DNA Structure I

The A-, B-, and Z- Conformers

© David Marcey, 1999

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I. General Topology

A-DNA sugar-phosphate backbone< >
B-DNA sugar-phosphate backbone< >
Z-DNA sugar-phosphate backbone< >

A-DNA bases< >
B-DNA bases< >
Z-DNA bases< >

II. Major and Minor Grooves

Rotating the molecule 90o reveals the grooves in A-DNA < >. The bases are shown in spacefill, the backbone in wireframe.
Rotating the molecule 90o reveals the grooves in B-DNA< >. The bases are shown in spacefill, the backbone in wireframe.
Rotating the molecule 90o reveals the grooves in Z-DNA< >. The bases are shown in spacefill, the backbone in wireframe.

III. Base Pairs

A single G-C base-pair in A-DNA
A single G-C base-pair in B-DNA
A single G-C base-pair in Z-DNA

Can you identify the major and minor grooves for each?

IV. Torsion Angles

Torsion angles in A-DNA guanine
delta< >
chi< >

Torsion angles in B-DNA guanine
delta< >
chi< >

Torsion angles in Z-DNA guanine
delta< >
chi< >


Parameters of A-, B-, and Z-DNA Double Helices (after Dickerson, et al., 1982)

Property A-Form B-Form Z-Form
Helical sense Right-handed Right-handed Left-handed
Repeating helix unit 1 base pair 1 base pair 2 base pairs
Rotation/base pair (degrees) 33.6 35.9 +/- 4.2 -60/2
Mean base pairs/turn 10.7 10.0 +/- 1.2 12
Inclination of base normals to helix axis (degrees) +19 -1.2 +/- 4.1 -9
Rise/base pair along helix axis (Å) 2.3 3.32 +/- 0.19 3.8
Pitch/turn of helix (Å) 24.6 33.2 45.6
Mean propeller twist (degrees) +18 +16 +/- 7 ~0
Glycosyl angle conformation anti anti anti at C, syn at G
Sugar pucker conformation C3'-endo O1'-endo to C2'-endo C2'-endo at C, C2'-exo to C1'-exo at G

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References:

  1. Dickerson, R.E., et al. (1982) The Anatomy of A-, B-, and Z-DNA. Science 216: 475-485.
  2. Wang, A. H.-J., et al. (1979) Molecular Structure of a Left-handed Double Helical DNA Fragment at Atomic Resolution. Nature 282: 680-686.
  3. B-DNA Chime tutorial at W.H. Freeman.

Comments or Suggestions to: David Marcey (marcey@clunet.edu)