Question

Describe how the various weak interactions together give the double helical structure of B-DNA.

Answer 1

Variation in the conformation of the nucleotides of DNA is associated with conformational variants of DNA. There are 6 different forms of DNA A, B, C, D, E and Z. Among these B, A and Z forms are important. The B form of DNA double helix which was described by Watson and Crick is the most predominant form under physiological conditions.

Each turn of the B form has 10 base pairs spanning a distance of 3.4 nm and double helix has a width of 2 nm. The base pairs are perpendicular to the axis of the helix. Each base pair is centered on the helix axis, so that when viewed from above, all cross each other, in projection at the central axis.

The two strands of B-DNA are held together by a number of weak interactions like Hydrogen bonds, stacking interactions and hydrophobic effects. Among these, the stacking interactions between nitrogeneous bases are the most significant interactions.

The strength of base stacking is dependent on the bases which is strongest for stacks of Guanine-Cytosine base pairs and weakest for stacks of Adenine-Thymine base pairs.

The hydrophobic effect stacks the bases on top of one another. The stacked base pairs attract one another through Van der waals forces. Apart from this, base stacking in DNA is favored by the conformations of rigid five membered rings of phosphate sugars in the backbone. The base stacking interactions, which are mainly non specific with respect ot the identity of the stacked base, make the major contribution to the stability of the double helix and gives its puckered structure.