A-RNA Structure

A-form

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)

Look at this spacefilling view of A-form RNA.

. 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 very deep.

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 but not perpendicular to the axis of the double helix. They are also displaced to the side of the axis. The result is a wide, short 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

. B-DNA also stacks in this way, but compare this with Z-DNA, which behaves much differently. Essentially all helical RNA is in A form, but DNA can also be found in A form under certain conditions (particularly in RNA-DNA hybrids. The 2'-OH of ribose (shown in white in this view

) favors the C3'-endo sugar pucker necessary for A-form geometry.

A-RNA

B-form DNA, left frame.
B-form DNA, 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.