Module 6 : Structure and Functions of Nucleic Acids

DNA-structure, properties and function

Structure of DNA :

• The discovery of DNA structure is one of the hall mark of the modern molecular biology.

• Based on the assumptions of Chargoff and utilizing X-ray diffraction data, obtained from
crystals of DNA by Rosalind Franklin and Maurice Wilkins, James Watson and Francis Crick
proposed a model for the structure of DNA in 1953.

• They established that DNA has a double helical structure comprising of two complementary
antiparallel polynucleotide strands, wound around each other in a rightward direction.

• The backbone of the helix is sugar-phosphate and the bases are in the interior of the helix and
extended at 900perpendicular to the axis of the helix. Bases from opposite helix pair with each
other. Purines form base pairs with pyrimidene as a thumb rule- A will pair with T, and C with G.
According to this pattern, known as Watson-Crick base-pairing.

Specific features of DNA structure :

• It is double helical structure. One polynucleotide chain forms one strand. Two such strands
form double helix.

• Chain has sugar phosphate backbone and the bases are arranged perpendicular to the chain.

• Two strands are antiparallel to each other: one in 5' ---> 3' direction and the other in the 3' ---
> 5' direction.

• A and T ; and G and C occur as complementary and form base pair with corresponding
complementary base in opposite strand.

• One turn of the helix is 36 A and 10 base pairs are found per turn with rise of 3.6A.

• On the surface of double helix two deep grooves are found which are called major and minor
grooves.

• Helix is right handed along the axis.

The bases pairs are hydrogen bonds with each other and impart stability to the structure. The
base-pairs composed of G and C contain three H-bonds, whereas those of A and T contain two H-
bonds. For this reason G-C base-pairs are stronger than A-T base-pairs. The outcome will be that
DNA having more GC base pairs will be more stable than the one having more AT pairs.

• Bases are stacked over each other in the double helix.

• Hydrophobic interactions between stacked bases also stabilize the DNA.

• The sugar phosphate backbone of each strand is negatively charged (due to phosphate group
(pKa being near to zero). These charges are stabilized by Mg2+.

Various conformations of DNA :

• One of the properties of the DNA is that it shows conformational flexibility, and could exist in
alternative structural forms. The Watson-Crick structure is the B-form DNA or B-DNA.

• The B from is the most stable structure for a random sequence DNA molecule under
physiological conditions and is therefore “the standard point of reference in any study of the
properties of DNA”.The B-DNA predominates in the cell.

• There are two other structural variants of DNA that have been well characterized in crystal
structures. They are the A-DNA and Z-DNA. These DNA variants differ in their helical sense,
diameter, base pairs per helical turn, helix rise per base pair, base tilt normal to the helix axis,
sugar pucker conformation, and glycosyl bond conformation.

Dimensions of different DNA :