Amide protein exchange and surface conformation of the basic pancreatic trypsin inhibitor in solution. Studies with two-dimensional nuclear magnetic resonance

Dickerson and his colleagues have described the structure of the DNA dodecamer C-G-C-G-A-A-T-T-C-G-C-G in the B form at a level that shows clearly several aspects of some base sequence-dependent departures from the ideal, regular helical structure of B-DNA. I argue that the detailed conformation is a consequence of simple steric repulsive forces between purine bases in consecutive base-pairs but on opposite backbones. These repulsions are a consequence of the “propeller twist” of the base-pairs, together with the larger size of the purine bases, and they may occur in either the major or the minor groove. The argument is conducted in terms of the structural mechanics of a deformable elastic system. These repulsive forces between the base-pairs are resisted by stresses in the helical backbones, which may be studied quantitatively via the variation in torsion angles δ along the backbones, at the points where the sugar rings are connected. There is also a correlation between the cross-chain purine repulsions and the perturbations in helical twist angle between successive base-pairs. The work suggests some comments on the proposed “alternating B” form, the Z form and the A form of DNA.