B-DNA tour

• Most common DNA conformation in vivo
• Narrower, more elongated helix than A.
• 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

Structural highlights

Start the tour with this view. Now look at this .The backbone is yellow and the bases are magenta. You can compare it with the other DNA forms by

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 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 .You are looking into the major groove and the colors of the base pairs alternate.

Each base pair stacks on the next similarly, as shown from . 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 . 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 may include any references to papers as in: the use of JSmol in Proteopedia ^[1] or to the article describing Jmol ^[2] to the rescue.

Function

Disease

Relevance

This is a sample scene created with SAT to , and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.