Chemistry Reference
In-Depth Information
equilibrium binding constant, which suggests that the terminal 3
guanines of
d[G
4
(T
4
G
4
)
3
] within the outside G-quartet facilitate
15
NH
4
+
ion binding to this site.
′
and 5
′
3.8 Cation Movement within G - Quadruplexes
NMR spectroscopy has been used extensively to measure the dynamics of cations
coordinated within G-quadruplexes. By analysing resonance linewidths in NMR
spectra of the quadrupolar nuclei
23
Na and
39
K, Braunlin and coworkers were able
to estimate the rotation times and resident bound lifetimes of dehydrated cations
within G - quadruplexes d[(T
2
G
4
T)
4
] and d[(G
4
T
4
G
4
)
2
].
258,259
Cations within these two
G-quadruplexes have rotation times that are on the order of nanoseconds. The
rotational immobilization exhibited by coordinated cations within G-quadruplexes
is in distinct contrast to the high rotational mobility of cations associated with the
surface of a G-quadruplex. Na
+
ions coordinated within the tetramolecular quadru-
plex d[(T
2
G
4
T)
4
] were shown to exchange more rapidly compared to Na
+
ions
coordinated within the bimolecular quadruplex d[(G
4
T
4
G
4
)
2
].
259
The lifetime of Na
+
ions coordinated within d[(G
4
T
4
G
4
)
2
] was estimated to be 250
s at 10 ° C.
259
The
residence lifetimes determined for Na
+
ions tightly bound within DNA quadru-
plexes are in distinct contrast to the kinetics of G-quartet base opening, which can
be as slow as days to weeks.
110,152,236,260
Thus, cations must move between bulk solu-
tion and the cation coordination sites within a G-quadruplex by passing along the
axial channel of the quadruplex, rather than by moving through transient side
openings in G-quartets.
Wu
et al.
have observed similar
23
Na NMR spectra for d[(TG
4
T)
4
] at two other
magnetic fi elds, 9.4 and 11.7T.
250
At 9.4T, a chemical shift separation between the
channel and surface (or bulk) Na
+
cations of 17 ppm corresponds to a frequency
separation of approximately 1800 Hz. This chemical shift difference suggests that
the residence time for Na
+
cations inside the G-quadruplex channel of d[(TG
4
T)
4
]
is ~0.6 ms at 25 ° C.
259
The fact that a separate
23
Na NMR signal is observed for the
channel Na
+
ions with M
n
+
(K
+
, Rb
+
and Sr
2+
) as an immediate neighbour suggests
that the movement of the added M
n
+
ions in and out of the G-quadruplex channel
must be slow on the
23
Na NMR timescale.
249
The smallest signal separation observed
for the different channel Na
+
ions is 0.6 ppm (corresponding to 95 Hz at 14.1T)
observed in the Na
+
/K
+
case. This indicates that the average residence time of K
+
ions inside the channel must be much longer than ~2 ms.
249
This is consistent with
the recent results that the residence time of
15
NH
4
+
ions in a d[(G
4
T
4
G
4
)
2
] quadru-
plex channel containing mixed Na
+
/
15
NH
4
+
ions is 36 ms,
163
and that the residence
time of Tl
+
ions in the same G-quadruplex is approximately 100 ms.
100,127
NMR studies utilizing
15
NH
4
+
ions as a probe for localizing cation binding sites
and for monitoring the movement of cations between different coordination sites
revealed that
15
NH
4
+
ions move along the central axis of the bimolecular quadruplex
d[(G
4
T
4
G
4
)
2
] and the solution, reminiscent of an ion channel.
161 - 165,248
The residence
time of
15
NH
4
+
ions at the inner site is 250 ms at 10 °C.
15
NH
4
+
ions were shown to
move between the three inner binding sites, and from the outer binding sites into
µ
