Structural highlights
- Most RNA and RNA-DNA duplex in this form
- Shorter, wider helix than B.
- Deep, narrow major groove not easily accessible to proteins
- Wide, shallow minor groove accessible to proteins, but lower information content than major groove.
- Favored conformation at low water concentrations
- Base pairs tilted to helix axis and displaced from axis
- Sugar pucker C3'-endo (in RNA 2'-OH inhibits C2'-endo conformation)
Take the Tour
The tour starts with the 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
