Primary structure of DNA

Polynucleotide chains are long, almost always un-branched polymer. A number of deoxyribonucleotides Eire
covalently linked one by one to form a polynucleotide chain, i.e., deoxyribonucleotide monomer units are the
building blocks of polynucleotide chain.

The successive deoxyribonucleotide units are covalently linked by phosphodiester bridges formed between the 5′
hydroxyl group of one nucleotide and the 3′ hydroxyl group of the next. This reaction also releases one molecule of
water.

Thus one by one deoxyribonucleotide joins by phosphodiester bond and, consequently, produces dimer, trimmer,
tetramer and so for in polymer which is known as polynucleotide. The backbone of polynucleotide chain consists of
alternating phosphates and pentose’s.

Secondary structure of DNA

In 1953 J. D. Watson and F. H. C. Crick proposed a precise three-dimensional model of DNA structure based on the X-
ray crystallography data of Franking and Wilkins and the base equivalences rule formulated by Chargaff.

The Watson-Crick model of DNA structure postulated that two right-handed polydeoxyribonucleotide chains or
strands are coiled in helical fashion around the same axis, thus forming a double helix.

 It consists of two polynucleotide chains where the sugar and phosphate group form the backbone and the
nitrogenous bases project inside the helix.

 The two polynucleotide chains have anti-parallel polarity i.e. if one strand has 5′ → 3′ polarity, the other
strand has 3′ → 5′ polarity.
  The bases on the opposite strands are connected through hydrogen bonds forming base pairs (bp). Adenine
always forms two hydrogen bonds with thymine from the opposite strand and vice-versa. Guanine forms
three hydrogen bonds with cytosine from the opposite strand and vice-versa. Therefore, a purine always
pairs with a pyrimidine on the other strand, giving rise to a uniform distance between the two strands of the
helix.

 The two strands coil in a right-handed fashion. Each turn of the helix is 3.4nm (or 34 Angstrom units)
consisting of 10 nucleotides. These nucleotides are at a distance of 0.34nm (or 3.4 Angstrom units).

 The helix is stable because of the base pairs that stack over one another and hydrogen bonds that hold the
bases together.

Structural forms of the double helix

The most common form of DNA which has right handed helix and proposed by Watson and Crick is called B-form of
DNA or B-DNA. In addition, the DNA may be able to exist in other forms of double helical structure. These are A and
Z forms of double helix which vary from B- form in spacing between nucleotides and number of nucleotides per turn,
rotation per base pair, vertical rise per base pair and helical diameter.

Besides these three form there are C form D form also present

B-Form of DNA (B-DNA):

Structure of B-form of DNA has been proposed by Watson and Crick. It is present in every cell at a very high relative
humidity (92%) and low concentration of ions. It has antiparallel double helix, rotating clockwise (right hand) and
made up of sugar- phosphate back bone combined with base pairs or purine-pyrimidine. 10 base pairs present per
turn

The base pairs are perpendicular to longitudinal axis of the helix. The base pairs tilt to helix by 6.3°. The B-form of
DNA is metabolically stable and undergo changes to A, C or D forms depending on sequence of nucleotides and
concentration of excess salts.

A- DNA

A-DNA is one of the possible double helical structures which DNA can adopt. A-DNA is thought to be one of three
biologically active double helical structures along with B-DNA and Z-DNA. It is a right-handed double helix fairly
similar to the more common B-DNA form, but with a shorter, more compact helical structure whose base pairs are
not perpendicular to the helix-axis as in B-DNA. It was discovered by Rosalind Franklin, who also named the A and B
forms. She showed that DNA is driven into the A form when under dehydrating conditions. Such conditions are
commonly used to form crystals, and many DNA crystal structures are in the A form. 11 base pairs present per turn.

Z- DNA

Z-DNA is one of the many possible double helical structures of DNA. It is a left-handed double helical structure in
which the helix winds to the left in a zigzag pattern, instead of to the right, like the more common B-DNA form. Z-
DNA is thought to be one of three biologically active double-helical structures along with A- and B-DNA. Having 12
base pairs per turn

C- DNA

C-DNA also known as C form DNA. It is one of the many possible double helical structures of DNA. This form of DNA
can be observed at some conditions such as relatively low humidity and the presence of certain ions, such as Li+ or
Mg2+.

D- DNA

The D-form of DNA is found rarely as extreme vanants. Total number of base pairs per turn of helix is eight.
Therefore, it shows eight-fold symmetry. This form is also called poly (dA-dT) and poly (dG-dC) form. There is
pronounced negative tilt of base pairs by 16.7° as compared to C form i.e. the base pairs are displaced backwardly
with respect to the axis of DNA helix.