Chemistry Reference
In-Depth Information
G-quadruplex. The crystal structure of the RNA G-quadruplex formed by the
sequence r(UG
4
U) in the presence of Sr
2+
ions (PDB ID 1J8G), which was deter-
mined at ultra-high resolution (0.61 Å), seems to have provided an answer to this
apparent enigma.
160
Four strands of r(UG
4
U) form a parallel stranded quadruplex,
similar to that described above for the analogous DNA sequence d(TG
4
T), but
in the case of r(UG
4
U) the four strands within each quadruplex are symmetry-
related molecules. The tetramolecular G-quadruplexes of r(UG
4
U) stack with
one another in opposite polarity (head-to-head or tail-to-tail) to form a pseudo-
continuous column. Sr
2+
ions are coordinated between
every other
pair of stacked
G-quartets without any other cations coordinated at the intervening positions. The
Sr
2+
ions are associated with eight carbonyl oxygen atoms of adjacent G-quartets in
a bipyramidal-antiprism geometry.
160
Thus, it appears that the electrostatic repul-
sions between Sr
2+
ions force these ions to leave vacant cation coordination sites
within G - quadruplexes.
3.7 Coordination of Cations within d[( G
4
T
4
G
4
)
2
]
3.7.1 Crystal Structures
The X-ray crystal structure at 1.86 Å resolution of the
Oxytricha nova
telomere end
binding protein (OnTEBP) in complex with DNA and in the presence of NaCl
has shown that d(G
4
T
4
G
4
) adopts a bimolecular G-quadruplex structure (PDB ID
1JB7)
158
that is identical to the structure formed in the absence of the protein.
99
Again, four guanine bases form four G-quartets, and four thymine residues form
loops that span across the diagonal of the terminal G-quartets (Figure 3.6a). The
structural features of the G-quadruplex in the protein-DNA complex are also very
similar to those of the NMR structure,
96,97
including the stacking of bases between
G-quartets and the alternating
syn
-
anti
orientations across glycosidic bonds. The
high-resolution X-ray diffraction data also reveals the positions of Na
+
ions in the
centre of the G-quadruplex.
158
The two central Na
+
ions are nearly coplanar within
the central G-quartets and are in distorted, octahedral coordination environments
(Figure 3.9a). The outer two Na
+
ions are positioned above and below the planes of
the outer G-quartets towards the T
4
loops, and are coordinated by two O2 atoms of
bases T5 and T7 in addition to the carbonyl oxygen atoms of the terminal G-quartet.
Na
+
-thymine O2 coordination is consistent with the earlier proposal that changes
observed by NMR in T nucleotide positions, when Na
+
ions are exchanged for K
+
or
15
NH
4
+
ions, are driven by the loss of thymine O2 coordination.
98
Electron density
maps also revealed potential cation binding sites between the outside G-quartets
and loops, which could not be unequivocally attributed to water molecules or
Na
+
ions.
158
The bimolecular G-quadruplex formed by d(G
4
T
4
G
4
) in the presence of K
+
ions
has been crystallized in two different space groups and their structures have been
refi ned to 2.0 and 1.49Å resolution.
99
One of these crystal structures (PDB ID
1JRN) has two G-quadruplexes per asymmetric unit, whereas the other crystal
