B-DNA tour: Difference between revisions

Revision as of 16:45, 21 February 2016

B-form DNAB-form DNA

Structural highlights

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

Take the Tour

Start the tour with this view. Now look at this .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 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. You can also .

Each base pair stacks on the next similarly, as shown from . This is the . 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 can compare it with the DNA forms by looking at this 3D red-blue stern picture of A, B, and Z DNA

ReferencesReferences

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 ^[1] JSmol in Proteopedia ^[2] or to the article describing Jmol ^[3] to the rescue.

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

James Nolan, Eric Martz

[1]

[2]

[3]

@@ Line 18: / Line 18: @@
 Now change the display to make it show the <scene name='72/725442/Space_filling_bbone/1'>sugar-phosphate backbone as pseudo-bonds</scene>  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 <scene name='72/725442/Zoom_pairs/1'>look at just four of the base pairs.</scene>.You are looking into the major groove and the colors of the base pairs alternate.
+You can <scene name='72/725442/Zoom_pairs/1'>look at just four of the base pairs.</scene>.You are looking into the major groove and the colors of the base pairs alternate. You can also <scene name='72/725442/Zoom_pairs_only/1'>looks at just the bases</scene>.
-Each base pair stacks on the next similarly, as shown from <scene name='72/725442/Zoom_pairs_top/1'>this top view</scene>.  A-form DNA also stacks in this way, but compare this with Z-DNA, which behaves much differently.
+Each base pair stacks on the next similarly, as shown from <scene name='72/725442/Zoom_pairs_top/1'>this top view</scene>. This is the <scene name='72/725442/Zoom_pairs_only_top/1'>same top view of just the bases</scene>.  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 <scene name='72/725442/Water_spine/1'>in this view</scene>. 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.