Hydrogen bonding is essential to the three-dimensional structure of DNA. These bonds do not, however, contribute largely to the stability of the double helix. Hydrogen bonds are very weak interactions and the orientation of the bases must be just right for the interactions to take place. While the large number of hydrogen bonds present in a double helix of DNA leads to a cumulative effect of stability, it is the interactions gained through the stacking of the base pairs that leads to most of the helical stability.
Hydrogen bonding is most important for the specificity of the helix. Since the hydrogen bonds rely on strict patterns of hydrogen bond donors and acceptors, and because these structures must be in just the right spots, hydrogen bonding allows for only complementary strands to come together: A- T, and C-G. This complementary nature allows DNA to carry the information that it does.
Chargaff's rule states that the molar ratio of A to T and of G to C is almost always approximately equal in a DNA molecule. Chargaff's Rule is true as a result of the strict hydrogen bond forming rules in base pairing. For every G in a double-strand of DNA, there must be an accompanying complementary C, similarly, for each A, there is a complementary paired T.
Each strand of DNA wraps around the other in a right-handed configuration. In other words, the helix spirals upwards to the right. One can test the handedness" of a helix using the right hand rule. If you extend your right hand with thumb pointing up and imagine you are grasping a DNA double helix, as you trace upwards around the helix with your fingers, your hand is moving up. In a left-handed helix, in order to have your hand move upwards with your thumb pointing up, you would need to use your left hand. DNA is always found in the right-handed configuration.
As a result of the double helical nature of DNA, the molecule has two asymmetric grooves. One groove is smaller than the other. This asymmetry is a result of the geometrical configuration of the bonds between the phosphate, sugar, and base groups that forces the base groups to attach at 120 degree angles instead of 180 degrees. The larger groove is called the major groove while the smaller one is called the minor groove.
Since the major and minor grooves expose the edges of the bases, the grooves can be used to tell the base sequence of a specific DNA molecule. The possibility for such recognition is critical, since proteins must be able to recognize specific DNA sequences on which to bind in order for the proper functions of the body and cell to be carried out. As you might expect, the major groove is more information rich than the minor groove. This fact makes the minor groove less ideal for protein binding.