DNA Conformers
David Marcey
© 2006
Directions
Use
the scrollbar to the right to scroll through the text of this
exhibit.
To reset the molecules in this exhibit, use the refresh button
of your browser to reload the page.
If
you resize your browser window, simply refresh the page in order
to restore proper viewing. |
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.
return
to beginning of exhibit
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 |
return
to beginning of exhibit
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.
return
to beginning of exhibit
|