Chemistry Reference
In-Depth Information
topology in the presence of K
+
ions.
98
A subsequent X-ray crystal structure of
d[(G
4
T
4
G
4
)
2
] in the Na
+
form, located in a cavity of the
Oxytricha nova
single - strand
telomere - binding protein complex,
158
revealed the same fold as the NMR structure.
A recent X-ray study of the K
+
form of d[(G
4
T
4
G
4
)
2
], which crystallizes in two crystal
forms,
99
also revealed identical folds to the NMR and the protein-associated struc-
tures. These results are likewise in accordance with the conformations deduced by
Raman spectroscopy.
237
The G-quadruplex formed by the related oligonucleotide d(G
3
T
4
G
3
) in the
presence of K
+
or Na
+
ions has been determined independently by the groups of
Feigon
168,238
and Shafer
239 - 241
by NMR in solution. d(G
3
T
4
G
3
) forms a bimolecular
quadruplex (Figure 3.6d). Three G-quartets are formed from the GGG tracts. The
conformation of guanine bases is
syn
-
syn
-
anti
-
anti
around each G-quartet. Adjacent
strands are alternately in parallel and antiparallel orientations. Glycosidic confor-
mations of the guanines are 5
′
-
syn
-
syn
-
anti
- (T
4
loop) -
syn
-
anti
-
anti
in one strand and
5
-
syn
-
anti
-
anti
- (T
4
loop) -
syn
-
syn
-
anti
in the other strand. The thymines in the loops
span across the diagonal of the outer G-quartets. Unlike d[(G
4
T
4
G
4
)
2
], the bimo-
lecular structure of d[(G
3
T
4
G
3
)
2
] is not symmetric, which results in separate signals
for each monomer strand in NMR spectra. The unique feature of this topology is
the stacking of the G-quartets, which includes both tail-to-tail and head-to-tail
arrangements. The structures of d[(G
4
T
4
G
4
)
2
] (Figure 3.6 a) and d[(G
3
T
4
G
3
)
2
] (Figure
3.6d) are closely related.
97,98,185,240,242
However, the precise structure and dynamics of
the T
4
loops of both G-quadruplexes are cation dependent. A comparison of the
Na
+
, K
+
and
15
NH
4
+
NMR structures of d[(G
4
T
4
G
4
)
2
] indicated that the coordination
of Na
+
ions within the planes of the outer G-quartets allows for the participation of
the O2 carbonyl of the third loop thymine (T7) in the coordination of Na
+
ions.
98
In contrast, coordination of K
+
or
15
NH
4
+
ions between the planes of the G-quartets
does not allow for coordination by the same loop thymine, which results in a differ-
ent loop structure. When formed in the presence of K
+
ions, there is also evidence
of greater motion in the diagonal loops of the quadruplexes with respect to the Na
+
structure.
97,98,185,238,241
The sequence d(G
4
T
4
G
3
), which has one 3
′
guanine missing from the sequence
d(G
4
T
4
G
4
), has been shown to form a G-quadruplex with a signifi cantly different
structure and a greater cation-dependent polymorphism than d(G
4
T
4
G
4
).
243
This
sequence can be considered as an intermediate between d(G
4
T
4
G
4
) and d(G
3
T
4
G
3
).
Our NMR study demonstrated that d(G
4
T
4
G
3
) forms a bimolecular G-quadruplex
in the presence of Na
+
ions. The topology of d[(G
4
T
4
G
3
)
2
], shown in Figure 3.6c,
exhibits an asymmetric bimolecular fold-back structure consisting of three stacked
G-quartets. The conformation of guanine bases is
syn
-
syn
-
anti
-
anti
around each G-
quartet. The guanine bases of the two outer G-quartets exhibit a clockwise donor-
acceptor hydrogen-bonding directionality, while those of the middle G-quartet
exhibit anticlockwise directionality. The glycosidic torsion angle conformations of
the guanine bases are 5
′
′
-
syn - anti - syn
- (
anti
- T
4
loop) -
anti - syn - anti
in one strand
and 5
- (
syn
) -
anti - syn - anti
- (T
4
loop) -
syn - anti - syn
in the other strand. The two T
4
loops both span diagonally across the outer G-quartets, but adopt different confor-
mations. Each strand has neighbouring parallel and antiparallel strands. The two
guanine residues not involved in G-quartet formation, G4 and G12 (i.e. the fourth
′
