Interaction between DNA and cationic diester-bonded Gemini surfactants

Article abstract of DOI:10.1016/j.molliq.2014.05.013

The formation of the polyion-complex between three cationic diester-bonded Gemini surfactants and DNA has been demonstrated systematically. This was studied through the electrostatic attraction between ammonium head groups of Gemini surfactants and the phosphate groups of DNA. Ethidium bromide exclusion assay indicates the interaction between DNA and diester-bonded Gemini surfactants. DNA binding abilities with the Gemini surfactant depends on tail length which has been demonstrated by agarose gel electrophoresis and circular dichroism (CD) measurements. Dynamic light scattering measurements reveal that the ester-bonded Gemini surfactants can induce the collapse of DNA into densely packed bead-like structures with smaller size. Molecular docking technique was also utilized to understand the mode and mechanism of interaction between DNA and the Gemini surfactants (pre-micellar form). In addition to electrostatic interactions between the negatively charged phosphate backbone of DNA and positively charged head groups of Gemini surfactants, self-association due to hydrophobic interactions between the alkyl tails of surfactant and the hydrogen bonding between the ester group of surfactant and nucleotide bases, result in the compaction of nucleotides.

Full text of DOI:10.1016/j.molliq.2014.05.013

MOLLIQ-04280; No of Pages 6
Journal of Molecular Liquids xxx (2014) xxx–xxx
Contents lists available at ScienceDirect
Journal of Molecular Liquids
journal homepage: www.elsevier.com/locate/molliq
1
Interaction between DNA and cationic diester bonded Gemini surfactants
b
b
c
2Q1 Zahid Yaseen a, , Sayeed Ur Rehman , Mohammad Tabish , Kabir-ud-Din
⁎
a
3
4
5
Department of Civil Engineering, Islamic University of Science and Technology, Awantipora, India
Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
Department of Chemistry, Aligarh Muslim University, Aligarh 202002, India
b
c
6
a r t i c l e i n f o
a b s t r a c t
OOF
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Article history:
The formation of the polyion-complex between three cationic diester bonded Gemini surfactants and DNA has 17
been demonstrated systematically. This was studied through the electrostatic attraction between ammonium 18
head groups of Gemini surfactants and the phosphate groups of DNA. Ethidium bromide exclusion assay indicates 19
the interaction between DNA and diester bonded Gemini surfactants. DNA binding abilities with the Gemini sur- 20
factant depends on tail length which has been demonstrated by agarose gel electrophoresis and circular dichro- 21
ism (CD) measurements. Dynamic light scattering measurements reveal that the ester bonded Gemini 22
surfactants can induce the collapse of DNA into densely packed bead-like structures with smaller size. Molecular 23
docking technique was also utilized to understand the mode and mechanism of interaction between DNA and the 24
Gemini surfactants (pre-micellar form). In addition to electrostatic interactions between the negatively charged 25
phosphate backbone of DNA and positively charged head groups of Gemini surfactants, self-association due to 26
hydrophobic interactions between the alkyl tails of surfactant and the hydrogen bonding between the ester 27
Received 15 March 2014
Received in revised form 7 May 2014
Accepted 21 May 2014
Available online xxxx
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Keywords:
DNA–cationic Gemini surfactant interaction
Compaction of nucleotides
Molecular docking
Cationic diester bonded Gemini surfactants
group of surfactant and nitrogenous bases, results in the compaction of nucleotides.
© 2014 Published by Elsevier B.V.
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1. Introduction
the practical usage of these surfactants [7]. Therefore, it is worthwhile 56
to develop biodegradable, eco-friendly and biocompatible surfactants 57
and study their interaction with DNA in aqueous solution in order to 58
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The modern treatment protocol, known as gene therapy, is an ap-
proach to treat the inherited disease by transfection that is transferring
a correct copy of the defective gene into the cells. In the field of
bionanotechnology, nonviral gene delivery has been a goal for many
years [1]. The inherent immunological risks with viral vectors provide
large incentives towards the development of nonviral vectors capable
of targeted and triggered release of DNA [2,3]. Various complex agents
such as cationic surfactants, lipids, poly-electrolytes, multivalent ions
and alcohols have been used in the development of new nonviral trans-
fection agents for decades [4]. Earlier, in vitro and in vivo delivery of inter-
feron-γ plasmid was achieved by using the m-s-m type model Gemini
surfactants, the so-called alkanediyl-α,ω-bis(dimethylalkylammonium
bromide), where m represents the carbon chain length of the alkyl tail
and s the number of carbon atom in the spacer and the dependence of
the carbon number (m) of the alkyl side chain and spacer on the trans-
fection efficiency was determined [5]. Bhadani and Singh [6] reported
check their potential in gene delivery.
59
The architecture of surfactant plays vital role in controlling the interac- 60
tion between DNA and surfactant. Incorporation of esters as the labile 61
linker in variety of lipids results in successful transfection [8–10]. It has 62
been shown that the orientation of the ester linkage can have significant 63
effect on the transfection efficiency [11]. Cationic Gemini surfactants, 64
structurally analogous to complex cationic lipids used for transfection 65
studies, have received increasing attention as simpler models for transfec- 66
tion complexes [12–17]. An in-depth study of these systems could be 67
beneficial for the better understanding of DNA–surfactant complex for- 68
mation. The first important step for any agent to prove its transfection po- 69
tential depends on its binding affinity, and mode of binding with DNA. 70
Recently synthesized Gemini surfactants [18–20] (Scheme 1), containing 71
cleavable diester group in the spacer part, referred to as m-E2-m type sur- 72
factant where m = 12, 14, and 16 is the number of carbon atoms in alkyl 7Q33
tail and E2 represents the diester group in the spacer part of Gemini sur- 74
factants (ethane-1,2-diyl bis(N,N-dimethyl-N-alkylammoniumacetoxy) 75
dichloride) have special importance due to having two ester groups 76
(E2). The surfactants m-E2-m have shown promising potential in solubi- 77
lization of various polyaromatic carcinogenic materials [19,20]. These 78
new diester-group-containing Gemini surfactants have low cmc (critical 79
micelle concentration) values, with cleavable nature, and low cytotoxicity 80
[19–21], which can be utilized in several technical areas including the 81
the binding affinity Uof thiNoesterCspaceOrs ofRimidaRzoliumEGemCini TED PR
sion experiments. Despite remarkable progress of cationic surfactants
in gene delivery, a number of limitations preclude enthusiasm including
cytotoxicity, environmental concerns and aquatic toxicity which limit
5Q2 2 surfactants by agarose gel electrophoresis and ethidium bromide exclu-
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Corresponding author. Tel.: +91 9797264038 (mobile).
E-mail address: zadn521@gmail.com (Z. Yaseen).
biomedical application of gene delivery.
82
http://dx.doi.org/10.1016/j.molliq.2014.05.013
0167-7322/© 2014 Published by Elsevier B.V.
Please cite this article as: Z. Yaseen, et al., J. Mol. Liq. (2014), http://dx.doi.org/10.1016/j.molliq.2014.05.013

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Z. Yaseen et al. / Journal of Molecular Liquids xxx (2014) xxx–xxx
C12H25-E2- C12H25
C14H29-E2-C14H29
C16H33-E2- C16H33
Scheme 1. Chemical structures of the ester bonded Gemini surfactants used in the present study.
83
84
85
86
87
88
89
90
91
92
93
In the present studies, we have investigated the interaction between
ethane-1,2-diylbis(chloroacetate). Ether was used in separation of 104
ethane-1,2-diylbis(chloroacetate), followed by washing with satu- 105
rated solution of sodium chloride. The organic phase was dried 106
over magnesium sulfate. In the next step, a mixture of ethane-1,2- 107
diylbis(chloroacetate) and N,N-dimethylalkylamine (molar ratio = 108
1:2.1) was refluxed for 10 h in ethyl acetate. Finally, the solvent was re- 109
moved under vacuum and white crystalline solid of the cationic Gemini 110
surfactants was obtained (Scheme 2). After recrystallization, the three 111
surfactants were characterized by 1H NMR and FT-IR [19–21]. The 112
data were in agreement with the literature values. The purity was 113
further ascertained on the basis of absence of minima in their surface 114
dicationic ester bonded Gemini surfactants m-E2-m and DNA. The ulti-
mate objective is to find out the mode of binding of these surfactants
with DNA and also to relate the correlation between the alkyl tail length
and DNA binding affinities. To achieve a deeper understanding of the in-
teraction, a host of techniques have been employed to obtain broader
and more integrated information. Based on these studies, we have
shown herein that there exists a strong interaction between the
diester-bonded Gemini surfactants and DNA. These studies reveal as
how the hydrophobic effects and the specific surface charges play im-
portant roles in bringing about profound changes in DNA structures.
tension–concentration isotherms [22].
115
94
95
2. Experimental
2.1. Materials
2.2. Sample preparation
116
96
97
98
99
Ethylene glycol, N, N-dimethylalkylamine, calf thymus DNA and
ethidium bromide (EB) were purchased from Sigma Aldrich (St. Louis,
USA). Plasmid pUC19 DNA (0.5 μg/μL, 2686 bp) was purchased
from GeNei (India). Tris buffer was purchased from Fisher Scientific.
1 mg of calf thymus DNA was dissolved in 1 mL of 0.1 M Tris buffer 117
(pH = 7.2) at 298 K and kept for 24 h with occasional stirring to ensure 118
formation of a homogenous solution. The concentration of the DNA was 119
determined spectrophotometrically using molar extinction coefficient of 120
6600 M−1 cm−1 at 260 nm [23]. The purity of the DNA solution was 121
checked from the absorbance ratio A260/A280. Since the attenuance ratio 122
of the above purified DNA lied in the range of 1.8 b A260/A280 b 1.9, no 123
100 The dimeric Gemini surfactants m-E2-m. 2Cl− were synthesized by
101 following a procedure described in the literature [18]. In brief,
102 chloroacetyl chloride (0.22 mol) was added drop wise to ethylene glycol
103 (0.1 mol) and the reaction mixture was heated at 50 °C for 8 h to obtain
further purification was needed.
124
HO
O
50O C, 8hr
Cl
O
+
O
Cl
2ClCH2COCl
N2
O
OH
O
O
CH3
H3C
R
CH3
R
reflux, 10h
ethylacetate
Cl
O
N+
O
O
Cl
O
N+
N
R
-
. 2 Cl
+
H3C
CH3
CH3
O
O
R = CmH2m+1 ( m=12, 14, 16)
Scheme 2. Synthesis protocol of ethane-1,2-diyl bis(N,N-dimethyl-N-alkylammoniumacetoxy) dichloride Gemini surfactants.
Please cite this article as: Z. Yaseen, et al., J. Mol. Liq. (2014), http://dx.doi.org/10.1016/j.molliq.2014.05.013

Z. Yaseen et al. / Journal of Molecular Liquids xxx (2014) xxx–xxx
3
125 2.3. Steady state fluorescence measurements
126
Fluorescence measurements were recorded on a Shimadzu
3. Results and discussion
178
179
3.1. Effect of Gemini surfactants on EB displacement assay
127 spectrofluorimeter-5000 (Japan). In EB exclusion assay, the excitation
128 with EB was set at 473 nm and emission in the range of 550–625 nm.
129 5 μg of pUC19 DNA in a volume of 10 μL was used for each experiment
130 and DNA was directly mixed with 1 μL of EB in the fluorescence cell;
131 buffer was added to make the final volume 3 mL.
Ethidium bromide (EB) [27], a phenathridine fluorescence dye, is a 180
typical indicator of intercalation that forms soluble complexes with 181
nucleic acids and emits intense fluorescence in the presence of DNA 182
due to the intercalation of the planar ring between the nucleotide 183
base pairs of DNA. To study the interaction between DNA and other 184
compounds, the changes in the spectra of EB on its binding to DNA are 185
often used. Fig. 1 shows the fluorescence emission spectra of DNA/EB 186
complex and the spectra after gradual addition of the Gemini surfac- 187
tants. The progressive addition of surfactant into the premixed DNA– 188
EB solution results in the displacement of intercalated EB from the 189
DNA/EB complexes, leading to gradual fluorescence quenching. The 190
concentrations of the surfactants (12-E2-12, 14-E2-14, 16-E2-16) re- 191
quired to displace ethidium bromide from the DNA, which brings de- 192
crease in fluorescence intensity, have been determined by plotting 193
relative fluorescence intensity F/Fο, at 590 nm vs. concentration of 194
surfactant (in mM), as shown in Fig. 1 (where Fο is the fluorescence in- 195
132 2.4. Agarose gel electrophoresis
133
134
135
136
Different concentrations of surfactants, 3 μL of 0.5 μg/μL of pUC19 DNA
and 2 μL of EB were mixed and incubated at room temperature for 1 h in a
total volume of 10 μL. Samples were electrophoresed using 1% agarose gel
and the DNA bands were visualized under UV transilluminator.
137 2.5. Circular dichroism measurements
138
Far UV-CD spectra were recorded on an applied Photo physics (U.K.)
tensity of DNA–EB complex and F is fluorescence intensity after adding 196
OOF
139 (model CIRASCAN) spectrophotometer equipped with a Peltier temper-
140 ature controller using a rectangular quartz cuvette of path length
141 10 mm. The spectra shown are average of three successive scans record-
142 ed at a scan speed 200 nm/min. The contribution of buffer on the mea-
143 sured ellipticity was subtracted as blank. The data were subjected to
144 noise reduction analysis. All the experiments were performed at ambi-
145 ent temperature (298 K) with air-equilibrated solutions and in Tris
146 buffer of pH 7.0.
surfactant to DNA–EB complex). It has been observed that quenching in 197
fluorescence intensity is less in case of 12-E2-12; however, the behavior 198
of decrease is almost similar in case of 14-E2-14 and 16-E2-16, though 199
14-E2-14 shows more quenching efficiency as compared to 16-E2-16. 200
Increasing tail length of the surfactant results in an increase in hydro- 201
phobicity of the surfactant and, as a consequence, increased compaction 202
efficiency. However, surfactants with too long chains may also provide 203
sufficient amount of steric strains to get adjusted on the helical structure 204
of DNA and also make the surfactant insoluble, therefore, be less effi- 205
cient in DNA compaction [28].
206
147 2.6. Dynamic light scattering measurements
The DNA–Gemini surfactant mixtures were made by mixing equal 207
amount of pUC19 DNA with different concentrations of the Gemini sur- 208
factants and incubated for 60 min at room temperature. These mixtures 209
were then subjected to electrophoresis after adding EB and the gel 210
images were captured on UV transilluminator. As shown in Fig. 2 211
(lane a), pUC 19 DNA was run without any surfactant as control. The 212
DNA + 12-E2-12 mixtures show noticeable fading of the bands and 213
the band intensity shows consistent decrease with increasing concen- 214
tration of the 12-E2-12 surfactant from 10 μM to 50 μM (lanes b–e). 215
148
Dynamic light scattering (DLS) measurements were performed
149 using a Laser-Spectroscatter 201 by RiNA GmbH, Berlin, Germany.
150 In DLS measurements, a beam of laser is guided towards the sample
151 under investigation, with a fixed detection arrangement of 90° to
152 the center of the cell area and the fluctuation in the intensity of
153 the scattered light is measured. DNA and Gemini surfactant solu-
154 tions were dissolved in Tris–HCl buffer and then mixed to obtain dif-
155 ferent DNA/surfactant molar ratios ([DNA] = 1 μM, [Gemini] = 0.2
156 to 5 μM).
0.9
157 2.7. Molecular docking
0.8
12-E2-12
158
The rigid molecular docking studies were performed by using HEX
14-E2-14
159 6.1 software [24], and PATCHDOCK [25]. HEX 6.1 is an interactive molec-
160 ular graphics program for calculating and displaying feasible docking
161 modes of DNA. The HEX 6.1 performs protein docking using Spherical
162 Polar Fourier Correlations. It necessitates the ligand and the receptor
163 as input in PDB format. The parameters used for docking include: corre-
164 lation type — shape only, FFT mode — 3D, grid dimension — 0.6, receptor
165 range — 180, ligand range — 180, twist range — 360, and distance
16-E2-16
0.7
0.6
0.5
0.4
0.3
UNCORRECTED PR
166 range — 40. PATCHDOCK is an algorithm for molecular docking. The
167 input is two molecules in PDB format and the output is a list of poten-
168 tial complexes sorted by shape complementary criteria. The crystal
169 structure of the B DNA dodecamer d(CGCGAATTCGCG)2 (PDB ID:
170 1BNA) was downloaded from the protein data bank. The initial struc-
171 tures of the surfactant molecules were generated by molecular
172 modeling software Avogadro 1.01 using MMFF94 force field. The mole-
173 cules of surfactants were optimized for use in the present docking
20
30
40
50
60
70 80 90 100
174 study. They had their minimized total energy of 8.5–9.9 kcal mol−1
,
log [surfactant], mM
175 respectively. Visualization of the docked pose has been done by
176 using PyMol [26] (http://pymol.sourceforge.net/) molecular graphic or
177 graphics program.
Fig. 1. Relative fluorescence intensity (F/Fo) observed at 590 nm vs. log concentration
(mM) plot of DNA–EB-surfactant and DNA–EB complexes (λexc = 473 nm).
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Z. Yaseen et al. / Journal of Molecular Liquids xxx (2014) xxx–xxx
Fig. 2. Agarose gel electrophoresis of reaction mixtures containing DNA and cationic Gemini surfactants. The concentration of plasmid DNA was 150 ng/μL. (A) Lane a, DNA only; lanes b–e,
DNA and 12-E2-12 (10, 20, 30, 50 μM); lanes f–i, DNA and 14-E2-14 (10, 20, 30, 50 μM); and lanes j–m, DNA and 16-E2-16 (10, 20, 30, 50 μM).
216 DNA + 16-E2-16 mixtures (Fig. 2, lanes j–k) also show slight reduction
217 in the intensity of bands as compared to control and the band intensity
218 decreases with increase in concentration of the surfactant. However,
219 DNA + 14-E2-14 mixtures (Fig. 2, lanes f–i) display noticeable fading
220 in the intensity of bands and there is almost complete disappearance
221 of the DNA band at 50 μM of the surfactant. Thus, all the DNA–Gemini
222 surfactant complexes exhibit a change in the intensity when compared
223 with the control. The faint or invisibility of the DNA bands in the pres-
224 ence of Gemini surfactants in the agarose gel even after long ethidium
225 bromide staining indicated that DNA–Gemini surfactant complexes
226 lost the ability of intercalation towards the intercalator ethidium bro-
227 mide. This may be assumed due to the compaction between DNA and
228 Gemini surfactants. The DNA compaction may lead to alteration in the
229 native structure of DNA in water. However, this form of DNA can still re-
230 tain the double-stranded structure [29]. Such condensation of DNA
231 leaves insufficient space available for ethidium bromide to intercalate
232 and hence lose the fluorescence. The driving force for the compaction
233 of DNA is electrostatic in nature, where positively charged head group
234 of the surfactant interacts with negatively charged phosphate group of
235 DNA. A possible explanation for the interaction between DNA and
236 Gemini surfactants in concentration dependent manner is that the
237 head group of Gemini surfactant itself experiences entropy loss due to
238 electrostatic interactions with DNA. In order to compensate this loss, a
239 large number of surfactant molecules have to be present to gain in hy-
240 drophobic interactions by self-association. This results in a highly com-
241 pact DNA–Gemini surfactant complex and makes itself inaccessible to
242 intercalators such as ethidium bromide.
indicates the change in helicity of DNA double helix. This suggests that 268
Gemini surfactant molecules get adsorbed on the surface of DNA and 269
result in its compaction. It is evident from the Fig. 3 that the change in 270
ellipticity of DNA double helix in presence of 14-E2-14 is more in 271
comparison to 12-E2-12 and 16-E2-16, suggesting its stronger binding 272
affinity with DNA.
273
3.2. DNA–surfactant interaction and hydrodynamic diameter
274
Dynamic light scattering (DLS) gives direct observation of the 275
surfactant induced conformational changes in DNA chain, and size dis- 276
tribution of DNA/surfactant complexes could be obtained [33]. The var- 277
iation in the hydrodynamic diameter as a function of the concentration 278
of Gemini surfactant is shown in Fig. 4. DLS measurements could not be 279
carried out for pure Gemini surfactants due to low scattering intensity. 280
To avoid interaction between the DNA molecules, low concentration 281
of DNA (1 μM) was used. A single peak in the intensity weighted size 282
distribution of the DNA solution is attributed to the translational mode 283
of the molecules and resulting in a mean hydrodynamic radius of 284
about 300 nm. It was observed that with the addition of 0.2 μM of 285
Gemini surfactant, there was a significant decrease in the size of DNA– 286
Gemini complexes. As can be seen, with further addition of Gemini sur- 287
factants, a progressive decrease of the hydrodynamic diameter appears 288
and finally becomes almost constant. Such an enormous decrease in the 289
hydrodynamic diameter of the DNA–Gemini complexes indicates that 290
the DNA undergoes a discrete conformational change from extended 291
coiled state to a compact state by the addition of Gemini surfactants. 292
The DNA molecule undergoes compaction that leads to a shift in the 293
translational mode of DNA to lower hydrodynamic radius by the addi- 294
tion of surfactant molecules. Dias et al. [34] reported a gradual change 295
of the DNA size in presence of CTAB (cetyltrimethyl ammonium bro- 296
mide) and the existence of two populations in the sample, one of ex- 297
tended DNA coil coexisting with the DNA compacted molecules. 298
However, in our case we have not found existence of two populations 299
because of the abrupt change in hydrodynamic diameter of DNA, at 300
very low surfactant concentrations. This may be attributed to the higher 301
compaction efficiency of the ester bonded Gemini surfactants as com- 302
pared to the conventional one head/one tail CTAB. Cationic surfactants 303
interact with DNA by a combination of initial electrostatic interaction 304
followed by a cooperative binding of surfactant ligands to the same 305
DNA molecules (driven by hydrophobic forces). The diester group con- 306
taining Gemini surfactants m-E2-m has cmc (critical micelle concentra- 307
tion) values in a range from 1.3 to 1.6 μM [19–21]. In the presence of a 308
polyelectrolyte, surfactants show the aggregational behavior much 309
below their cmc values. The compaction of DNA is depicted due to the 310
surfactant self-assembly in the vicinity of the macromolecule; the sur- 311
factant self-assemblies are multivalent counterions which induce elec- 312
trostatic attractions between different parts of a DNA molecule due to 313
ion correlation effects [35,36]. In addition to this, ester bonded Gemini 314
surfactants also have tendency to participate in hydrogen bonding be- 315
tween the oxygen atom of the ester group in the spacer part of Gemini 316
243
To investigate the changes in the secondary structure of DNA upon
244 binding with cationic Gemini surfactants, circular dichroism experi-
245 ments were performed. This technique is useful to probe non-covalent
246 DNA–ligand interactions [30,31]. The secondary structure of DNA is
247 perturbed markedly by the intercalation of small molecules leaving its
248 signature through the changes in the intrinsic CD spectra of DNA.
249 Fig. 3 shows the CD spectra of DNA in buffer at pH 7, having a positive
250 peak at ~277 nm and a negative peak at ~244 nm, characteristic of the
251 right handed B form [32]. The peak position at 244 nm corresponds to
252 the helical superstructures of the polynucleotide that provide an asym-
253 metric environment for the nucleotide bases of DNA whereas peak at
254 position 277 nm occurs due to stacking interaction between the bases
255 of DNA. It is evident from Fig. 3 that there is noticeable change in the
256 negative peak at 244 nm, with only a slight change in the intensity of
257 the positive peak at 277 nm as the concentration of Gemini surfactants
258 increased from 20 to 60 μM, indicating change in the conformation of
259 DNA. Slight change in the intensity of the CD peak at 277 nm has been
260 associated with alteration of hydration layer of the helix in the vicinity
261 of phosphate or the ribose ring as the concentration of surfactant in-
262 creased. On progressive addition of surfactants, the Tris (buffer) ions
263 near the hydration layer of DNA helix may get exchanged with surfac-
264 tant molecules. Hydrophobic alkyl chain of surfactants changes the ex-
265 tent of hydration near the phosphate group of DNA double helix and
266 hence results in little perturbation in DNA helix. The peak at 244 nm
267 becoming more negative with progressive addition of surfactants
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Z. Yaseen et al. / Journal of Molecular Liquids xxx (2014) xxx–xxx
5
400
(a)
12-E2-12 [
0
20
350
300
250
200
150
100
50
20
40
60
12-E2-12+ DNA
14-E2-14+ DNA
16-E2-16+DNA
0
-20
240
260
280
300
0
1
2
OOF
3
4
5
Wavelength (nm)
[surfactant] ( M)
(b)
Fig. 4. Average hydrodynamic diameter Dh of DNA–Gemini surfactant complexes as a
function of the surfactant concentration.
20
14-E2-14 (
0
20
40
60
and the nitrogen bases in the nucleotide of DNA, leading to stronger in- 351
teraction between the two components.
352
3.3. Computational analysis of DNA–surfactant interaction
353
0
Molecular docking technique is an attractive tool in order to under- 354
stand the mechanistic details and mode of interaction between biopoly- 355
mers and ligands, which can corroborate the experimental results. In 356
this context docking studies were performed in an attempt to ascertain 357
the type and the amount of interaction between the Gemini surfactants 358
(in monomer form) and the DNA, as surfactant molecules bind to the 359
polymer in pre-micellar region. In our experiments rigid molecular 360
structure of DNA duplex with a sequence d(CGCGAATTCGCG)2 361
dodecamer (PDB ID: 1BNA) was taken and the ligand has been made 362
flexible to attain different conformations in order to predict the best 363
fit orientation, and the best energy docked structure was analyzed. 364
The docked structure, as shown in Fig. 5, suggests that the Gemini sur- 365
factants could bind to DNA by interacting with the phosphate backbone. 366
The molecular-modeling predicted lowest energy conformation in 367
which the head group of Gemini surfactant fits snugly into the curved 368
contour of the targeted DNA in the minor groove and the tails of the sur- 369
factant molecules align themselves in parallel fashion to the DNA helix. 370
Moreover, the ester groups of spacer part of the Gemini surfactants are 371
situated near the Adenine ↔ Thymine region of DNA double helix. 372
The ester groups in Gemini surfactant were stabilized by hydrogen 373
bonding between the oxygen atoms and the hydrogen atoms of deoxy 374
adenosine (DA5 and DA6 of strand A) of dodecamer. The resulting rela- 375
-20
220
240
260
280
300
wavelength (nm)
(c)
16-E2-16 (
20
20
40
60
80
0
UNCORRECTED PR
tive binding energy of docked DNA–Gemini surfactant complex was 376
found to be ~ −160–180 kJ mol−1, the negative values indicate higher 377
binding potential of the Gemini surfactants with DNA. For comparison 378
purpose, we have also run the docking program (HEX 6.1) on 379
C12H25N+(CH3)3. Br−, monomeric analog of 12-E2-12, and the Gemini 380
surfactant C12H25N+(CH3)2(CH2)8(CH3)2N+C12H25·2Br− and the ener- 381
gies evaluated were −114.2 and −140.11 kJ/mol, respectively. Thus 382
more binding energies in case of m-E2-m surfactants with DNA give 383
evidence of hydrogen bonding between the ester bonded Gemini 384
-20
220
240
260
280
300
Fig. 3. Circular dichroism spectra of ct-DNA in presence of different concentrations of
(a) 12-E2-12, (b) 14-E2-14, and (c) 16-E2-16 Gemini surfactants.
wavelength (nm)
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Z. Yaseen et al. / Journal of Molecular Liquids xxx (2014) xxx–xxx
(a)
(b)
Fig. 5. Poses of molecular docked model of 12-E2-12 Gemini surfactant with DNA [dodecamer duplex of sequence d(CGCGAATTCGCG)2 (PDB ID: 1BNA)].
[5] I. Badea, R. Verrall, M. Baca-Estrada, S. Tikoo, A. Rosenberg, P. Kumar, M. Foldvari, J. 421
385 surfactants and DNA. We see that there is a mutual complement be-
386 tween spectral techniques and molecular modeling, which provides
387 valuable information about the mode of interaction of the Gemini sur-
388 factants with DNA.
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389 4. Conclusions
390
The present work reports a study of the interaction of diester bonded
391 cationic Gemini surfactants with DNA. Intercalation ability of ethidium
392 bromide decreases in presence of the Gemini surfactants in ethidium
393 bromide exclusion assay, which indicates the compaction potential of
394 Gemini surfactants. This is also in agreement with the results obtained
395 from gel electrophoresis. The outcome from circular dichroism mea-
396 surements establishes that the Gemini surfactants interact with DNA
397 in a groove binding fashion. These Gemini surfactants show chain
398 length dependent binding capability as evidenced by fluorescence, elec-
399 trophoresis and CD studies. The extent of interaction with DNA in case
400 of 14-E2-14 is more as compared to 12-E2-12 and 16-E2-16. Due to
401 the presence of positive charge on the head groups of Gemini surfac-
402 tants, electrostatic binding of these self-organizing molecules to the an-
403 ionic DNA phosphate is facilitated. Although the binding leads to
404 entropy loss that is compensated due to hydrophobic interaction be-
405 tween the alkyl tails of surfactant, results in compaction of DNA are
406 also revealed from DLS study. Large negative values of binding energy
407 evaluated from molecular docking shed light on the possibility of hydro-
408 gen bonding also between the ester group of Gemini surfactants and
409 nitrogenous bases of DNA.
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Please cite this article as: Z. Yaseen, et al., J. Mol. Liq. (2014), http://dx.doi.org/10.1016/j.molliq.2014.05.013