DNA Conformers
David Marcey
© 2021
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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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