DNA Conformers

David Marcey
© 2006

I. Introduction
II. Table of Parameters
III. References


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I. Introduction

To the left are shown the three primary conformers of double stranded DNA, including A-, Z-, and B-DNA (the backbones are indicated by purple traces). Although B-DNA is the primary in vivo conformation, DNA-RNA hybrid molecules adopt the A conformation in cells, and Z-DNA may arise in GC rich stretches of chromosomal DNA. Whereas A- and B-DNA are right handed helices, Z-DNA is left handed. A-DNA forms under non-physiological conditions when B-DNA is dehydrated.

There are large differences in the depths of the grooves in the three conformers. Whereas B-DNA has major and minor grooves of similar depths, A-DNA has a cavernous major groove and a minor groove that is quite shallow. Z-DNA has the opposite arrangement, with a deep minor groove and a major groove into which the bases are extruded. In B-DNA, the bases are nearly perpendicular to the helical axis, which runs through the center of each base pair. In A-DNA, the helical axis runs through the major groove, the base pairs being pushed toward the surface of the minor groove. The A-DNA bases are tilted significantly (13o - 19o) with respect to the helical axis.

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II. Table of Conformer Parameters

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

ble 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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III. References

Dickerson, R.E., et al. (1982) The Anatomy of A-, B-, and Z-DNA. Science 216: 475-485.

Wang, A. H.-J., et al. (1979) Molecular Structure of a Left-handed Double Helical DNA Fragment at Atomic Resolution. Nature 282: 680-686.

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