Chemistry Reference
In-Depth Information
Figure 3.7
Sodium ion localization within G-quadruplexes as revealed by X-ray crystal struc-
tures of d[(TG
4
T)
4
] with eight strands forming two sets of four G-quartets
157
Figure 3.7, multiple cation coordination geometries are possible and observed (see
below).
The determination of G-quadruplex crystal structures of d[(TG
4
T)
4
] has pro-
vided a detailed view of cation coordination that is unmatched by other DNA
structures.
157
The X-ray crystal structure of d[(TG
4
T)
4
] was refi ned to a resolution
of 0.95 Å (PDB ID 352D). This crystal structure confi rmed that d(TG
4
T) forms a
tetramolecular parallel-stranded G-quadruplex in the presence of Na
+
ions (Figure
3.8 a).
157
The asymmetric unit of the d[(TG
4
T)
4
] crystal consists of four G-
quadruplexes, with two quadruplexes being coaxially stacked in a 5
orientation,
such that a continuous stack of eight G-quartets is formed.
157,246
Seven Na
+
ions are
coordinated along the axial channel formed by the O6 atoms of eight G-quartets
(Figure 3.8a). Close inspection of the crystal structure reveals that the central Na
+
in this channel is positioned equidistant between the planes of two stacked G-quar-
tets. The coordination geometry of this particular Na
+
is bipyrimidal, with eight
equidistant guanine O6 atoms. Na
+
ions located away from this central position are
displaced incrementally further from this perfect symmetrical bipyrimidal coordina-
tion. At the ends of this channel, terminal Na
+
ions are in fact located in the planes
of the end G-quartets, coordinated by the carbonyl groups of only four guanine
residues (Figure 3.8a). Displacement of the Na
+
ions from the central eight-coordi-
nate geometry to the in-plane four-coordinate geometry is believed to arise from
electrostatic repulsion between adjacent Na
+
ions. The mutual repulsion of Na
+
ions
along the central axis of the G-quadruplex has also been hypothesized to be the
origin of an out of plane bending observed for the terminal G-quartets of the eight
stacked quartets.
157
′
to 5
′
