Z-DNA model tour

Structural highlights

• 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.
• 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

Take the Tour

The tour starts with the Default view. Now look at this space filling view.The backbone is yellow and the bases are magenta. 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 it show the sugar-phosphate backbone as pseudo-bonds connecting the phosphate atoms. Now the bases are easier to see. 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 here.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 top view of just the bases.. Note the stacking of red base pairs on each other is much different than the stacking of red on blue.

You can compare it with the other DNA forms by looking at this 3D red-blue stereo picture of A, B, and Z DNA