Article
Inorganic Chemistry, Vol. 49, No. 24, 2010 11425
be located. H atoms of the coordinated water and hydroxo
bridge were found from a Fourier difference map and treated
with a riding model. The oxygen atoms of the perchlorate
counterions were found to be disordered over two alternative
positions, and their refined site occupancies were 0.55(4) and
0.45(4). Complex 4: the crystallographic data were acquired
from a selected irregular block cut off from a large dark red
crystal taken from the crystalline sample. The crystals of this
complex showed low scattering power. From 6251 poorly
diffracted reflections, only 2572 reflections were observed with
I > 2σ. However, non-H atoms could be refined with aniso-
tropic displacement parameters, except for oxygen atoms of the
perchlorate counterions and water solvate. Hydrogen atoms of
the water molecules and hydroxo bridge were not found in the
Fourier map. Further relevant crystallographic data for com-
plexes 1 and 4 are summarized in Supporting Information,
Table S1.
kH/kD.14 The reactions were monitored under a 125-fold excess of
substrate at 400 nm for complexes 1, 3, and 4.
Preparation of Plasmid DNA. Plasmid DNA pBSK II
(Stratagene) was obtained and purified according to standard
techniques.40,41 Briefly, Escherichia coli DH5alpha cells were
transformed with pBSK II. One colony was incubated overnight
in 5 mL of Lysogeny broth (LB) medium medium42,43 supple-
mented with 0.1 mg/mL of ampicillin at 37 ꢀC with aeration; and
then 1 mL was inoculated in 300 mL of LB medium supple-
mented with 0.1 mg/mL of ampicillin and incubated for 8 h at
37 ꢀC with aeration. From these cultures plasmid DNA was
purified using Qiagen Plasmid Maxi Prep Kit. DNA was
quantified by spectrophotometry using the ratio of the absor-
bance at 260 and 280 nm.40 The plasmid preparation was
analyzed by gel electrophoresis to ensure that it consisted of
approximately 90% intact supercoiled plasmid DNA.
DNA Cleavage Activity Assays. The ability of 1-4 to cleave
DNA was examined by following the conversion of supercoiled
plasmid DNA (F I) to open circular DNA (F II) or linear DNA
(F III) using agarose gel electrophoresis to separate the cleavage
products.41,44
Theoretical Calculations. The geometry optimization of the
four cationic complexes 1-4 was performed using the B3LYP
hybrid density functional theory in combination with the 6-31G(d,
p) and LACVP* basis sets using Gaussian03.38,39 To ensure that
the geometry was minimized, a frequency calculation was per-
formed (B3LYP, LANL2DZ), finding only one weak, low energy
imaginary frequency corresponding to a minor rotatory vibration
of the methyl group.
In general, 400 ng of pBSK II (∼30 mmol L-1 bp) buffered
with PIPES (10 mmol L-1, pH 6.5) were treated with 1-4 in
CH3CN (25% reaction volume) for different time reactions at
50 ꢀC. Thereafter, each reaction was quenched adding 5 μL of a
loading buffer solution (0.25% bromophenol blue, 50% glycer-
ol and 250 mmol L-1 ethylenediamine tetraacetic acid (EDTA)
at pH 8.0) and then subjected to electrophoresis on a 0.8%
agarose gel containing 0.3 mg mL-1 of ethidium bromide in 0.5x
TBE buffer (44.5 mmol L-1 TRIS, 44.5 mmol L-1 boric acid and
1 mmol L-1 EDTA) at 90 V for approximately 1.5 h. The
resulting gels were visualized and digitized using a DigiDoc-It
gel documentation system (UVP, U.S.A.). The proportion of
plasmid DNA in each band was quantified using KODAK
Molecular Imaging Software 5.0 (Carestream Health, U.S.A.).
The portion of supercoiled DNA (F I) was corrected by a factor
of 1.47,45 since the ability of ethidium bromide to intercalate
into this DNA topoisomeric form is decreased relative to open
circular and linear DNA. To elucidate whether the mechanism
of DNA cleavage performed by complexes 1-4 is hydrolytic or
oxidative, different inhibitors of reactive oxygen species (ROS)
were added to the DNA treatments prior to the complexes.
These inhibitors were dimethyl sulfoxide (DMSO, 10%), KI
(500 mmol L-1), superoxide dismutase (SOD, 15 Units), and
NaN3 (500 mmol L-1). In addition, assays in the presence of the
DNA minor groove binder distamycin46 (50 μmol L-1) and the
DNA major groove binder methyl green47 (50 μmol L-1) were
also performed to clarify the DNA groove binding preference of
the complex-DNA interaction. The plasmid DNA was pre-
treated with distamycin and methyl green for 30 min and then
treated with the complex as described above. The kinetics of
plasmid DNA cleavage performed by 1-4 were evaluated
following the loss of supercoiled DNA fraction along the
Kinetic Assays for Complexes. Phosphodiesterase-like activity
was determined for complexes 1-4 by measuring hydrolysis of the
substrate bis-(2,4-dinitrophenyl)phosphate (2,4-bdnpp) in an UV-vis
Varian Cary 50 BIO spectrometer. The data were accompanied by
monitoring the release of 2,4-dinitrophenolate at 400 nm. The
rates were measured in real time at various pH values, and the
extinction coefficients of the product 2,4-dinitrophenolate were
measured at different pH’s under the same experimental condi-
tions of the kinetic measurements at different pH’s/(λ = 400 nm/ε,
M-1 cm-1) (3.5/2125; 4.0/3410; 4.5/7180; 5.0/10080; 5.5/11400;
6.0/12,000; 6.5-10.0/12,100). Reactions were monitored to less
than 5% of conversion of substrate to product, and the data were
treated by the initial rate method. The effect of pH on the rate of
hydrolysis of 2,4-bdnpp between pH 3.6 and 10.25 (buffers - MES;
HEPES and CHES 0.05 mol L-1) was investigated by using fixed
concentrations of substrate ([S]final = 5 ꢀ 10-3 mol L-1), and
complex ([C]final = 4 ꢀ 10-5 mol L-1 for complexes 1 and 3 and
4 ꢀ 10-5 mol L-1 for complex 4), with excess of substrate at 25 ꢀC
(I = 0.05 mol L-1 with LiClO4). Substrate dependence ([S]final
=
5 ꢀ 10-4-7 ꢀ 10-3 mol L-1) of the catalytic rate was measured at
the optimum pH for each complex. The data were treated using the
Michaelis-Menten non-linear regression (V0 vs [bdnpp]). Isoto-
pic effects of deuterium on the hydrolysis of 2,4-bdnpp promoted
by complexes 1, 3, and 4 were investigated monitoring parallel
reactions, where the buffer solutions MES pH and pD 6.50 were
prepared in H2O and D2O, respectively to determine the relation
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