Chemistry Reference
In-Depth Information
Figure 3.9
(Plate 6)
Localization of cations within bimolecular G-quadruplexes: (a) Na
+
ions
(pink balls) within the d[(G
4
T
4
G
4
)
2
] quadruplex in crystals of the
Oxytricha nova
telomere
end-binding protein with telomere DNA (PDB ID 1JB7);
158
(b) K
+
ions (grey balls) within
d[(G
4
T
4
G
4
)]
2
as revealed by X-ray crystal structure at 2.0 Å resolution (PDB ID 1JRN);
99
(c) K
+
ions (grey balls) within d[(G
4
T
4
G
4
)
2
] as revealed by X-ray crystal structure at 1.5 Å reso-
lution (PDB ID 1JPQ);
99
(d) fi ve Tl
+
ions (red balls) within d[(G
4
T
4
G
4
)
2
] as revealed by X-ray
crystal structure at 1.55 Å resolution (PDB ID 2HBN);
129
(e) ammonium ions within
d[(G
4
T
4
G
4
)
2
] as established by NMR measurements in solution;
162
(f) two ammonium ions
within d[(G
3
T
4
G
4
)
2
] established by NMR studies in solution.
176
Individual strands are shown
in wire frame model, while guanine bases are presented in stick representation to demonstrate
the extent of out of plane bending. Na
+
ion can be localized within the plane of a G-quartet
or between two adjacent G-quartets. The larger K
+
, Tl
+
and
15
NH
4
+
ions are exclusively
coordinated between two adjacent quartets (See colour plate section)
structure (PDB ID 1JPQ) has only one G-quadruplex per asymmetric unit. All three
G-quadruplex structures exhibit the same bimolecular diagonal loop folding topol-
ogy. This fold is identical to the structure determined for the same DNA sequence
ten years earlier by NMR in the presence of both Na
+
and K
+
ions (Figure 3.6a).
96 - 98
The central two G-quartets in each G-quadruplex are approximately coplanar. One
guanine base in each terminal G-quartet is slightly more tilted than the others and
stacks effectively with the adjacent 3
- thymine base (Figures 3.9 b and 3.9 c). The
average rise between adjacent G-quartets is consistently 3.3 Å.
99
A linear row of fi ve
equidistant K
+
ions lies along the helical axis within the central core of all three G-
′
