Chemistry Reference
In-Depth Information
quadruplex crystal structures (Figure 3.9b). All K
+
ions have full occupancy. The
average K
+
- K
+
distance is 3.38 Å. All three G-quadruplexes have three octahedrally
coordinated K
+
cations that are located equidistant between the planes of two adja-
cent G-quartets, with each K
+
and eight O6 atoms forming a square antiprismatic
arrangement. The outer K
+
ions are located within the loops, where they also achieve
octahedral coordination with the outer G-quartet O6 carbonyl oxygen atoms and
the O2 atoms from the adjacent thymine bases, together with two oxygen atoms
provided by water molecules. These potassium ions have only slightly increased
mobilities (i.e. thermal factors) compared to the three central K
+
ions.
99
The crystal structure of the Tl
+
form of the d[(G
4
T
4
G
4
)
2
] has been solved to
1.55 Å resolution (PDB ID 2HBN).
129
This G - quadruplex contains fi ve Tl
+
ions
(Figure 3.9d). The relative positions of these fi ve cations are very similar to those
found in the K
+
crystal structure. The average distance between Tl
+
ions is 3.6 Å .
Three Tl
+
ions are spread between adjacent G-quartet planes. They are coordinated
by eight oxygens (one O6 from each of the surrounding guanines). Two Tl
+
ions are
coordinated in each of the two thymine loops (Figure 3.9d). They are coordinated
by four guanine O6 atoms from the outer G-quartet plane and two thymine carbonyl
groups. A water molecule was identifi ed and located within the thymine loops and
in close proximity to the loop-associated Tl
+
ion.
129
3.7.2 NMR Studies
Ammonium ions have been shown to stabilize G-quartets to an extent that is similar
to that observed for Na
+
.
5,125
Hud and Feigon
et al.
used this fact to exploit
15
NH
4
+
ion as a solution-state probe of monovalent cation coordination sites.
162,248
These
authors used
1
H -
1
H and
1
H -
15
N NMR correlation experiments to localize
15
NH
4
+
ions within the bimolecular G-quadruplex d[(G
4
T
4
G
4
)
2
]. Dipole - dipole interactions
(ROE) between the protons of the bound
15
NH
4
+
ions and G-imino protons revealed
that d[(G
4
T
4
G
4
)
2
] coordinates three
15
NH
4
+
ions within its symmetric architecture
(Figure 3.9e). In fact, only two distinct chemical shift environments were detected
for bound
15
NH
4
+
ions. One of them was assigned to the two symmetry-related outer
sites, while the other was in the centre of the bimolecular G-quadruplex structure.
The observed ROE cross-peak intensities also revealed that
15
NH
4
+
ions in
d[(G
4
T
4
G
4
)
2
] are positioned equidistant between stacked G-quartets (Figure
3.9 e).
162,176
NMR spectroscopy has also been used to monitor the competition between
Na
+
and
15
NH
4
+
ions for coordination within G-quadruplexes at specifi c sites. For
the G-quadruplex formed by d(G
4
T
4
G
4
) in the presence of
15
NH
4
Cl, Na
+
ions were
shown to replace
15
NH
4
+
ions at all three of the above mentioned outer- and inner-
binding sites as the NaCl concentration is increased.
163
Moreover, Na
+
ions pre-
ferentially replace
15
NH
4
+
ions coordinated at the inner site of d[(G
4
T
4
G
4
)
2
]
quadruplexes.
163
The 11 - mer d(G
3
T
4
G
4
), a single base deletion of d(G
4
T
4
G
4
), has been shown by
NMR spectroscopy to fold into an unusual asymmetric, bimolecular structure in the
presence of
15
NH
4
+
, K
+
and Na
+
ions (Figure 3.6b).
244
Multinuclear NMR studies
