Nucleic Acids

DNA RNA
(deoxyribonucleic acids) (ribonucleic acids)

Central Dogma of Biology

DNA RNA Proteins Cellular Action

replication

transcription translation
DNA
DEFINITION: - NUCLEIC ACID

Nucleic acid is macromolecule with acid property & it

was isolated from the nucleus of cells & hence it is named
as nucleic acid. It is made up of C, H, O, N & P.

•The nucleic acid was first

isolated in 1868 by
Miescher from nuclei of
our cell. He called it
nuclein.

•Altmann (1889) gave

Friedrich Miescher
name nucleic acid.
 The Building Blocks of DNA

Nucleotide

Nucleotides have Purine or

three components:- Pyrimidine
O Base
Nitrogenous
5'
Base -O P O -N-glycosidic bond
O
1'
Five – carbon O- 4'
H H

sugar H 3' 2' H

O H(OH)
Phosphate
Phosphate
Pentose sugar

Nucleoside
PYRIMIDINE
PURINES
 DNA and RNA nucleobases

NH2 O

7 6
N 5 1 N N
N N NH
8

4 2 N N
9N N N H
N NH2
H H
3
Purine Adenine (A) Guanine (G)
NH2 O
O
4
5 3 H3C
N N NH
NH

6 2
N1 N O N O
H N O
H H H

Pyrimidine Cytosine (C) Thymine (T) Uracil (U)

(DNA only) (RNA only)
 NUCLEOSIDES
Nucleosides are composed of ribose or deoxyribose and
a nitrogenous purine or pyrimidine base

In each nucleoside, a B – N glycosidic bond connects C

– 1 of the sugar to N – 1 of the pyrimidine or N – 9 of the
purine.

BASE RIBONUCLEOSIDE DEOXYRIBONUCLEOSIDE

Adenine Adenosine Deoxy adenosine
Guanine Guanosine Deoxy guanosine
Cytosine Cytidine Deoxy cytidine
Uracil Uridine (Rarely found)
Thymine (Rarely found) Deoxy thymidine
 Preferred conformations of nucleobases and sugars in
DNA and RNA
NH2 NH2

N N

HO N O O N
HO
O
O

OH
OH
Anti conformation Syn conformation

Sugar puckers:
5.9 A
HO HO HO
BASE 3' BASE
5' 2' 5'
O 1' O 1'
7.0 A 3' H (OH)
HO H (OH)
2' endo (B-DNA) 3' endo (RNA)
 Nomenclature of nucleobases, nucleosides,
and mononucleotides

nucleobase (Deoxy) 5’-mononucleotide

nucleoside

Adenine (A) 2’-Deoxyadenosine Deoxyadenosine 5’-monophosphate

(dA) (5’-dAMP)
Guanine (G) 2’- Deoxyguanosine Deoxyguanosine 5’-monophosphate
(dG) (5’-dGMP)
Thymine (T) 2’- Deoxythymidine Deoxythymidine 5’-monophosphate
(dT) (5’-dTMP)
Cytosine (C) 2’- Deoxycytidine Deoxycytidine 5’-monophosphate
(dC) (5’-dCMP)
Uracil (U) Uridine (U) Uridine 5’-monophosphate (5’-UMP)
 Nucleosides Must Be Converted to
5’-Triphosphates to be Part of DNA and RNA

O
HO
HO P O Base
Base
O Kinase HO O
ATP
OH OH
Monophosphate

ATP Kinase

O O O O O
HO P O P O P O HO P O P O
Base Kinase Base
HO OH OH O HO OH O
ATP
OH OH
Triphosphate Diphosphate
 Linking in DNA biopolymer: DNA primary structure

DNA is
Arranged
5’ to 3’
Connected by
Phosphates
Structural differences between DNA and RNA

DNA RNA

O O

H3C
NH NH

N O N O
H H
Thymine (T) Uracil (U)

HO CH2 HO CH2
O Base O Base
H H H H
H H
H H
O H O OH

2'-deoxyribose ribose
 Structure of DNA

The correct structure of DNA

was first deduced by J.D.
Watson & F.H. C Crick in
1953.
 X Ray Diffraction Studies

X ray diffraction studies showed that:

 DNA Polymers are helical

 It has two periodicities primary one of
0.34n.m. and secondary one of 3.4
n.m.
 It also indicated that the molecule
contains two strand

Thus the X ray diffraction studies

indicated that DNA was an ordered
structure
Maurice Wilkins
Chargaff's Rule
Chargaff's Rule
• Erwin Chargaff’s studies and subsequent
investigations led to the establishment of
following conclusions:

1.DNA Specimen isolated from different tissues

of the same species have the same base
composition

2. The base composition of DNA varies from one

species to another

3. The base composition of DNA in a given species

does not change with age, nutritional state or
the environmental change
Watson and Crick
Watson and Crick
 Forces stabilizing DNA double helix

1. Hydrogen bonding (2-3 kcal/mol per base pair)

2. Stacking (hydrophobic) interactions (4-15 kcal/mol per

base pair)

3. Electrostatic forces.
Alternative Forms of DNA
 Alternative Forms of DNA
Characteristics Features
A B Z
Helix sense Right handed Right handed Left handed
Residue per turn 11 10 (10.4) 12
Rise per base pair 2.560 A 3.380 A 3.710 A
Rotation per base pair +32.70 +36.00 300
Helical Diameter 230 A 200 A 190 A
Anti for CT
Glycosidic bonds anti anti
Syn for GA
Pitch per turn 280 A 340 A (33.8) 45.60 A
Tilt per bases from 190 90
1.20
normal to helix axis
Shape Broadest Intermediate Most Elongated
Wide and Quite
Major Grooves Narrow and very deep Flat
deep
Very broad and Narrow and Quite Very narrow very
Minor Grooves
Shallow Deep deep
75% relative humidity 92% -
Conditions
High Salt Conc. & ions Low Ions High Salt Conc.
 The sugar puckering in A-DNA is 3’-endo

5.9 A

O
5' 2' BASE
O O
O 3' BASE
1' 5'
7.0 A 3' H (OH) O 1'
O 2'
H (OH)
2' endo (3' exo) B-DNA 3' endo (A-DNA)
 B-DNA
23.7 A
•Sugars are in the 2’ endo
right handed helix conformation.
HO
• helical axis passes through 5' 2' BASE

base pairs O 1'

7.0 A 3' H (OH)
HO
• planes of bases are nearly
perpendicular to the helix axis. •Bases are the anti conformation.
NH2
• 3.4 A rise between base pairs
N

Wide and deep HO N O

O

OH
•Bases have a helical twist of 36º
(10.4 bases per helix turn)
Narrow and deep
• Helical pitch = 34 A
 A-form helix: dehydrated DNA; RNA-DNA hybrids

Right handed helix

•Sugars are in the 3’ endo
conformation.

• planes of bases are tilted

20 ° relative the helix axis.
•Bases are the anti conformation.

• 2.3 A rise between base pairs

25.5 A •11 bases per helix turn

• Helical pitch = 25.3 A

Top View
 B-type duplex is not possible for RNA

HO CH2
O Base
H H
H
H
O OH

ribose

steric “clash”
 A-DNA has a shallow minor groove
and a deep major groove

Major groove

N O H2N
Major groove

e N NH• N Helix axis •

bos N To d O H2N
i N eo N
x yr xy
o NH2 O rib
de os
e e N NH N
To Minor groove os N To d
ir b N eo
y xy
e ox NH2 O rib
os
d e
To Minor groove

B-DNA A-DNA
 Z-form double helix: polynucleotides of alternating purines and
pyrimidines (GCGCGCGC) at high salt

Left handed helix • Backbone zig-zags because sugar

puckers alternate between 2’ endo
pyrimidines and 3’ endo (purines)

• planes of the bases are

tilted 9° relative the helix • Bases alternate between anti
axis. (pyrimidines) and syn conformation
(purines).
• 3.8 A rise between base pairs

•12 bases per helix turn

18.4 A • Helical pitch = 45.6 A

• Flat major groove
• Narrow and deep minor groove
Sugar and base conformations in Z-DNA alternate:
5’-GCGCGCGCGCGCG
3’-CGCGCGCGCGCGC

C: sugar is 2’-endo, base is anti

G: sugar is 3’-endo, base is syn

NH2
O

N HN

H2N N
HO
N O
5' 2' N
HO HO
O 1' 3' N
5'
3' H
O 1'
HO

C G H
B A Z
Sructural Parameter A-DNA B-DNA Z-DNA
Direction of helix
Right handed Right handed Left handed
rotation
Residue per helical
11 10.5 12
turn
Axial rise per residue 2.55 Å 3.4 Å 3.7 Å
Pitch (length) of the
2.82 Å 34 Å 44.4 Å
helix
Base pair tilt 20° -6° 7°
Rotation per residue 32.7° 34.3° -30°

Diameter of helix 23 Å 20 Å 18 Å
Configuration dA, dT,
anti anti anti
dC
of glycosidic bond dG anti anti syn
Sugar Pucker dA, dT,
C3' endo C2' endo C2' endo
dC
dG C3' endo C2' endo C3' endo
 Alternative Forms of DNA

Figure : B-form (left), A-form (middle) and Z-DNA (right).

Comparisons of B-form, A-form and Z-DNA
Any Questions?????

Thank you
 Question

• DNA was extracted from cells of

• Staphylococcus and found to have 37%
• cytosine. What percent of guanine does
• this species have?
• 1) 37%
• 2) 13%
• 3) 74%
• 4) 26%
 Question
• What percent of thymine does this
• species have?
• 1) 37%
• 2) 13%
• 3) 74%
• 4) 26%