Chemistry Reference
In-Depth Information
most highly occupied sites (20-35%) were located within the G-tract major groove
while the occupancy in the minor groove were estimated to be around 10%.
The situation concerning penetration of Na
+
ions into the spine of hydration is
still an open question among X-ray crystallographers. The existence of just a single
alkali metal ion coordination site in the Rb
+
-form crystal structure argues against a
view that ions can invade the minor groove hydration spine along the entire length,
or the existence of a mixed water-ion spine of hydration. In a recent high-resolution
(1.1Å) structure determination of the Dickerson-Drew duplex no experimental
evidence for the presence of Na
+
ions in the minor groove was found.
63 - 65
A series of
23
Na NMR quadrupolar relaxation studies have been carried out
on B - DNA.
66,67
A general conclusion from these studies is that monovalent counte-
rion binding to DNA is loose and delocalized, without any dehydration or sequence-
specifi c features. In an optimally designed test for sequence-specifi c Na
+
binding
in the minor groove Denisov and Halle have used a magnetic relaxation dispersion
(MRD) technique, where the
23
Na relaxation rate is measured over nearly two
decades of resonance frequency.
67
Comparison of Na
+
MRD data from three
dodecamers with different nucleotide sequences: CGCGAATTCGCG (abbreviated
A
2
T
2
), CGAAAATTTTCG (A
4
T
4
) and CGCTCTAGAGCG (TA) showed that the
most tightly bound Na
+
ions reside in the minor groove. However, the occupancies
are quite low corresponding to a binding constant
K
Na
of 0.03 M
− 1
for TA and 0.1 M
− 1
for the other two dodecamers, and imply that Na
+
binding in the minor groove is a
rare event and is not likely to be detected by X-ray diffraction. These results are
not necessarily inconsistent with higher occupancy at the cryogenic temperature
(120-160 K) used in recent crystallographic studies. Even a modest binding enthalpy
of 5 kJ mol
− 1
could increase the binding constant from 0.1 M
− 1
at 277 K to 1.7 M
− 1
at
120 K, which is suffi cient to give 50% occupancy in a single binding site, as found
for Rb
+
at the ApT step in A
2
T
2
.
61
The authors conclude that groove bound Na
+
ions,
with an occupancy of only a few percent at room temperature, are not likely to
contribute importantly to the ensemble of DNA structures under physiological
conditions.
67
1.5.3 Divalent Cations
At physiological concentrations the binding of divalent cations to DNA is both
cation dependent and sequence dependent. From a sequence standpoint, specifi city
is contributed to by both the local molecular nucleophilicity (see above) and the
hydrogen bond environment. These H-bond interactions refl ect the greater hydra-
tion properties of divalent cations over monovalent. Generally, it is diffi cult to assess
how contributions of base sequence or cation type infl uence groove specifi city
because of crystal packing effects. Chiu and Dickerson have examined a database
of 28 cation-bound B-DNA structures spanning ten different crystal packing envi-
ronments and showed that there is a correlation between experimental conditions
and the number of observed cations.
68
Hence, the locations of cations can be com-
pared safely only between structures having similar crystallizing conditions, data
collection methods and resolutions. Despite these diffi culties, the authors fi nd a
