Chemistry Reference
In-Depth Information
Figure 3.8
(Plate 5)
Cation coordination within G-quadruplex structures adopted by d(TG
4
T)
as revealed by X-ray crystallography: (a) Na
+
ions (pink balls) within the 0.95 Å resolution
structure (PDB ID 352D);
157
(b) Na
+
ions in the structure crystallized using lithium sulfate as
the main precipitating agent (PDB ID 2O4F);
246
(c) arrangement involving both Ca
2+
(green
balls) and Na
+
(pink balls) cations crystallized in a mixed ion environment (PDB ID 2GW0);
139
(d) Tl
+
(red balls) and Na
+
(pink ball) ions within the 2.2 Å resolution structure (PDB ID
1S45);
247
(e) Tl
+
(red balls) and Na
+
(pink balls) ions within the 2.5 Å resolution structure
(PDB ID 1S47);
247
(f) Tl
+
(red balls) and Na
+
(pink balls) ions within the G-quadruplex exhibit-
ing a T-quartet at the 3
-end of the strands (shown at the top of this structure) (PDB ID
1S47).
247
Individual strands are shown in a wire frame model, while guanine bases are pre-
sented in stick representation to demonstrate the extent of out of plane bending. Cations are
shown as coloured balls. Na
+
with the smallest ionic radius can vary in coordination geometry
from being within the plane of a G-quartet to being equidistant between two adjacent G-
quartets. The larger ions are exclusively coordinated between two adjacent quartets (See
colour plate section)
′
Analysis of details of the more recent crystal structure of d(TG
4
T) determined
to 1.5 Å resolution (PDB ID 2O4F) shows that G-quartets within a bimolecular
structure are not coplanar and are tilted with respect to the column axis towards
the 5
- ends (Figure 3.8 b).
246
The crystallization of d(TG
4
T) from a solution contain-
ing both Li
+
and Na
+
ions showed only Na
+
ions within the core of the quadruplex.
A single bound Li
+
ion has been observed at the surface of the bimolecular structure,
but not within the G-quadruplex core.
246
The high - resolution crystal structures of
d(TG
4
T) also revealed the location of cations and water molecules located around
the outside of the G-quadruplex.
′
