DNA and its structure
• DNA or Deoxyribonucleic acid is the genetic material of most of
the living organisms (some viruses have RNA as the genetic
material).
• It is a polynucleotide, i.e., a polymer of nucleotides.
• A DNA nucleotide or deoxyribonucleotide comprises of 3
components:
(i) Nitrogenous base (A,T,G or C)
(ii) Deoxyribose (a pentose sugar)
(iii) Inorganic phosphate (phosphate group), (PO4)3-
• The structure of DNA was elucidated by James Watson & Francis
Crick. It is known as the Watson & Crick Double Helix after them.
• They published their research in Nature Journal in 1953 &
received a Noble Prize in 1962.
• Their research was supported by the X-ray diffraction pattern of
DNA given by Rosalind Franklin & Maurice Wilkins.
Structure of a deoxyribonucleotide
• In DNA nucleotide, the 9th N of Purines or the 6th N of Pyrimidines is joined to the 1st
OH (1’-OH) of Deoxyribose sugar by N-glycosidic linkage, a covalent bond.
• The 3’-OH of deoxyribose is attached to a phosphate group by ester linkage.
DNA Bases: Purines and Pyrimidines
Salient features of DNA Double Helix
• A DNA molecule comprises of 2 polynucleotides strands running in an
anti-parallel fashion.
• The first nucleotide of a DNA chain has a free 5’-CH2OH, thus it is known
as the 5’- end.
• The terminal end of a DNA chain has a free 3’-OH group, thus it is known
as the 3’-end.
• During formation of a polynucleotide chain, the 3’-OH group of first
nucleotide is joined to the 5’-CH2OH of the next, through a phosphate
group. This is known as a Phosphodiester linkage.
• Base Complementarity: In nucleic acids, a purine base always pairs with a
pyrimidine base through Hydrogen Bonds. The bases A & T are said to be
complementary to each other. Similarly, G & C are complementary.
Pairing occurs as follows:
A & T form 2 hydrogen bonds
G & C form 3 Hydrogen bonds
• The chain of nucleotides formed due to phosphodiester linkage forms
the sugar-phosphate backbone of DNA.
• Diameter of double helix: 20 e Å (2nm).
• DNA base pairs are arranged like steps of a ladder.
• Twisting of DNA double helix:
The DNA molecule has a central axis, around which the 2
polynucleotides strands are twisted at an angle of 36◦.
Every turn of the twisted helix has an angle of 360◦, covering a distance
of 34nm.
Each turn has around 10 base pairs (bp), thus the distance between 2
consecutive base pairs is ~3.4nm.
Each bp is slightly tilted w.r.t. to the next, at an angle of 3.6◦.
DNA molecule is negatively charged due to the presence of phosphate
groups.
This charge is neutralized by binding to positively charged Histone
proteins in Chromatin.
Major groove (12 Å ) and minor groove (10 Å)
Chargaff’s Rule
• The sum of purine bases in DNA is equal to the sum of pyrimidine
bases, due to base complementarity.
A+G =1
T+C
• This means, the %age of A is always equal to that of T.
• Likewise, the %age of G is always equal to that of C.
• The G+C content is an important criterion in determining the
Genome Size & evolutionary development of organisms.
• Higher GC content imparts stability to the DNA, since DNA with
higher GC has higher melting temperature (Tm)
• E.g.: In plants, monocots have a higher GC content than dicots.
Prokaryotes have a higher GC content than eukaryotes.
Complementary pairing between purines &
pyrimidines
Dna Double helix
A, B and Z DNA
Packaging of DNA