890
N. Raman et al. / Spectrochimica Acta Part A 78 (2011) 888–898
DNA.
the entire DNA molecule. The docked poses were generated by the
exhaustive search and optimization step. FRED selects the single
best pose from the set of candidates. This pose is then scored and
the score is used to rank ligands in the output hit list. The consensus
structure step allows multiple scoring functions to vote for the best
docked structure in a rank-by-vote approach.
[DNA]
εa − εf
[DNA]
εb − εf
1
=
+
(1)
K (ε − ε )
[
]
b
b
f
where εa, εf, and εb are the apparent, free and bound metal com-
plex extinction coefficients, respectively. A plot of [DNA]/(εb − εf)
versus [DNA], gave
a
slope of 1/(εb − εf) and
a y-intercept
equal to [Kb/(εb − εf)]−1, Kb is the ratio of the slope to the y-
2.6. Antimicrobial activity studies
intercept.
The in vitro antibacterial and antifungal activities of the ligand
and its complexes were tested against the bacteria Staphylococcus
aureus, Pseudomonas aeruginosa, Escherichia coli, Staphylococcus epi-
dermis and Klebsiella pneumoniae and the fungi Aspergillus niger,
Fusarium solani, Culvularia lunata, Rhizoctonia bataicola and Can-
dida albicans. For the detection of the biocidal activities, the filter
paper disc agar diffusion method was used. Pure Streptomycin
and Nystatin were used separately as standards for antibacterial
and antifungal activity tests respectively. The stock solution was
prepared by dissolving the 1 mg of sample in 10 mL of DMSO to
give the concentration of 100 g/mL and the solution was seri-
ally diluted in order to find the minimum inhibitory concentration
(MIC) value. The suitable medium (nutrient agar for bacteria and
potato dextrose agar medium for fungi) was inoculated with the
test organisms. The standard solutions of Streptomycin and Nys-
tatin were prepared in DMSO to give concentration of 100 g/mL.
The sterilized blank paper discs of 6 mm diameter were impreg-
nated with tested compounds and placed on the surface of the
agar plates previously spread with 0.1 mL of overnight culture of
microorganisms. The incubation was carried out 24 h for bacteria
and 72 h for fungi at 30 ◦C. During the period, the test solution
diffused and the growth of the inoculated microorganisms was
affected. The inhibition zone was developed, at which the concen-
tration was noted.
2.3.2. Electrochemical methods
Cyclic voltammetry were performed on a CHI 620C electro-
chemical analyzer with three electrode system of glassy carbon as
the working electrode, a platinum wire as auxiliary electrode and
Ag/AgCl as the reference electrode. Solutions were deoxygenated
by purging with N2 prior to measurements.
2.3.3. Viscosity measurements
Viscosity experiments were carried on an Ostwald viscometer,
immersed in a thermostated water-bath maintained at a constant
temperature at 30.0 0.1 ◦C. CT DNA samples of approximately
0.5 mM, were prepared by sonication in order minimize complex-
ities arising from CT DNA flexibility [16]. Flow time was measured
with a digital stopwatch three times for each sample and an average
the ratio of metal(II) complexes to DNA, where Á is the viscosity of
CT DNA solution in the presence of complex, and Áo is the viscos-
ity of CT DNA solution in the absence of complex. Viscosity values
were calculated after correcting the flow time of buffer alone (t0),
Á = (t − t0)/t0 [17].
2.4. pUC19 DNA cleavage study
The oxidative cleavage experiment was performed using super
coiled pUC19 plasmid DNA Form I (2 L, 10 M) in Tris–HCl buffer
(50 mM) with 50 mM NaCl (pH 7.2) which was treated with the
metal complex (30 M) and ascorbic acid (10 M) followed by
dilution with the Tris–HCl buffer to a total volume of 20 L. The
samples were incubated for 1 h at 37 ◦C. A loading buffer con-
taining 25% bromophenol blue, 0.35% xylene cyanol, 30% glycerol
(3 L) was added and electrophoresis performed at 40 V for each
hour in Tris–acetate–EDTA (TAE) buffer using 1% agarose gel con-
taining 1.0 g/mL ethidium bromide. The cleavage of DNA was
monitored using agarose gel electrophoresis. The gel was visual-
ized by photographing the fluorescence of intercalated ethidium
bromide under a UV illuminator. The cleavage efficiency was mea-
sured by determining the ability of the complex to convert the super
coiled (SC) DNA to nicked circular form (NC) and linear form. Inhibi-
tion reaction was also carried out by prior incubation of the pUC19
DNA with DMSO (4 L) (hydroxyl radical scavenger) and sodium
azide (100 M) (singlet oxygen scavenger).
3. Results and discussion
The Schiff base ligand, L and its Cu(II), Ni(II),Co(II) and Zn(II)
complexes were synthesized and characterized by spectral and ele-
mental analysis data. The complexes were found to be air stable. The
ligand was soluble in common organic solvents but their complexes
were soluble only in CHCl3, DMF and DMSO.
3.1. Elemental analysis and molar conductivity measurements
The results of elemental analysis for the metal complexes were
in good agreement with the calculated values (Table 1) showing
that the complexes have 1:2 metal–ligand stoichiometry of the type
ML2Cl2 wherein L acts as a bidentate ligand.
The formation of these complexes may proceed according to the
equation given below:
MCl2·nH2O + 2L → [ML2Cl2] + nH2O
2.5. Molecular modeling studies
where M = Cu(II), Ni(II), Co(II) and Zn(II).
The metal(II) complexes were dissolved in DMSO and the
molar conductivities of 10−3 M of their solution at room
temperature were measured. The lower conductance values
(18.25–21.47 ꢀ−1 cm−2 mol−1) of the complexes support their
non-electrolytic nature. It also indicates that the chloride anions
bind to the metal ions as ligands and do not ionize.
The interaction of the metal complexes with DNA was also stud-
ied by molecular modeling with special reference to docking. All
calculations were performed in Open Eye with Fast Rigid Exhaus-
tive Docking using the FRED docking software package. The main
function employed for the calculation program was Chemguass
2. Prior to docking, the structure of the metal complexes was
constructed and geometry optimized by MM2 force field. The crys-
tal structure of the complex of netropsin with B-DNA dodecamer
d(CGCGAATTCGCG)2 (NDB code GDLB05), was downloaded from
Protein Data Bank. During the docking analysis, the binding site
of the netropsin drug in the minor groove of the above complex
was assigned as the binding site for our metal complexes across
3.2. Mass spectra
The mass spectrum of Schiff base ligand showed peak at m/z 471
corresponding to [C28H30N4O3] ion. Also the spectrum exhibited
peaks for the fragments at m/z 200, 150, 122 and 77 corresponding