B-DNA Structure

B-form

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

Look at this spacefilling view of B-form DNA.

. The backbone is yellow and the bases are magenta. You can compare it with the other DNA forms by looking at this Red-Blue Stereo picture of A, B, and Z. Note that the major groove (at the top, when you have just clicked the button) is wide and easily accessible.

Now change the display to make the 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.

Zoom in on a few base pairs with this button

. Hydrogen bonds between the bases are shown in white. You are looking into the major groove. Each base pair stacks on the next similarly, as shown from this view

. 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. 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.

B-DNA

A-form RNA, left frame.
A-form RNA, right frame.
Z-form DNA, left frame.
Z-form DNA, right frame.

Reference:
R. E. Dickerson, H. R. Drew, B. N. Conner, R. M. Wing, A. V. Fratini & M. L. Kopka (1982) The anatomy of A-, B-, and Z-DNA. Science 216: 475-485. [Medline Abstract]

Back to intro to DNA-RNA structure.