Opening image: The Watson-Crick double helix. The 20-bp DNA is shown here as a stick model. Hydrogen bonds between the base pairs are shown as dashed green lines.

The DNA double helix consists of a stack of planar base pairs between two spiraling sugar-phosphate backbones. Base pairs prefer to stack on one another rather than being exposed to water. JSmol's ability to rotate molecules allows you to appreciate the helical shape of the DNA molecule.

Now we see the double helix displayed as a ball-and-stick model. Toggle spacefilling on and off.

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 π-π contact with its 3′ and 5′ neighbors. In fact, the distance separating the planes of the base is about 3.4 Å, a distance corresponding to the thickness of the π-electrons in an aromatic ring. We'll discuss π-stacking in more detail in a later tutorial.

The stacked bases form a spiral staircase. Examine the stacking by moving the model around with the cursor. Then rotate for a view along the axis of the double helix.

The Sugar-Phosphate Backbone

The sugar-phosphate chains wrap around the core. They cannot be separated without unwinding the duplex.

We will occasionally display the sugar phosphate chain as a tube drawn through the phosphorus atoms.

Animate backbone trace. You can use the "Default Settings" button to return to spacefill.

One point has been overlooked so far; how can we decide if the double helix is right-handed or left-handed?

Go to an orthogonal view of the model. The sense of a helix is intrinsic (it does depend on the end from which it is viewed). As you look down the length of the double helix, note that the strands rotate in a clockwise direction as they move away from you. This means that B-DNA is a right-handed helix.

Grooves on the Double Helix

Another point before we leave this lesson. B-DNA has two deep exterior grooves. The broader groove is referred to as the major groove. The minor groove is about half as wide as the major groove. The best model to illustrate this point is a spacefilling model:

Toggle rotation. Take a moment to examine the depth of each groove by tilting the helix.

Toggle a model of the solvent-accessible surface.