Interaction of antitumor drug Sn(CH3)2Cl2 with DNA and RNA

Article abstract of DOI:10.1016/j.molstruc.2005.04.008

Sn(CH₃)₂Cl₂ exerts its antitumor activity in a specific way. Unlike anticancer cis-Pt(NH₃)₂Cl ₂ drug which binds strongly to the nitrogen atoms of DNA bases, Sn(CH₃)₂Cl₂ shows no major affinity towards base binding. Thus, the mechanism of action by which tinorganometallic compounds exert antitumor activity would be different from that of the cisplatin drug. The aim of this study was to examine the binding of Sn(CH₃) ₂Cl₂ with calf thymus DNA and yeast RNA in aqueous solutions at pH 7.1-6.6 with constant concentrations of DNA and RNA and various molar ratios of Sn(CH₃)₂Cl₂/DNA (phosphate) and Sn(CH₃)₂Cl₂/RNA of 1/40, 1/20, 1/10, 1/5. Fourier transform infrared (FTIR) and UV-visible difference spectroscopic methods were used to determine the Sn(CH₃)₂Cl₂ binding mode, binding constant, sequence selectivity and structural variations of Sn(CH₃)₂Cl₂/DNA and Sn(CH₃) ₂Cl₂/RNA complexes in aqueous solution. Sn(CH ₃)₂Cl₂ hydrolyzes in water to give Sn(CH ₃)₂(OH)₂ and [Sn(CH₃) ₂(OH)(H₂O)_n]⁺ species. Spectroscopic evidence showed that interaction occurred mainly through (CH₃) ₂Sn(IV) hydroxide and polynucleotide backbone phosphate group with overall binding constant of K(Sn(CH₃)₂Cl ₂-DNA)=1.47×10⁵ M^-1 and K(Sn(CH ₃)₂Cl₂-RNA)=7.33×10⁵ M ^-1. Sn(CH₃)₂Cl₂ induced no biopolymer conformational changes with DNA remaining in the B-family structure and RNA in A-conformation upon drug complexation.

Full text of DOI:10.1016/j.molstruc.2005.04.008

Journal of Molecular Structure 750 (2005) 22–27
www.elsevier.com/locate/molstruc
Interaction of antitumor drug Sn(CH3)2Cl2 with DNA and RNA
a,
Shohreh Nafisi , Amir Sobhanmanesh , Majid Esm-Hosseini ,
b
b
*
Kamran Alimoghaddamc, Heidar Ali Tajmir-Riahid
aDepartment of Chemistry, Azad University, Tehran Central Branch, Tehran 14169 63316, Iran
bDepartment of Chemistry, Urumieh University, Urumieh, Iran
cHematology, Oncology and BMT research Center, Tehran University of Medical Science, Shariati Hospital, Kargar Ave., Tehran 14117 13131, Iran
dDepartment of Chemistry-Biology, University of Quebec at Trois-Rivieres, C. P. 500, TR, Que., Canada G9A 5H7
Received 2 March 2005; revised 16 April 2005; accepted 19 April 2005
Available online 31 May 2005
Abstract
Sn(CH3)2Cl2 exerts its antitumor activity in a specific way. Unlike anticancer cis-Pt(NH3)2Cl2 drug which binds strongly to the nitrogen
atoms of DNA bases, Sn(CH3)2Cl2 shows no major affinity towards base binding. Thus, the mechanism of action by which tinorganometallic
compounds exert antitumor activity would be different from that of the cisplatin drug. The aim of this study was to examine the binding of
Sn(CH3)2Cl2 with calf thymus DNA and yeast RNA in aqueous solutions at pH 7.1–6.6 with constant concentrations of DNA and RNA and
various molar ratios of Sn(CH3)2Cl2/DNA (phosphate) and Sn(CH3)2Cl2/RNA of 1/40, 1/20, 1/10, 1/5. Fourier transform infrared (FTIR) and
UV–visible difference spectroscopic methods were used to determine the Sn(CH3)2Cl2 binding mode, binding constant, sequence selectivity
and structural variations of Sn(CH3)2Cl2/DNA and Sn(CH3)2Cl2/RNA complexes in aqueous solution. Sn(CH3)2Cl2 hydrolyzes in water to
give Sn(CH3)2(OH)2 and [Sn(CH3)2(OH)(H2O)n]C species. Spectroscopic evidence showed that interaction occurred mainly through
(CH3)2Sn(IV) hydroxide and polynucleotide backbone phosphate group with overall binding constant of K(Sn(CH3)2Cl2–DNA)Z1.47!
105 MK1 and K(Sn(CH3)2Cl2–RNA)Z7.33!105 MK1. Sn(CH3)2Cl2 induced no biopolymer conformational changes with DNA remaining
in the B-family structure and RNA in A-conformation upon drug complexation.
q 2005 Elsevier B.V. All rights reserved.
Keywords: DNA; RNA; Drug; Sn cation; Binding constant; Conformation; FTIR; UV–Visible spectroscopy
1. Introduction
Sugar-organotin(IV) cation complexation discussed by
Nagy et al. [8–10].
The mechanism of biological action of organotin(IV)
complexes has not yet been fully understood and being the
subject of much controversy. Several studies have been
reported on the interaction of tin complexes with DNA by a
number of different techniques [3,11,12]. The results of Tin-
119 Mossbauer titration of dimethyl(IV)tin hydroxide with
DNA showed that the bases and phosphodiester groups of
DNA do not exhibit consistent affinity for the tin cation in
SnMe2(OH)2 which is formed at physiological pH [13,14].
Further, Mossbauer spectroscopy for SnIVRn–DNA con-
densates confirmed bidentate coordination of the phosphate
groups and the formation of mixed hydroxo complexes in
the weakly acidic, neutral and strongly basic pH ranges.
Two vicinal phosphodiester groups (from DNA duplex)
were cis-coordinated and gave an octahedral geometry for
Sn cation [15]. The coordination of Me2Sn(IV) to mono-
nucleotides showed direct Sn-phosphate binding and no
direct Sn-base interaction [16]. The UV and circular
It is well known that organotin(IV) compounds display
strong biological activity. An overview of organotin
chemistry is recently reported and their antitumor activities
have been discussed [1,2]. They are known to exert
therapeutic effects on various tumor cells [3]. Diorganotin
(IV) derivatives and mainly those of dialkyltin(IV) appear to
be the most effective [4,5]. The biological and anticancer
activities of organotin compounds have been studied by
Saxena in 1989 [1]. The activity of a wide range of bio-
organotin(IV) compounds were investigated by Molloy [6].
The applications of tin and tin organometallic compounds in
pharmacy were studied by Tsangoris and Williams [7].
*
Corresponding author. Tel.: C98 21 2408164; fax: C98 21 2408164.
E-mail address: drshohreh@yahoo.com (Sh. Nafisi).
0022-2860/$ - see front matter q 2005 Elsevier B.V. All rights reserved.
doi:10.1016/j.molstruc.2005.04.008

S. Nafisi et al. / Journal of Molecular Structure 750 (2005) 22–27
23
dichroism spectra of Me2SnCl2 solution added to calf
thymus DNA at neutral pH suggested cation binding to
phosphodiester residue, with no alteration of DNA confor-
mation [17]. The 31P-NMR results demonstrated that
phosphate groups of DNA act as binding sites for
dimethyltin(IV) between pH 4.5 and 7 [3,18]. However,
there has been no report on the interaction of tin or organotin
complexes with RNA in aqueous solution. Therefore, it was
of interest to examine the binding of Sn(CH3)2Cl2 to DNA
and RNA bases and the backbone phosphate group. FTIR
and UV–Visible spectroscopic methods were often used to
characterize the nature of drug–DNA and drug–RNA
interactions [19–21].
Infrared spectra were recorded on a Thermo Nicolet
NEXUS model 870 FTIR with a DTGS detector and KBr
beam splitter. Solution spectra were taken using AgBr
windows with resolution of 4 cmK1 and 128 scans. Each set
of infrared spectra was taken (three times). The water
subtraction was carried out with 0.1 mM NaCl solution used
as a reference at pH 6.5–7.5 [22]. A good subtraction was
achieved as shown by a flat baseline around 2200 cmK1
where the water combination mode is located. The spectra
were analyzed with OMNIC software. The FTIR difference
spectra [(DNA solutionCdrug solution)K(DNA solution)]
and [(RNA solutionCdrug solution)K(RNA solution)]
were produced, using the bands at 968 cmK1 for DNA and
862 cmK1 for RNA as internal references. The vibrations at
968 (DNA) and 862 cmK1 (RNA) are due to the sugar C–C
and sugar phosphate stretching modes and show no spectral
changes upon Sn(CH3)2Cl2 complexation. These intensity
ratios were used to determine drug binding to DNA and
RNA bases or the backbone phosphate groups. Similar
intensity variations have been used to determine the drug
binding to DNA and RNA bases and the backbone
phosphate groups [23,24].
We now report a comparative study of DNA and RNA
interactions with Sn(CH3)2Cl2 in aqueous solution using
different cation concentrations (0.3–12.5 mM) with DNA or
RNA concentration of 6.25 mM. Fourier transform infrared
(FTIR) and UV–Visible spectroscopic methods were used to
obtain structural information regarding the cation binding
mode, apparent binding constant, and the effects of cation
complexation on the biopolymer secondary structure.
2. Experimental
3. Results and discussion
2.1. Materials and methods
3.1. FTIR spectra of Sn(CH3)2Cl2–DNA complexes
Highly polymerized type I Calf thymus DNA sodium salt
(7% Na content)waspurchasedfromSigmaChemicalCo. and
was deproteinated by the addition of CHCl3 and isoamyl
alcohol in NaCl solution. Baker yeast RNA sodium salt was
purchased from Sigma and used as supplied. Sn(CH3)2Cl2 was
fromMerckCompany.Otherchemicalswereofreagentgrade.
The infrared spectral features related to this discussion
are presented in Fig. 1. Intensity ratio variations for several
DNA in-plane vibrations as a function of Sn(CH3)2Cl2
concentrations are shown in Fig. 2A. Evidence for drug
binding to A-T, G-C or phosphate comes from spectral
changes in DNA in-plane vibrations at 1710 (G, T; mainly
guanine), 1662 (T, G, A, C; mainly thymine), 1610 (A, C;
mainly adenine), 1492 (C, G; mainly cytosine), 1226 (PO2
asymmetric) and 1088 cmK1 (PO2 symmetric) [23–30].
At rZ1/40, decrease of intensity was observed for the
guanine band at 1710 (20%), thymine at 1662 (25%),
adenine at 1610 (50%), cytosine at 1492 (20%), PO2
asymmetric at 1226 (20%) and symmetric at 1088 cmK1
(20%), upon addition of Sn(CH3)2Cl2 (Fig. 2A). However,
no major shifting was observed for these vibrations on
cation interaction (DnZ2 cmK1) (Fig. 1). The observed
spectral changes are due to DNA aggregation in the
presence of organotinhyroxo complexes. Cation binding to
DNA bases and the phosphate group causes major increase
of intensity and shifting of these vibrations, while the loss of
intensity has been attributed to DNA aggregation, conden-
sation or helix stabilization [29–31].
2.2. Preparation of stock solutions
Na–DNA or Na–RNA were dissolved to 0.5% w/w,
12.5 mM DNA (phosphate) in water solution at 5 8C for
24 h with occasional stirring to ensure formation of
homogeneous solution. The solutions of Sn(CH3)2Cl2 at
different concentrations (2.5, 1.25, 0.625, 0.312 mM) were
also prepared. Mixtures of drug and polynucleotides were
prepared by adding Sn(CH3)2Cl2 dropwise to the poly-
nucleotide solutions with constant stirring to give the
desired drug/polynucleotide(P) molar ratios of 1/40, 1/20,
1/10, and 1/5 at a final DNA and RNA concentration of
0.25% w/w or 6.25 mM DNA(phosphate) or RNA(pho-
sphate). Solution pH was adjusted between 6 and 7 with
NaOH solution (0.1 M). The IR spectra were recorded 3 h
after initial mixing of drug and polynucleotide solutions.
The drug molar ratio more than 1/5 causes DNA gel
formation and precipitation.
As Sn(CH3)2Cl2 concentration increased (rZ1/20 and
1/10), the guanine band at 1710 gained minor intensity
(10%) (Fig. 2A). Similar intensity increase was also
observed for the thymine band at 1662 (13%) and adenine
band at 1609 cmK1 (15%) and cytosine band at 1492 cmK1
(10%) (Fig. 2A). The asymmetric phosphate vibration at
The absorption spectra were recorded on a LKB model
4054 UV-VIS spectrometer, using various Sn(CH3)2Cl2
concentrations of 5 mM to 0.05 mM with final DNA(P) and
RNA concentration of 0.1 mM.

24
S. Nafisi et al. / Journal of Molecular Structure 750 (2005) 22–27
Fig. 2. Intensity ratio variations for several DNA and RNA in-plane
vibrations as a function of Sn(CH3)2Cl2 concentration. (A) Intensity ratios
for the DNA bands at 1710 (G, T), 1662 (T, G, A, C),1609 (A), 1492 (C,G),
1226 (PO2 asymmetric stretch) and 1088 cmK1 (PO2 symmetric stretch)
referenced to the DNA band at 968 cmK1; (B) intensity ratios for the RNA
bands at 1698 cmK1 (G, U), 1653 cmK1 (U), 1609 cmK1 (A), 1489 cmK1
(G, C) and 1241 cmK1 (PO2 stretch) referenced to RNA band at 862 cmK1
.
rZ1/40) (Fig. 2A). Since, larger intensity increases were
observed for the PO2 bands at 1226 and 1088 cmK1
(compared with those of the bases vibrations), it is
reasonable to assume that some degree of cation-PO2
interaction occured at higher metal ion concentrations (1/20
and 1/10). However, such interaction with phosphate group
would be through OH groups of the Sn-hydroxo complexes
formed in aqueous solution. As cation concentration
increased (rZ1/5), no further spectral changes observed,
which is indicative of no more Sn–DNA complexation at
high cation concentration (Fig. 2A).
Fig. 1. FTIR spectra in the region of 1800–600 cmK1 for free calf-thymus
DNA and free Sn(CH3)2Cl2, and Sn(CH3)2Cl2–DNA adducts in aqueous
solution at pH 6.5–7.5 (top four spectra) and difference spectra for
Sn(CH3)2Cl2–DNA adducts obtained at various Sn(CH3)2Cl2–DNA
(phosphate) molar ratios (bottom two spectra).
3.2. FTIR spectra of Sn(CH3)2Cl2–RNA complexes
The infrared spectra of Sn(CH3)2Cl2–RNA adducts with
various molar ratios of Sn(CH3)2Cl2–RNA (phosphate)
were recorded. The spectral changes (intensity and shifting)
of several RNA in plane vibrations at 1698 cmK1 (G, U;
mainly guanine), 1653 cmK1 (U, G, A and C; mainly
uracil), 1609 cmK1 (A), 1489 cmK1 (C) and 1241 cmK1
1226 cmK1 shifted to 1225 cmK1 and exhibited intensity
increase (20%) together with the symmetric PO2 vibration at
1088 cmK1 with increase in intensity (15%) (this increase in
intensity was compared with the intensity of the bands at

S. Nafisi et al. / Journal of Molecular Structure 750 (2005) 22–27
25
At rZ1/40, the intensity of the bands at 1698 cmK1 (G)
(58%), 1653 cmK1 (59%), 1609 cmK1 (A) (61%),
1489 cmK1(C) (65%) and 1241 cmK1 (PO2) (58%)
decreased, respectively, (relative to free RNA) (Fig. 2B).
The major decrease in intensity can be due to RNA
aggregation in the presence of organotinhydroxo com-
plexes. The intensity variations were associated with the
shift of the bands at 1698 (mainly G) to 1690 cmK1, 1609
(A) to 1607 cmK1 and 1241 (PO2 stretch) to 1240 cmK1
(Fig. 3). No shifting was observed for the uracil band at
1653 cmK1 and cytosine band at 1489 cmK1. The observed
spectral changes can be due to drug interaction (indirectly)
with the guanine and to a lesser extent with adenine bases
(Fig. 3).
As concentration increased (rZ1/20), no major intensity
changes observed, but the guanine band at 1698 shifted to
1685 cmK1 (DnZ13 cmK1) (Fig. 3). The major shifting
observed for the guanine band at 1698 cmK1 is due to the
Sn–RNA interaction indirectly via guanine N7 and O6.
Similar spectral changes were observed in the Ag-RNA
interaction [31]. At this concentartion, the uracil band
at 1653 shifted to 1660 cmK1, adenine band at 1609 shifted
to 1607 cmK1 and the cytosine band at 1489 shifted to
1485 cmK1. The observed spectral changes can be due to tin
indirect drug interactions with G-C and A-U base pairs.
As drug concentration increased (rZ1/10, 1/5), major
increases in the intensities of RNA bands were observed in
the Sn(CH3)2Cl2–RNA complexes (Figs. 2B and 3). These
intensity variations were also associated with the shifting of
the bands at
1698 (G) to 1694 cmK1 (rZ1/10); 1687 cmK1 (rZ1/5);
1653 (U) to 1654 cmK1 (rZ1/10); 1659 cmK1 (rZ1/5);
1609 (A) to 1607 cmK1 (rZ1/10); 1605 cmK1 (rZ1/5);
1489 (C) to 1490 cmK1 (rZ1/10); 1484 cmK1 (rZ1/5);
1241 (PO2) to 1239 cmK1 (rZ1/10); 1236 cmK1
(rZ1/ 5); (Fig. 3).
These spectral changes can be attributed to the Sn
binding to G-C and A-U base pairs as well as PO2 group.
3.3. DNA and RNA conformations
No conformational transition was observed in Sn(CH3)2
Cl2–DNA complexes. In the free DNA spectrum, the marker
bands at 1710–1717 cmK1 (G), 1222–1227 cmK1 (asym-
metric PO2 stretching), 893 and 860 cmK1 (sugar-phosphate
stretching) and 836 cmK1 (phosphodiester mode) (Fig. 1),
are due to B-DNA conformation [38–42]. When B to A
transition occurs, the DNA marker bands are shifted to
1710–1700, 1225–1240, 825–800 cmK1, respectively, and a
new band appears at about 870–860 cmK1 [40–42]. In the B
to Z conformational transition, the sugar-phosphate band at
836 cmK1 appears at about 800–780 cmK1, and the guanine
band displaces to 1690 cmK1, while the PO2 stretching
vibration shifts to 1216 cmK1. Since, the sugar-phosphate
Fig. 3. FTIR spectra in the region of 1800–600 cmK1 for free yeast RNA
and yeast RNA, free Sn(CH3)2Cl2, and Sn(CH3)2Cl2–RNA adducts in
aqueous solution at pH 6.5–7.5 (top four spectra) and difference spectra for
Sn(CH3)2Cl2–polynucleotides adducts obtained at various Sn(CH3)2Cl2–
RNA (phosphate) molar ratios (bottom two spectra).
(PO2 asymmetric stretch) [21,22,30–37] were monitored at
different drug concentrations (Figs. 2B and 3).
It should be noted that, Sn(CH3)2Cl2 hydrolyzes in water
to produce Sn(CH3)2(OH)2 species that can bind indirectly
to RNA bases, phosphate and deoxyribose.

26
S. Nafisi et al. / Journal of Molecular Structure 750 (2005) 22–27
bands at 836 and 893 cmK1 exhibited no major shifting in
the spectra of the Sn(CH3)2Cl2–DNA adducts, the DNA
remains in the B-family structure. However, minor spectral
changes (shifting and intensity changes) in the region of
1060–600 cmK1 of Sn(CH3)2Cl2–DNA complexes can be
attributed to the alterations of the sugar-phosphate geometry
while DNA remains in the B-family structures (Fig. 1).
RNA remains in the A-family structure in the Sn–RNA
adducts. The marker bands for A-RNA conformation at 862,
810 cmK1 (due to ribose-phosphate vibrations), 1241(PO2
stretch) and 1698 (G) [42] did not show major shifting in the
spectra of Sn–RNA complexes, indicating of RNA remain-
ing in A-conformation (Fig. 3). The minor intensity
variations for RNA marker bands at 862, 810 and
800 cmK1 are related to a perturbations of the sugar-
phosphate backbone geometry upon drug interaction
(Fig. 3), while RNA remains in A-conformation.
proportionally increased as a function of 1/[free drug]
(Fig. 4), and thus, the overall binding constants
are estimated to be KZ1.47!105 MK1 for Sn(CH3)2Cl2–
DNA and KZ7.33!105 MK1 for Sn(CH3)2Cl2–RNA
complexes. The extra stability of Sn–RNA adducts
(KZ7.33!105 MK1) over Sn–DNA complexes (KZ
1.47!105 MK1) can be attributed to the less double helical
structure of RNA, which provides greater accessibility for
drug interaction with RNA bases. Similar association
constants were reported for DNA and RNA complexes
with AZT [20,21], Taxol [45], chlorophyll, chlorophyllin
[23,25,46] and biogenic polyamines [47].
On the basis of our spectroscopic results the following
conclusions are made (a) Sn(CH3)2Cl2 hydrolysis in
aqueous solution to give metal hydroxo species. (b) DNA
and RNA aggregation occurred in the presence of organotin
complexes. (c) Metal hydorxo complexes bind DNA mainly
through the backbone phosphate group indirectly (via cation
hydroxyl groups) with overall binding constant of KZ
1.47!105 MK1. (d) RNA binding is mainly through
backbone phosphate group with minor interaction with
RNA bases at high drug concentration and KZ7.33!
105 MK1. (e) The indirect cation bindings results in a partial
helix stabilization with no alterations of the B-DNA or
A-RNA structure.
3.4. Absorption spectra of Sn(CH3)2Cl2–DNA complexes
The calculation of the overall binding constants were
carried out using UV spectroscopy as reported.[43,44] The
double reciprocal plot of 1/[drug complexed] vs. 1/[drug] is
linear and the binding constant (K) is calculated from the
ratio of the intercept on the vertical coordinate axis to the
slope (Fig. 4). Concentrations of complexed drug were
determined by subtracting absorbance of uncomplexed
DNA and RNA at 260 nm from those of the complexed
DNA and RNA. Concentrations of drugs were determined
by subtraction of complexed drug from total drug used for
the experiment. Our data of 1/[drug complexed] almost
Acknowledgements
We greatly appreciate the financial support received
from AZAD university, Tehran Central Branch, Iran and
Hematology, Oncology and BMT Research Center, Shariati
Hospital, University of Tehran, Iran and the Natural
Sciences and Engineering Research Council of Canada
(NSERC).
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