Base Stacking

Let's consider the substance -- or rather the core -- of the Watson-Crick double helix. While the bases on opposite strands are paired with their corresponding partner through hydrogen-bonding interactions, most of the stability of the helix is proposed to result from the stacking of the bases on "top" of each other. Indeed, the helical twist of the DNA requires that the stacked bases be offset, a conformation that allows a base to be in direct pi-pi contact with its 3' and 5' neighbors. In fact, the distance separating the planes of the base is about 3.4 Ã…, a distance corresponding to the thickness of the pi-electrons in an aromatic ring. We'll discuss pi-stacking in more detail in a later tutorial.