Journal of Inorganic Biochemistry 91 (2002) 405–412

www.elsevier.com / locate / jinorgbio

Synthesis, characterization and DNA binding studies of a ruthenium(II)

complex
Vaidyanathan Ganesan Vaidyanathan, Balachandran Unni Nair*
Chemical Laboratory, Central Leather Research Institute, Adyar, Chennai, 600 020, India
Received 20 December 2001; received in revised form 18 April 2002; accepted 20 April 2002

Abstract

[Ru(bzimpy) 2 ]Cl 2 , where bzimpy is 2,6-bis(benzimidazol-2-yl) pyridine was synthesized and characterized by ESI-MS, UV–Visible,
1
H NMR and fluorescence spectra. Absorption titration and thermal denaturation experiments indicate that the complex binds to DNA
with moderate strength. Viscosity measurement shows that the mode of binding could be surface binding. Fluorescence study shows that
the fluorescence intensity of the complex decreases with increasing concentrations of DNA, which is due to the photoelectron transfer
from guanine base to 3 MLCT of the complex. Photoexcitation of the complex in the MLCT region in the presence of plasmid DNA has
been found to give rise to nicking of DNA.
 2002 Elsevier Science Inc. All rights reserved.

Keywords: Ruthenium(II) complex; DNA binding; Photocleavage

1. Introduction complexes have the ability to display enantioselective

Studies pertaining to DNA cleavage by synthetic re-
agents are of considerable interest because of their utility
as tools in molecular biology. This has resulted in the
development of both sequence specific DNA cleavers [1–
3] and DNA foot printing agents [4–8]. In most of the
cases, the cleavage of DNA was carried out by metal
complexes or organic dyes. In recent years, there has been
substantial interest in understanding the binding properties
of metal complexes, particularly polypyridyl complexes of
ruthenium, with biomolecules like DNA [9–33]. Since
ruthenium complexes are water soluble, coordinatively
saturated and inert to substitution, they are ideally suited
for application as sensitive non-covalent probes for poly-
mer structure. Moreover, polypyridyl complexes of
ruthenium are intensely colored due to localized metal to
ligand charge transfer transition (MLCT). This MLCT
transition is particularly important as it is perturbed when
the complex interacts with DNA, providing a spectroscopic
probe. It has been shown that these complexes can bind to
DNA by different modes such as intercalation in the major
groove or electrostatic interaction [34–38]. Some chiral
*Corresponding author. Tel.: 191-44-443-0273; fax: 191-44-491-
1589.
E-mail address: bcun@rediffmail.com (B.U. Nair).
DNA binding, discriminating between the right- and left-
handed DNA [39]. It has also been shown that some
ruthenium complexes induce DNA cleavage upon irradia-
tion and thus act as photochemical endonucleases [40,41].
These types of metal–ligand complexes have been consid-
ered as potent nucleic acid probes and therapeutic agents.
Some of the ruthenium complexes induce DNA cleavage
via singlet oxygen upon irradiation [41]. However, the
excited states of some ruthenium(II) complexes have been
shown to promote DNA strand break via electron transfer
[41–43]. Barton et al. have shown that [Ru(bpy) 2 (dppz)] 21
exhibits no luminescence in aqueous buffer. However, on
intercalation with DNA, it shows an enhancement in
luminescence [44]. Kelly et al. showed that the emission
intensity of [Ru(tap) 3 ] 21 decreases on addition of DNA
[41]. These observations indicate that modification of
ligand environment would lead to changes in binding
affinities, photophysical properties and DNA cleaving
properties of the metal complex. So far, ruthenium(II)
complexes having extended aromatic planar bidentate
ligands have been extensively studied. On the other hand,
only a few studies on ruthenium complexes having non-
planar bidentate ligands have been reported [45]. As far as
ruthenium(II) complexes having tridentate ligands are
concerned, only a few are reported [46]. A tridentate
ligand like bzimpy is not expected to form a Ru(II)

0162-0134 / 02 / $ – see front matter  2002 Elsevier Science Inc. All rights reserved.
PII: S0162-0134( 02 )00448-8
406 V.G. Vaidyanathan, B.U. Nair / Journal of Inorganic Biochemistry 91 (2002) 405 – 412
complex which can interact intercalatively with DNA.
Weakly binding complexes are preferred for development
of DNA footprinting agents. In this paper, we report the
synthesis and characterization of ruthenium(II) complex 1
having non-planar tridentate ligand, 2,6-bis(benzimidazol-
2-yl)pyridine (bzimpy). The DNA binding and cleavage
studies have been carried out for the complex.
2. Experimental
2.1. Reagents
All common chemicals, solvents as well as ruthenium
chloride trihydrate and 1,2-diaminobenzene were pur-
chased either from SRL (Mumbai, India) or Ranbaxy
(Mumbai, India). Pyridine 2,6-dicarboxylic acid was ob-
tained from Aldrich. The Calf Thymus DNA was pur-
chased from Sigma. Tris and agarose were purchased from
SRL. pBR322 DNA was obtained from Bangalore Genei,
Bangalore. Millipore water was used for preparing buffer.
2.2. Synthesis
[Ru(dmso) 4 Cl 2 ] [47] and 2,6-bis(benzimidazol-2-yl)
pyridine (bzimpy) [48] were prepared according to the
literature procedures.
[Ru(bzimpy) 2 ] 21 (1) A mixture of [Ru(dmso) 4 Cl 2 ]
(0.484 g, 1 mmol) and bzimpy (0.622 g, 2 mmol) in
methanol (25 ml) were refluxed for 1 h to give a clear red
solution. After most of the methanol was removed in a
rotary evaporator, a red precipitate was obtained by
addition of diethyl ether. The precipitate was filtered and
dried under vacuum. It was recrystallized from acetonitrile.
Found: C, 57.23; H, 3.15; N, 17.5; Calc. for
C 38 H 26 N 10 RuCl 2 : C, 57.41; H, 3.29; N, 17.62. vmax / cm 21 .
3401 (N–H), 3057 (C–H), 1615 (C=N). lmax / nm (´ / M 21
cm 21 ) methanol 352 (46 970), 498 (6815). 1 H NMR
[(CD 3 ) 2 SO]: d 9.09 (t, 2H), 8.89 (s, 1H), 8.2 (d, 1H), 7.45
(d,1H), 7.4 (d, 1H).
2.3. Measurements
UV–Visible spectral measurements of the complex, and
DNA binding studies were carried out on Perkin Elmer
Lambda 35 spectrophotometer at 25 8C. Elemental analysis
was carried out using a Heraeus-CHN-Rapid Analyzer at
RSIC, IIT, Madras. The emission spectra were recorded on
a Hitachi 650-40 spectrofluorimeter. Electrospray ionisa-
tion (ESI) mass spectrum of the complex was recorded
with a Hewlett Packard-1100 mass spectrometer equipped
with an electron spray source. Infra red spectrum of the
complex was recorded on a Perkin Elmer FT-IR spec-
trometer. NMR spectra were recorded on a Bruker spec-
trometer.
All the experiments involving the interaction of complex
1 with DNA were carried out using 10 mM Tris buffer at
pH 8.0. Solutions of calf thymus DNA in the buffer gave a
ratio of UV absorbance at 260 and 280 nm of 1.9:1,
indicating that DNA was free from protein [49]. The DNA
concentration per nucleotide was determined by absorption
spectroscopy using the molar absorption coefficient (6600
M 21 cm 21 ) at 260 nm [50]. The absorption titration was
carried out by keeping the concentration of complex
constant (10 mM) and varying the concentration of DNA
from 20 to 100 mM. The absorbance at 498 nm was
recorded after each addition of DNA. The intrinsic binding
constant Kb , was determined according to the following
equation:
[DNA] /(´A 2 ´F ) 5 [DNA] /(´B 2 ´F ) 1 1 /Kb (´A 2 ´F )
(1)
where ´A , ´F and ´B correspond to A obsd / [Ru], the
extinction coefficient for the free ruthenium complex and
the extinction coefficient for the ruthenium complex in the
fully bound form, respectively. A plot of [DNA] /(´A 2 ´F )
versus [DNA], gives Kb as ratio of slope to intercept.
Thermal denaturation studies were carried out for DNA
(100 mM) in the presence and absence of the complex 1
(10 mM). Viscosity measurements were carried out using
an Ostwald type viscometer, thermostated at 25 8C. The
flow times were recorded with a manually operated timer
for different concentrations of complex varying from 5 to
37.5 mM, maintaining the concentration of DNA constant
(150 mM). The buffer flow time was recorded as t8. The
relative viscosities for DNA in the presence (h ) and
absence (ho ) of the complex were calculated using the
relation h 5(t2t8) /t8, where t is the observed flow time in
seconds. The values of relative viscosity (h /ho )1 / 3 were
plotted against 1 /R (R5[DNA] / [Ru]).
Fluorescence measurements were carried out by keeping
the concentration of complex constant (10 mM) and
varying the concentration of DNA from 15 to 100 mM.
The complex 1 was excited at 498 nm and the fluorescence
spectra were recorded between 500 and 700 nm.
Cyclic voltammetry for complex 1 was carried out on an
EG&G PAR 173 potentiostat / Galvanostat analyzer at
25 8C. Tetrabutylammonium perchlorate (TBAP) (0.1 M)
was used as supporting electrolyte. The sample in dried
DMSO was purged with nitrogen prior to measurement. A
standard three-electrode system was comprised of a glassy
carbon electrode as working electrode, platinum electrode
as auxiliary electrode and a saturated calomel electrode as
reference electrode (SCE). A separate solvent blank with
0.1 M TBAP was used as a bridge between experimental
solution and the reference electrode.
Gel electrophoresis of plasmid DNA (pBR322 DNA)
was carried out with 25 ml reaction mixture containing 4
ml of 100 mg / ml plasmid DNA, 5 ml of 0.1 mM complex
1 and remaining buffer. A 5-ml aliquot of NaN 3 solution
 V.G. Vaidyanathan, B.U. Nair / Journal of Inorganic Biochemistry 91 (2002) 405 – 412
was added to one of the samples. The metal DNA solutions
were preincubated for 1 h in the dark and the samples were
kept in the spectrofluorimeter sample chamber. The sample
was then irradiated at 49565 nm. The samples were
subsequently analyzed by 0.8% agarose gel electrophoresis
(Tris–boric acid–EDTA buffer, pH 8.0) at 50 V for 4 h.
The gel was stained with 0.5 mg / ml ethidium bromide.
The stained gel was illuminated under a UV lamp and
photographed with Polaroid film using a Kodak DC-40
camera.
3. Results and discussion
3.1. Synthesis and characterization of complex 1
The synthetic route presented here is straightforward and
provides a good yield of the desired product in pure form.
This complex gave a satisfactory elemental analysis, and
was characterized by 1 H NMR and 13 C NMR. The ESI-
MS spectrum of the complex (Fig. 1) shows the base peak
2
at m /z 759 due to [RuL 21
2 Cl ] ion pair. The complex also
shows a peak at m /z 723 due to the complex cation
[RuL 2 ] 21 . The ESI-MS spectrum thus confirms the au-
Fig. 1. ESI-MS spectrum of [Ru(bzimpy) 2 ] 21 .
407
thenticity of the complex. It is interesting to note that the
same ligand has been shown to behave like a mono anion
(through the loss of a proton from one of the –NH groups)
in the case of Mn(II) complex of this ligand. Such a proton
loss has been confirmed by crystal structure determination
[51]. In the present case, the ESI mass spectrum clearly
shows that the ligand coordinates as a neutral tridentate
ligand without the loss of a proton from the –NH group.
The electronic absorption spectrum of complex 1 is
characterized by intense ligand centered transition in the
UV region and a metal to ligand charge transfer (MLCT)
transition in the visible region. The peaks at 352 nm in
complex 1 are characteristic of intraligand )–)* transition
of the bzimpy ligand. The lower energy band observed at
498 nm (´ 56815 M 21 cm 21 ) is assigned as MLCT
Ru(dp )–bzimpy(p *) transition.
The optimized structure of [Ru(bzimpy) 2 ] 21 has been
obtained using the Extensive Systematic Force Field
method (ESFF) available in the InsightII package. From
the optimized structure (Fig. 2), the bond length of Ru–N
has been found to be 2.154 A ˚ for equatorial bonds and
˚
2.05 A for axial bonds (Table 1). The reduction in bond
length in the axial position could be due to backbonding of
Ru(II) and p * orbital of the pyridine moiety. The bond
lengths reported here are comparable to Ru–N bond
lengths of [Ru(bpy) 3 ] 21 and [Ru(NH 3 ) 6 ] 21 having 2.05
and 2.10 A, ˚ respectively [52,53]. From the cyclic vol-
tammetry experiment, the formal potential of Ru 21 / Ru 31
has been found to be 1.6 V versus SCE. However the
electrochemical wave was found to be irreversible, hence
the potential reported here can only be taken as an
approximate value. Based on the ligand environment, the
electrochemical properties of the corresponding complexes
vary. The oxidation, which corresponds to abstraction of
an electron from the t 2g metallic centered, highest occupied
molecular orbital (HOMO) occurs at a more positive
potential. The potential reported here is comparable to the
potentials of TAP and HAT complexes of ruthenium
[41,54,55].
3.2. Effect of binding of complex to DNA on absorption
spectra
In the presence of increasing concentrations of DNA, the
p – p * transition of the complex was significantly per-
turbed, indicating interaction of the complex with DNA
(Fig. 3). With increasing DNA concentrations no shift in
the energy of the spectral transition was found but percent
hypochromism increased and eventually reached saturation
at [DNA] / [Ru]514. The intercalative binding of small
molecules to a DNA helix has been characterized by large
changes in the absorbance (hypochromism) and an appreci-
able shift in wavelength (red shift) due to the interaction of
a DNA p stack and complex p system. The percentage
hypochromicity of MLCT band of 1 upon binding to DNA
408 V.G. Vaidyanathan, B.U. Nair / Journal of Inorganic Biochemistry 91 (2002) 405 – 412

Fig. 2. (a) The optimized structure of [Ru(bzimpy) 2 ] 21 . (b) Redrawn structure for the sake of clarity in numbering of atoms.

was found to be 13% (hypochromicity, H% 5 [(´f 2 ´b ) / able to those observed for many other ruthenium complex-
´f ) 3 100], where ´f and ´b are the molar absorption es (1310 4 –4310 4 M 21 ) [56], but smaller than that
coefficients for the free and bound forms of the complex). observed for [Ru(phen) 2 (dppz)] 21 (.10 6 M 21 ) [44] which
The observed hypochromism in the visible spectrum of the binds intercalatively. This result is expected, since bzimpy
complex with DNA, however was less than the metalloin- does not possess a greater planar area like dppz or taptp
tercalators (Table 1). From the plot of [DNA] /(´a 2 ´f ) [57], and hence intercalation of its ruthenium complex to
versus [DNA], the intrinsic binding constant of the com- DNA is unlikely.
plex with DNA was calculated to be 1.860.2310 4 M 21 .
The moderate binding constant for this complex is compar-
3.3. Emission spectroscopy
Table 1
˚ of Ru(bzimpy) 21
Angle (8) and bond lengths (A) (from the optimized The emitting excited state of ruthenium polypyridyl
2
structure) complexes is generally triplet excited state and metal to
ligand charge transfer in character, with excited electron
N(1)–Ru–N(5) 77.97 Ru–N(1) 2.05
N(5)–Ru–N(2) 77.97 Ru–N(2) 2.05 localized on only one ligand. Deexcitation may also occur
N(4)–Ru–N(6) 77.97 Ru–N(3) 2.05 by radiationless deactivation both by solvent interaction
N(6)–Ru–N(3) 77.97 Ru–N(4) 2.05 and through a higher lying metal-centered state. In the
Ru–N(5) 2.154 present case, [Ru(bzimpy) 2 ] 21 exhibits luminescence with
Ru–N(6) 2.154
maxima at 602 nm in Tris buffer at ambient temperature.
 V.G. Vaidyanathan, B.U. Nair / Journal of Inorganic Biochemistry 91 (2002) 405 – 412 409

Fig. 3. Absorption spectra of complex (10 mM) in the absence (top) and presence of calf thymus DNA (2, 4, 6 mM). Arrow shows that the absorbance
changes upon increasing DNA concentration.

On increasing the concentration of CT DNA, the intensity DNA to the 3 MLCT of the complex, as reported in the
of [Ru(bzimpy) 2 ] 21 decreases and saturates at the ratio of case of Ru(TAP) 21
3 [41] and Ru(bpz) 21
3 [58].
[DNA] / [Ru]516. Fig. 4 depicts the variation of emission
intensity from the excited [Ru(bzimpy) 2 ] 21 at 602 nm as a 3.4. Photocleavage of DNA
function of [DNA] / [Ru]. The quenching of luminescence
excited state of [Ru(bzimpy) 2 ] 21 by DNA is consistent The irradiation of pBR322 plasmid DNA in the presence
with a photoelectron transfer from the guanine base of of [Ru(bzimpy) 2 ] 21 was studied so as to determine the

Fig. 4. Changes in the luminescence intensity at 602 nm of the excited [Ru(bzimpy) 2 ] 21 (10 mM) in 10 mM Tris buffer, pH 7.5, as a function of
concentration of DNA to ruthenium complex ratio for calf thymus DNA.
410 V.G. Vaidyanathan, B.U. Nair / Journal of Inorganic Biochemistry 91 (2002) 405 – 412

Fig. 5. Light-induced nuclease activity of [Ru(bzimpy) 2 ] 21 . Dark and light experiments: lanes 1 and 2, untreated pBR322 DNA (100 ng) in the dark and
upon irradiation (40 min); lanes 3, 4 and 5, pBR322 DNA1[Ru(bzimpy) 2 ] 21 (100 mM) in the dark and upon irradiation for 20 and 40 min; lane 6,
pBR322 DNA1[Ru(bzimpy) 2 ] 21 15 ml NaN 3 (10 mM) irradiated for 20 min.

efficiency with which they sensitize DNA cleavage. This
can be achieved by monitoring the transition from the
naturally occurring, covalently closed circular supercoiled
form (Form I) to the open circular relaxed form (Form II).
This occurs when one of the strands of the plasmid is
nicked, and can be determined by gel electrophoresis of the
plasmid. Extended irradiation results in a build up of nicks
on both strands of the plasmid, which eventually results in
its opening to the linear form (Form III). When circular
plasmid DNA is subjected to gel electrophoresis, relatively
fast migration will be observed for the supercoiled form
(Form I). Form (II) will migrate slowly and Form III will
migrate between Form II and Form I. [Ru(bzimpy) 2 ] 21
was found to bring about the photocleavage of the super-
coiled pBR322 DNA. Control experiments suggest that
untreated DNA does not show any cleavage in the dark
and even upon irradiation as shown in lane 1 and 2 (Fig.
5), respectively. For pBR322 DNA treated with
[Ru(bzimpy) 2 ] 21 in the dark, no cleavage is observed
(lane 3). On the other hand, formation of the relaxed
circular form of DNA was observed when DNA was
irradiated for 20 min in the presence of complex 1 (lane
4). Increasing the irradiation time to 40 min resulted in
further relaxation of the duplex forming Form III with
disappearance of Form I. The photonicking of DNA was
not affected by azide (lane 6); hence the role of singlet
oxygen in the nicking of DNA is ruled out in the present
case. The photonicking of DNA could be due to guanine
base oxidation by the photoexcited metal complex. The
probable mechanism for the photocleavage was further
supported by the observed luminescence quenching of
complex 1. This type of photocleavage of DNA has also
been reported in the presence of [Ru(TAP) 3 ] 21 and
Ru(bpz) 21
3 .
3.5. Thermal denaturation study
The melting of DNA can be used to distinguish between
those molecules which bind via intercalation and those
which bind externally. The melting temperature T m , at
which 50% of the DNA has become single-stranded, can
be determined from the thermal denaturation curves of
DNA. In the absence of any added complex, the melting
transition of CT DNA is sharp. Intercalation of organic
dyes or metallointercalators generally results in a consider-
able stabilization of the DNA duplex with a corresponding
large increase in melting temperature (T m ). In the presence
of intercalators, the T m rises sharply until all the intercalat-
ing sites are saturated, after which the stabilization is due
to electrostatic binding, and T m increases less steeply.
Thermal denaturation experiments carried out on CT DNA
in the absence of any added complex revealed that the T m
for the duplex is 6562 8C under our experimental con-
ditions. Addition of [Ru(bzimpy) 2 ] 21 to DNA increased
T m of DNA by 460.5 8C. For metallointercalators like
[Ru(phen) 2 (dppz)] 21 and [Ni(phen) 2 (dppz)] 21 , the DT m
was strikingly high. These complexes show binding con-
stants in the order of 10 6 [42,59] (Table 2). The above
change in melting temperature indicates that the binding
strength of the complex with DNA is only moderate. This

Table 2
UV spectral parameters and binding constants of the interaction of various metal complexes with DNA
Complex DT m (8C) % Hypochromicity Kb (M 21 ) Reference
21
[Ru(tpy)(bpy) OH 2 ] 4.260.5 2.3 660 [64]
[Ru(tpy)(DPPZ)OH 2 ] 21 14.160.8 9.6 7.0310 5 [64]
[Ru(bpy) 2 (taptp)] 21 24 1.7310 5 [57]
[Ru(pztp) 2 (phen)] 21 10–12 1.1310 4 [56]
Ethidium bromide 13 26 .10 7 [65,66]
[Co(phen) 2 (DPPZ)] 31 861 10 5 –10 6 [59]
[Ni(phen) 2 (DPPZ)] 21 861 10 5 –10 6 [59]
[Ru(phen) 2 (DPPZ)] 21 560.5 20 10 6 –10 7 [67]
 V.G. Vaidyanathan, B.U. Nair / Journal of Inorganic Biochemistry 91 (2002) 405 – 412 411

Fig. 6. Plot of relative viscosities (h /ho )1 / 3 versus 1 /R (R5[DNA] / [Ru]).

is consistent with binding constant and also from the guanine base to 3 MLCT of the complex. The occurrence of
optimized structure, which does not show any extended electron transfer is further supported by photonicking of
planarity in the ligand structure. DNA by the complex.

3.6. Viscosity measurement

4. Abbreviations
Another convincing test for the intercalation comes from
viscometry studies that test the ability of small molecules CT DNA calf thymus DNA
to lengthen DNA, which occurs when DNA base pairs bzimpy 2,6-bis(benzimidazo-2-yl)pyridine
separate to accommodate the ligands. In the presence of SCE saturated calomel electrode
increasing concentrations of complex 1, the viscosity TBAP tetrabutyl ammonium perchlorate
initially increased and decreased later (Fig. 6). This type of
change in viscosity could be due to the presence of two
phases of binding between Ru(II) complex and DNA. This Acknowledgements
type of binding can be explained by the effects like change
in conformation. However, the CD spectrum of DNA in The authors thank R. Amutha for her help with molecu-
the presence of complex 1 (CD spectrum not shown) does lar simulations. V.G.V. acknowledges CSIR for a research
not show any appreciable change in conformation of DNA. fellowship.
So in the present case, the possibility of conformational
change has been ruled out. McMillin et al. [60] have
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