STRUCTURE OF NUCLEIC ACIDS :

DNA (DE-OXY RIBO NUCLEIC ACID

)

By Dr. Ichha Purak

University ProfessorDepartment of Botany

Ranchi Women’s College,Ranchi

http://www.dripurak.com/

Discovery of DNA Friedrick Miescher (1869) , a Swiss chemist first identified

nuclein from nuclei of human white blood cells which was later

on renamed as Nucleic acid . It was rich in phosphorus having

no sulphur so was different than protein.

Russian Biochemist Phobebus Levene (1910) is credited to

discover Phosphate-Sugar-Base as three components of

Nucleotide . He also mentioned DNA as polynucleotide (Any one

of four adenine,Cytocine,Thymine /Guanine ).

He also stated difference between Ribose and Deoxyribose Sugar• From

HISTORY OF DNAHISTORY OF DNA William Astbury (1938) detected a periodicity of 3.4 angstroms

Rosalind Franklin (1952) performed - X- ray diffraction analysis of DNA crystal

Franklin and Wilkins (1950-1953) confirmed 3.4 periodicity and noted uniform diameter of 20A○ (2nm)

The images of DNA taken by Franklin gave clue to Watson and Crick about the width of double helix and spacing of N-bases

Watson and Crick (1953 ) proposed the DNA double helical model based on Franklin’s X-ray crystallography Analysis and other evidences

1962: Nobel Prize in Physiology and Medicine

James D.Watson

Francis H.Crick

Maurice H. F.Wilkins Rosalind Franklin

X-ray Crystallography of DNA by Franklin and Wilkins(1950-52) showing helical symmetry

Franklin’s X ray diffraction Photograph of DNA

•DNA is one of the two nucleic acids ( RNA and DNA )

•DNA is long, unbranched and spirally coiled in Eukaryotes and circular in prokaryotes as well as mitochondria and plastids

• In Prokayotes DNA is present only in Nucleoid and is Monocistronic, but in Eukaryotes DNA is present in Nucleus, Mitochondria and Plastids and is Polycistronic.

•DNA is genetic material ,carries heredity characters over generations through DNA Replication ( DNA DNA )and Transcription ( DNA RNA ) followed by Translation

•Nucleic Acids are fibre like molecules ( Length is many times the breadth )

•Nucleic Acids are polymers of Nucleotides.

•DNA is a macromolecule of high Molecular Weight •Nucleotides consists of sugar, Phosphoric Acid and bases ( Purine /Pyrimidine)

•

POLYNUCLEOTIDE

J D Watson and Francis Crick (1953 ) have

proposed a double helical structure (Model)

of DNA , for which they have received the

Nobel Prize of 1962.

According to this Model some facts about DNA are as

follows :

DNA has a double helical structure made by

twisting around of 2 very long thin polymeric strands

around a common (imaginary) axis.

The original DNA model by Watson and Crick. Photo: Cold Spring Harbor Laboratory Archives

Imaginary axis is shown by a line passing through the centre longitudinally

DNA has two sugar phosphate back bones with paired bases in between

DNA Double Helix

Two strands are antiparallel in their back bones, complementary in sequence of bases and are joined by Hydrogen (H) bonds

OO=P-O O

PhosphatePhosphate GroupGroup

NNitrogenous baseNitrogenous base (A, G, C, or T)(A, G, C, or T)

CH2

O

C1C4

C3 C2

5

SugarSugar(deoxyribose)(deoxyribose)

Each strand is polymer of deoxy ribonucleotides having phosphate ,sugar and N-base

1

2

3

4

5

6

Each Deoxyribonucleotide is made up of a Deoxyribose sugar, a phosphate, a Nitrogenous Base, which may be either a Purine or Pyrimidine

Deoxy ribose sugar has formula C5 H10 O4 and is derived from Ribose sugar C5H10O5 by loss of one oxygen atom at C-2 position

Phosphate (PO4) is derived from Phosphoric acid (H3PO4)

Figure : Nucleotides have three components.A nucleotide consists of a phosphate group, a pentose sugar (ribose or deoxyribose), and a nitrogen-containing base, all linked together by covalent bonds. The nitrogenous bases have two different chemical forms: purines have two fused rings, and the smaller pyrimidines have a single ring.© 2008 by Sinauer Associates, Inc. All rights reserved. Used with permission.

17

Deoxyribose – C5 H10 O4

Ribose- C5H10O5

Adenine-6-amino PurineGuanine- 2-amino 6 oxy Purine Cytocine- 6- amino pyrimidineThymine- 5- methyl 6 oxy pyrimidineUracil- 6-oxy pyrimidine

Nitrogenous Bases are either Pyrimidine -6 membered ring (Basic Skeleton 4C-2N ) or Purine- two rings (Basic Skeleton 5C-4N ) .

Cytosine ( C ) and ( T ) are pyrimidines of DNA and Adenine ( A ) and Guanine (G ) are the Purines of DNA

In a deoxyribonucleotide phosphate is attached at C-3 or C-5 of deoxy ribose sugar and base is attached to

C-1 of sugar

A) Sugar+ Base forms Nucleoside ( S-B )

B) Sugar + Base + Phosphate forms Nucleotide ( P-S-B )

Sugar and Phosphate of the nucleotides are linked together forming exterior of frame work of the strands.

PO4 are linked between two sugar molecules at C3 & C5 position by formation of Phosphodiester bonds. PO4 are exposed to exterior as they are ( - ) vely charged and are hydrophilic.

In DNA deoxyribo nucleotides are held together by phosphodiester bonds.

What chemical forces hold the two DNA strands together? Two strands are connected to each other by means

of base pairing which comprise the steps of the

ladder. Base pairing takes place between one purine

and one pyrimidine by H bonds. Although H bonds

are weak but many H bonds give stability to the

double helical structure.

The two strands of DNA are oriented in opposite

directions. One strand runs in 3’-5’ direction and the

other in 5’-3’ direction. This antiparallel orientation also

supports the double helical nature of DNA molecule.

There lies close similarity of measurements of AT and

GC pairs, distance of A-T is about 1.11 nm and that of

G-C is 1.08nm. The angle between C-1 of deoxyribose

sugar and N of base is about 51°.

Base Pairing

• Hydrogen bonds

Individually weak electrostatic bonds but collectively become strong and provide stability to double helix

Hydrogen bonds between bases

Also important that the purine-pyrimidine base pairs are of similar size.

DNA strands also held together by base stacking:

Van der Waals interactions with neighboring base

pairs

The evidence for this opinion is based on interference

by urea and foramide ,are unable to separate double

strand themselves but require heat in addition

Double stranded helix structure is also promoted by

having phosphates on outside ,interact with water and

K+ and Mg+ +

ions

30

Bases are projected inwards and lie perpendicular to the long sugar & phosphate chains.

Bases are attached to C -1 of sugar and for attachment N at 3 position of pyrimidine and N at 9 position of Purine is used.

During base pairing Adenine always pairs with Thymine by 2 H bonds and Guanine pairs with Cytosine b y 3 H bonds. A=T G Ξ C

Diameter of double helical structure is constant because of strict pyrimidine (small ) and Purine (large ) base pairing. Diameter of B- DNA is 20 A ° (2 nm)

For one complete turn 34 A° space is required and 10 bp (base pairs ) are present in each complete turn. Each base pair lies at an angle of 36 ° from next base pair

Two strands of DNA run in antiparallel direction. One in 3’ 5’ direction and other in 5’ 3’ direction. The direction depends on attachment of first PO4 group to C3 or C5 of deoxyribose sugar.

Two strands are coiled around a common axis in such

a way ( like a rope ) that deep (major ) and shallow

(Minor) grooves are resulted. Proteins can bind with

DNA at these locations. Major grooves are 22A° and

Minor grooves are 12 A°

34 Å

3.4 Å

20 Å

MinorGroove

MajorGroove

GC

CG

AT

TA

CG

GCAT

TA

TA

AT

GCCG

GC

Strands areantiparallel

Two strands are coiled around each other in such a way that they can not be separated unless ends are permitted to revolve ( just like a rope ) Such coiling is known as Plectonic coiling.

Due to strict base pairing rules , two strands are complementary to each other in sequence of bases. This feature helps in determining heredity through DNA Replication and Transcription.

• DNA code consists of only 4 symbols A T G C

Erwin Chargaff (1949-1953) Digested many

DNAs and subjected products to chromatographic separation RESULTS

The sum of Purines is equal to sum of Pyrimidines

A = T, C = G , A + G = C + T (purine = pyrimidine) but A+T ≠ G +C ( Not equal )

Base ratio A + T/ G+C varies from one species to other and is not always equal to one but is constant for a species.

Chargaff’s RuleChargaff’s Rule AdenineAdenine must pair with ThymineThymine

GuanineGuanine must pair with CytosineCytosine

The amount of Adenine must be equal to amount of Thymine and amount of Guanine must be equal to Cytosine in a given DNA molecule

G CT A

Figure : Chargaff's rule.In DNA, the total abundance of purines is equal to the total abundance of pyrimidines.© 2008 by Sinauer Associates, Inc. All rights reserved. Used with permission

DNA with high percentage of G ≡ C pairing ( Mitochondrial DNA ) have more density

than those with high A = T pairing. (Nuclear DNA )

Upon heating upto 80-90 º C or more 2 strands of DNA uncoil and separate

( DNA Denaturation ). On cooling the strands come closer and are held together ( DNA Renaturation or Annealing ) The two separated strands can act as template for synthesis of new complementary strand.This property is used in PCR ( Polymerase Chain Reaction) which is in vitro process for DNA amplification

DNA is generally double stranded, but is single stranded exceptionally in some Viruses viz. ȹ- 174 & S-13

Both strands of DNA are right handed spirals except Z DNA ( Left handed spiral )

Alternative Forms of DNA

DNA can exist in several conformational isomers

B form is the “normal” conformation

A form is found in high salt conc

Z form Left-handed helix and 12 bp/turn (Z for zigzag)

DNAs are of various types A B C D E & Z , of which B DNA is the most common form . The different types of DNA differ in number of base pairs per turn, pitch, angle, diameter of Helix and handed ness etc.

TYPE HANDED NESS

BASE PAIRS /TURN

PITCH DIAMETER

AngleBetween 2 bp

A RIGHT 11 28º 23Aº 32.7º

B RIGHT 10 34º 20Aº 36º

Z LEFT 12 69º 18Aº 30º

C RIGHT 9.33 31º 19Aº 38.6º

TYPES OF DNA

A11

B 10

Z12Residues/Turn

Clock -wiseTurn Anti Clock-wise Turn

Figure : DNA can assume several different secondary structures.These structures depend on the base sequence of the DNA and the conditions under which it is placed.

Used with permission. © 2005 by W. H. Freeman and Company. All rights reserved

Right vs. Left Handed Helices

B Z

DFFERENCES BETWEEN DNA AND RNA

S N DNA RNA

1 DNA is polymer of Deoxyribonucleotides

RNA is polymer of Ribonucleotides

2 DNA has Deoxyribose sugar RNA has Ribose sugar3 Deoxyribose Sugar has OH- only

at C3 & C5Ribose sugar (C5H10O5) has OH- at C2,C3 &C5

4 DNA is Generally Double Stranded Exception In Bacteriophage Ф- 174 and S-13

RNA is generally single stranded Exception tRNA & rRNA at some places are double stranded

5 DNA has Pyrimidines Cytosine and Thymine

RNA has Pyrimidines Cytosine and Uracil

6 DNA is Genetic Material RNA generally Non Genetic but in some Viruses it is Genetic Material

7 DNA is stable in alkaline condition RNA is not stable8 DNA is Synthesized by Replication

using both strands of DNA as templates during Interphase

RNA is synthesized by transcription using one strand of DNA as Template

9 A- T and C-G are the Base Pairs In helical regions A-U and C-G are the Base Pairs

10 The helix geometry of DNA is of B-FormProtects itself against enzymes

The helix geometry of RNA is of A-FormIs destroyed by enzymes and produced again

11 DNA performs long term storage and transfer of Genetic Information

RNA performs the function of a messenger between DNA and the proteins.

.

RIBOSE

1

OHOCH2

H

H

OH

H

OH

H

OH23

4

5OHOCH2

H

H

OH

H

OH

H

H

1

23

4

5

2-DEOXY-RIBOSE

O N

H N

O

H

CH3

THYMINE

O N

H N

O

H

URACIL

RNA DNA

Molecular Differences between Ribonucleic Acid (RNA)& 2-deoxy-ribonucleic acid (DNA).

Ribose replaces deoxyribose; uracil replaces thymine

RNA

Nucleosides and Nucleotides

SUMMARY OF THE PRESENTATION DNA STRUCTURE

DNA ( De oxy Ribo Nucleic Acid ) is one of the two

Nucleic Acid

The Repeating Units of DNA are De-oxy Ribonucleotides

Each Deoxy Ribonucleotide has 3 components Deoxy

Ribose Sugar, Phosphate and Any one N Base ( A/G/T/C)

DNA is double helical in Nature , two strands are coiled

around a common imaginary axis

Double helical structure is like a ladder having steps

made by base pairs which are projected inwards

Successive De oxy ribonucleotides are linked with

each other by Phospho diester bond which is formed

by linkage of phosphate with two OH groups of two

sugar residuesAmount of Purines is always equal to amount of

Pyrimidines(Charguff’s Rule)

Adenine always pairs with Thymine by two Hydrogen

bonds and Guanine always pairs with Cytosine by three

Hydrogen bonds

Two strands run in opposite directions.

Two strands are complementary to each other in

sequence of bases because of strict base pairing rules ,

A=T, G Ξ C. This feature helps in maintaining the

diameter of double helix constant ( Pyrimidine→Purine

Pairing) and also making DNA as Genetic Material

through Replication and Transcription.DNA with high percentage of G ≡ C pairing ( Mitochondrial DNA )

have more density than those with high A = T pairing. (Nuclear DNA )

DNA with high percentage of G ≡ C pairing ( Mitochondrial DNA )

have more density than those with high A = T pairing. (Nuclear DNA )

DNA may have millions of Nucleotides

PART OF DNA DOUBLE HELIX

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