Z-DNA Structure

Z-form

Helix has left-handed sense
Can be formed in vivo, given proper sequence and superhelical tension, but function remains obscure.
Narrower, more elongated helix than A or B.
Major "groove" not really groove
Narrow minor groove
Conformation favored by high salt concentrations, some base substitutions, but requires alternating purine-pyrimidine sequence.
N2-amino of G H-bonds to 5' PO: explains slow exchange of proton, need for G purine.
Base pairs nearly perpendicular to helix axis
GpC repeat, not single base-pair
- P-P distances: vary for GpC and CpG
- GpC stack: good base overlap
- CpG: less overlap.
Zigzag backbone due to C sugar conformation compensating for G glycosidic bond conformation
Conformations:
- G; syn, C2'-endo
- C; anti, C3'-endo

Look at this spacefilling view of Z-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 so wide that it is not really a groove any more.

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. But notice that the base pairs do not stack upon each other equivalently. The backbone also is not a continuous curve, it "zig-zags" back and forth (hence "Z"-DNA) In this view,

the molecule is shown in stick representation, with the backbone in yellow and sets of base pairs in red and blue. Notice how the blue bases stack well on the adjacent blue ones, but not on adjacent red ones, and vice versa. So it is the dinucleotide unit, rather than mononucleotide that is the repeating unit of the structure. This explains the need for alternating purines and pyrimidines to form Z-DNA. You can see the same view without the backbone

. Going 5' to 3', there is good stacking within the GpC dinucleotide, but not between them (CpG). A top view also illustrates the stacking arrangement.

. You can also see this view without the backbone

Z-DNA

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