Chemistry Reference
In-Depth Information
solution. The relatively large size of
15
NH
4
+
ions in comparison to Na
+
ions is likely
to hinder their movement through the quadruplex and provides a rationale for its
longer residence time compared with Na
+
ions. The signifi cant difference in the
residence times of
15
NH
4
+
and Na
+
ions bound inside the bimolecular G-quadruplex
d[(G
4
T
4
G
4
)
2
] revealed that
15
NH
4
+
ion movement from the inner to the outer binding
sites of d[(G
4
T
4
G
4
)
2
] is accelerated by ca. 7.5 times in the presence of Na
+
ions.
163
The residence time of
15
NH
4
+
ions within the inner coordination site is reduced from
270 ms in the presence of
15
NH
4
+
ions alone, to 36 ms in the presence of both
15
NH
4
+
and Na
+
ions at 25 ° C.
163
The partial occupancy by Na
+
ions is strongly correlated
with the acceleration of
15
NH
4
+
ion movement through the G-quadruplex, whereas
bulk ion concentration does not exert a noticeable infl uence on the rate of
15
NH
4
+
ion movement from the inner to the outer coordination sites. Even a low concentra-
tion (i.e. 5 mM) of Na
+
ions decreases the residence time of
15
NH
4
+
ions bound at
the inner coordination site to the minimum value of 36 ms. Further increases in Na
+
concentrations, to the point that one or two coordination sites of d[(G
4
T
4
G
4
)
2
] are
completely occupied by Na
+
ions, does not lead to further increase in the rate of
15
NH
4
+
ion movement. Thus, the residence time of 36 ms for
15
NH
4
+
ions bound at
the inner coordination site provides a good estimate for the limiting rate for its
movement from the inner to an outer binding site. The much slower rate of
15
NH
4
+
ion movement observed when all three coordination sites of d[(G
4
T
4
G
4
)
2
] are occu-
pied by
15
NH
4
+
ions is apparently due to the added restriction that their movement
to an adjacent site within the G-quadruplex requires a concerted movement of
another
15
NH
4
+
ions out of the adjacent site (i.e. double
15
NH
4
+
ion movement).
163
Vacant coordination sites are likely to exist, at least transiently, during
15
NH
4
+
ion
movement. However, the lifetime of these vacancies must be short compared with
the lifetime of occupied sites.
An NMR study on
15
NH
4
+
ion movement within d[(G
3
T
4
G
4
)
2
] demonstrated
the absence of
15
NH
4
+
ion movement between the two binding sites along the central
ion cavity of the G-quadruplex structure in solution.
165
15
NH
4
+
ions do move between
the two binding sites, U and L, and bulk solution.
15
NH
4
+
ion movements from the
binding sites U and L into the bulk solution are characterized by lifetimes of 139 ms
and 1.7 s at 298 K, respectively. The 12 times faster movement from binding site U
demonstrates that
15
NH
4
+
ion movement is controlled by the structure of T
4
loop
residues, which through diagonal- versus edge-type orientations impose distinct
steric restraints for cations to leave or enter the G-quadruplex. Activation energy
for the UB process is 15.8 kcal mol
− 1
.
165
The d[G
4
(T
4
G
4
)
3
] quadruplex exhibits four G-quartets with three
15
NH
4
+
ion -
binding sites (termed O
1
, I and O
2
).
164
The analysis of 2D NMR data has demon-
strated unambiguously that there is no unidirectional
15
NH
4
+
ion movement through
the central cavity of the d[G
4
(T
4
G
4
)
3
] quadruplex.
164
15
NH
4
+
ions move back and
forth between the binding sites within the G-quadruplex and exchange with ions in
bulk solution.
15
NH
4
+
ion movement is controlled by the thermodynamic preferences
of individual binding sites, steric restraints of the G-quartets for
15
NH
4
+
ion passage
and diagonal versus edge-type arrangement of the T
4
loops. The cross - peak volumes
were observed for mixing times as long as 3 s, which was due to slow
15
N longitudinal
relaxation and slow
15
NH
4
+
ion movement within the d[G
4
(T
4
G
4
)
3
] quadruplex. The
