Cell Division - process is essential for growth,
development, and tissue repair in multicellular
organisms.
• Genetic Inheritance : Offspring inherit their genetic
information from their parents, with half of their DNA
coming from each parent.