B-DNA tour

Source ^[1]

Structural highlights

• Most common DNA conformation in vivo
• Narrower, more elongated helix than A-form
• Wide major groove easily accessible to proteins
• Narrow minor groove
• Favored conformation at high water concentrations (hydration of minor groove seems to favor B-form)
• Base pairs nearly perpendicular to helix axis
• Sugar pucker C2'-endo

Take the Tour

The tour starts with the Default view. Now look at this space filling view.The backbone is yellow and the bases are magenta. Note that the major groove (in the middle, when you have just clicked the button) is wide and easily accessible.

Now change the display to make it show the sugar-phosphate backbone as pseudo-bonds connecting the phosphate atoms. Now the bases are easier to see. Notice how they are stacked upon each other and are nearly perpendicular to the axis of the double helix. Note also that the backbone forms a smooth, continuous curve.

You can look at just four of the base pairs..You are looking into the major groove and the colors of the base pairs alternate. You can also look at just the bases.

Each base pair stacks on the next similarly, as shown from this top view. This is the same top view of just the bases. A-form DNA also stacks in this way, but compare this with Z-DNA, which behaves much differently.

DNA is usually found in the B form under physiological conditions. The B-form conformation is stabilized by water molecules bound to the minor groove. You can see them as red dots in this view. Sometimes kinks are found in the B helix at transcriptional control regions. These kinks can either be intrinsic to the DNA sequence or caused by transcription factor binding.

You can compare it with the DNA forms by looking at this 3D red-blue stereo picture of A, B, and Z DNA