Chemistry Reference
In-Depth Information
Figure 1.13
Coordination of Mg
2+
at the CpG step near one end of the Dickerson-Drew
Duplex.
63
(Reprinted from
Chem. Biol.
,
9
, 3, M. Egli, DNA-cation interactions: Quo vadis?,
10. Copyright 2002, with permission from Elsevier.)
strong correlation between divalent cation binding and base sequence for the 28
structures examined. For four high-resolution (0.99 Å) structures, the minor groove
affi nity for Mg
2+
is GG
AC, with cations
positioned in the centre of the groove. For the major groove, the order for Mg
2+
is
GG
>
A G
>
AC and for Ca
2+
is GG
>
A T
∼
A G .
68
Treshko
et al.
63
have redetermined the crystal structure of the Dickerson-Drew
duplex at 1.1 Å resolution. Three ordered Mg
2+
ions are present in the asymmetric
unit, two hexahydrates and one pentahydrate complex. One Mg
2+
is located in the
major groove, close to the end of the duplex (Figure 1.13). The ion contacts the N7
and O6 edges of residue G
2
and G
22
from opposite strands via coordinated water
molecules. None of the contacts between Mg
2+
ions and DNA atoms on the fl oor of
the major groove involve inner-sphere coordination.
65
Hud and Feigon have studied the localization of Mn
2+
in A - tract DNA by
1
H
NMR spectroscopy, using a series of self-complementary dodecamer oligonucle-
otides that contain the sequence motifs A
n
T
n
and T
n
A
n
, where
n
= 2, 3 or 4 fl anked
by 5
>
A G
∼
GT and for Ca
2+
is GG
>
- GC base pairs.
69
At an Mn
2+
to duplex ratio of 10
− 3
most of the aro-
matic base protons are severely broadened, however, in contrast to the Mn
2+
NMR
data referred to above, the adenine H2 resonances exhibit the largest broadening.
The authors conclude that Mn
2+
is localized in the minor groove with the position
and degree of localization being highly sequence-dependent. In addition, G
2
- H8 in
the sequence CGT is broadened by 7 Hz/
′
- CG or 5
′
M MnCl
2
while G
1
- H8 in the sequence
GCT is broadened less than 2 Hz, a fi nding that is in agreement with the observa-
tion that the affi nity of 5
µ
′
- GT
>>
5
′
- GC (see above).
