This document summarizes the structure of DNA. It describes that DNA is composed of polynucleotide chains containing nucleotides with pentose sugars, phosphate groups, and nitrogenous bases. The two strands of DNA run in opposite directions and are held together through hydrogen bonding between complementary purine-pyrimidine base pairs. The Watson-Crick model established that DNA forms a right-handed double helix with the bases stacking internally and the sugar-phosphate backbones forming the exterior spiraling strands.

1. Structure of DNA
BIBHU PRASAD RATH
LECT. IN BOTANY

2. What is DNA; Why it is there
• DNA is a type of nucleic acids.
• These are the structures those control the
quality and quantity of protein synthesis in
organisms.
• These are present both inside and outside
(mitochondria, chloroplast) the nucleus.
• These biomolecules carry genes those are
coded informations.

3. Components of DNA
Polynucleotide chains of DNA carry nucleotides as monomers. Nucleotide
comprises;
a. Pentoses
The ribose sugar in DNA is a 2 deoxyribose.
b. Nitrogenous bases
These are heterocyclic, planner, relatively water insoluble aromatic
molecules. These are; pyrimidines and purines
c. Phosphate [PO4
3-]
It is an ion of phosphoric acid [H3PO4]. Phosphate groups are found in every
nucleotide. As these carry negative charges frequently DNA is acidic.
These can be attached to the 3̕̕ or 5̕ C of the pentose.

4. Pyrimidines;
Single ring compounds, nitrogen in 1 and 3
positions of a benzene ring. In DNA two
types of pyrimidines are found
1. Thymine ; 5-methyl, 2,4-dioxy pyrimidine
2. Cytosine ; 2-oxy, 4-amino pyrimidine
Purines ;
Double ring compounds, comprise a five
membered imidazole ring and a
pyrimidine ring joined at 4th and 5th
position. These are of two types
1. Adenine ; 6-amino purine
2. Guanine ; 6-oxy, 2-amino purine

5. Watson-Crick model
This model is based on the crystallographic studies
• DNA is a helically twisted double stranded macromolecule.
• The two strands are antiparallel to each other.
• Spirally twisted DNA has two types of alternative grooves i.e. major and minor.
• One turn of DNA has about 10 base pairs with a length of 34Å. Hence each base pair has a
pitch of about 3.4 Å.
• The sugars are joined together by phosphate groups that form phosphodiester
bonds between the third and fifth carbon atoms of adjacent sugar rings.
• Glycosidic Bond - In DNA, refers to the nitrogen-carbon linkage between the 9' nitrogen of
purine bases or 1' nitrogen of pyrimidine bases and the 1' carbon of the sugar group.
• The two strands are held together by weak hydrogen bonds. The two strands are
complementary as the purines lie opposite to pyrimidines. Adenine forms two hydrogen
bonds with thymine and cytosine forms three bonds with guanine.
• Purine-pyrimidine pairing is about 20 Å thick.

6. ADENINE AND THYMINE BONDING

7. GUANINE AND CYTOSINE BONDING

8. Special characters of DNA
• DNA is composed of polynucleotide chains
• Two strands of the double helix are wound around each other in an anti-parallel orientation and
have complementary sequences
• Double helix is stabilized by base pairing and base stacking
• Base can flip out from the double helix
• DNA is usually right handed double helix
• Double helix has major and minor grooves
• Major groove is rich in chemical informations
• Double helix exists in multiple conformations
• DNA sometimes can form a left handed helix
• DNA can denature and reassociate
• Some DNA molecules are circular

9. Types of DNAs
A - DNA B - DNA Z - DNA
• COILING IS RIGHT HANDED
• PITCH OF A HELIX TURN 28Å
• MEAN BASE PAIR PER TURN 11
• RISE PER BASE PAIR 2.3Å
• DIAMETER 26Å
• RIGHT HANDED
• 34Å
• 10
• 3.4Å
• 20Å
• LEFT HANDED
• 45Å
• 12
• 3.8Å
• 18Å

10. Factors affecting DNA stability
This stability is important because it prevents the two DNA strands from breaking
apart spontaneously and plays an important role in the way DNA is copied.
a. Hydrogen bonding
It contributes a little to the stability.
b. Base stacking interaction
Base pairs stack together through Van der Waal force of attraction. It contribute
significantly to the overall stability.
c. Ionic interaction
Arrays of negative charges of the phosphate groups along the strands repel each
other to keep the complementary backbones apart. Negative charges are on
the exterior surface to minimize this repulsive effect. Divalent cations like
Mg2+ bind to these anionic phosphates to shield them from one another.

11. MOLECULAR BIOLOGY BY JAMES D. WATSON
STRUCTURE OF DNA