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Materials Science and Engineering C 29 (2009) 539545

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Materials Science and Engineering C


j o u r n a l h o m e p a g e : w w w. e l s ev i e r. c o m / l o c a t e / m s e c

New approach to immobilization and specic-sequence detection of nucleic acids


based on poly(4-hydroxyphenylacetic acid)
Tatiana A.R. Silva a, Lucas F. Ferreira a, Letcia M. Souza a, Luiz R. Goulart b,
Joo M. Madurro a, Ana G. Brito-Madurro a,
a
b

Institute of Chemistry, Federal University of Uberlndia, Uberlndia, 38400-902, Brazil


Institute of Genetics and Biochemistry, Federal University of Uberlndia, Uberlndia, 38400-902, Brazil

a r t i c l e

i n f o

Article history:
Received 28 May 2008
Received in revised form 12 September 2008
Accepted 23 September 2008
Available online 9 October 2008
Keywords:
Modied electrode
Hybridization
Nucleic acids
Polymer lm

a b s t r a c t
Immobilization and hybridization of oligonucleotides or specic-gene PCR product (DENV-1), a conserved
genomic sequence of the dengue virus, onto graphite electrode modied with poly(4-hydroxyphenylacetic
acid), were carried out with success using both direct electrochemical oxidation of guanine or redox
electroactive indicator ethidium bromide.
Studies of oligonucleotides hybridization with the complementary target showed a decrease of both guanosine
and adenosine current peaks, when compared with the peak previously obtained before the hybridization.
Immobilized ssDNA, DENV-1, was hybridized with various concentrations of target DNA. The interaction
between DENV-1 hybridized onto the modied graphite electrodes surface and the intercalator, ethidium
bromide, was observed by differential pulse voltammetry, monitoring the current change generated to the DNA
intercalator accumulated onto the modied electrode after DNA hybridization. For the determination of
complementary target, the proposed method exhibited a good dynamic range (1242 nmol L 1) and a low
detection limit (7.12 nmol L 1).
AFM images showed that the oligonucleotides or single-stranded DNA, DENV-1, before hybridization, had
roughness values lower than the double stranded obtained after hybridization.
The new surface obtained in these work, as well as the possibility of utilization of the same to monitor
hybridization events is a promising strategy for the development of DNA electrochemical biosensors.
2008 Elsevier B.V. All rights reserved.

1. Introduction
The chemical modication of the surface of electrodes offers great
potential to help in the identication between target compounds that
have similar characteristic redox, increasing the efciency and
applicability of electrochemical sensors [1]. The ability to control
and to modify the properties of the surfaces of the electrodes can
provide a variety of attractive effects, which can effectively collaborate
for the solution of problems presented by traditional electrochemical
sensors [2]. The use of polymer lms offers several advantages in the
construction of sensors, since they are relatively cheap materials, the
techniques for the production are simple, they can be deposited on
various types of substrates and the choice of different molecular
structures provides the construction of lms with different characteristics [3]. The modication of the molecular composition of the
electrode aims at improving sensitivity, selectivity and/or stability
allowing the tailoring of its response in order to meet analytical needs
[46].

Corresponding author. Tel.: +55 34 32394442; fax: +55 34 32394208.


E-mail address: agbrito@iqufu.ufu.br (A.G. Brito-Madurro).
0928-4931/$ see front matter 2008 Elsevier B.V. All rights reserved.
doi:10.1016/j.msec.2008.09.048

The techniques currently used in the deposition of lms on


different areas are quite diverse. The methods of LangmuirBlodgett
and electrochemical polymerization are the most commonly used for
the construction of biosensors [3,7]. The advantage of the last method
is the control of the electrochemical deposition of the lm as
thickness, morphology and homogeneity in the formation of the
chain, ranging up the potential and the number of scans on the work
electrode [3,8].
The modication of surfaces with polymer lms has been used in
the development of biosensors to protect the surface of the electrodes
against impurities, block interferents, incorporate mediators and
provide biocompatibility [7]. The stage of the immobilization of
biomolecules or indicators on the surface of the electrode plays an
important role in obtaining the sensitivity, selectivity and stability of
the biosensor. These characteristics are achieved by means of a
chemical control and coverage of the area, thus ensuring reactivity,
accessibility and stability to the biomolecules immobilized [9].
The use of conducting and non-conducting lms is suitable for the
immobilization of DNA probes [9]. This feature is due to the ability of
being easily processed by the modied electrodes, with increase in the
contact area of the biomolecules with the electrode, which allows
greater accommodation of the molecule, simulating its natural

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T.A.R. Silva et al. / Materials Science and Engineering C 29 (2009) 539545

environment, favoring the conversion of the biological signal to fast


analytical signal with high stability and reproducibility [8,10]. Due
to the various characteristics presented by polymer lms, several
studies are found in the literature aimed at the construction of
biosensors [1113].
Since, as a whole, DNA is highly redox-inactive, an electrochemical
hybridization indicator is usually employed (indirect method). They can
bind DNA through reversible physical intercalation between base pairs
or through electrostatic interaction, in well-dened binding sites [14].
The effect is a differential accumulation of the indicator in the DNA layer
near the surface of the electrode when a ssDNA or a dsDNA is attached,
which correlates with different voltammetric peak currents [15]. The
most common indicators are heterocyclic dyes (e.g., ethidium bromide,
methylene blue, anthracyclines, phenotiazines and acridine derivatives),
anticancer drugs (e.g., daunomycin) and organomettalic complexes
(mainly from Co, Fe, Os, Pt and Ru). DNA hybridization biosensor holds
an enormous potential for pharmaceutical, clinical and forensic
application and disease diagnosis [16].
Dengue virus is a member of the Flaviviridae family and is one
of the most signicant causes of arthropod-borne diseases on
Earth. Dengue virus exists as four antigenically distinct serotypes
(Dengue 14) and is transmitted among humans by the Aedes aegypti
mosquito. Dengue is recognized in over 100 countries and territories,
and the worldwide annual infection rate is estimated to be between
50 and 100 million infections per year [17].
Recently, we investigated the electropolymerization of 4hydroxyphenylaceticacid on the surface of graphite electrodes, the
electrochemical and morphological properties of the polymer lm
formed and their applications in incorporation and electrooxidation of
nitrogenated bases of DNA. These electrodes modied with poly(4hydroxyphenylacetic acid) were found to be efcient in immobilizing
purine bases. Adenosine monophosphate and guanosine monophosphate presented an increase in the current values of the anodic
potential peak when compared to bare graphite electrodes. This
parameter is very important to guarantee the sensibility of the DNA
biosensor [18].
In this work, poly(4-hydroxyphenylacetic acid) was used as matrix
for the detection of a 18-mer synthetic oligonucleotide and a
conserved genomic sequence of the dengue virus (dengue 1 or
DENV1), aiming at contributing for biosensor development, once the
prevention of the disease has widely focused on mosquito eradication
strategies, which were of very limited success.
This is the rst report on oligonucleotide and DNA fragment
immobilization and detection of complementary target onto graphite
electrode modied with poly(4-hydroxyphenylacetic acid).
2. Experimental
2.1. Chemicals
All reagents used were of analytical grade. Ultra high purity water
(Millipore Milli-Q system) was used in the preparation of the solutions.
Oligonucleotide probes and target were synthesized by Invitrogen Life
Technologies with the following sequences: probe: poly(G) 5GGGGGGGGGGGGGGGG-3, poly(A) 5-AAAAAAAAAAAAAAAA-3, poly
(C) 5-CCCCCCCCCCCCCCCC-3, poly(T)5-TTTTTTTTTTTTTTTT-3, poly
(GA) 5-GGGGGGGGAAAAAAAA A-3, poly(CT) 3-CCCCCCCCTTTTTTTT5. Stock solutions of the probe (6.4 10 2 mmol L 1) and target
oligonucleotides (1.8 10 1 mmol L 1) were prepared in water and
stored at 20 C until use. Buffer components (CH3COOH and CH3COONa
or Na2HPO4 and NaH2PO4) were purchased from Sigma-Aldrich
Chemical, USA (ACS purity) and prepared at pH 4.7 and pH 7.4
respectively. Monomer solutions, 4-hydroxyphenylacetic acid, were
prepared in 0.5 mol L 1 HClO4 solution, immediately before their use. All
reagents were used as received. The experiments were conducted at
room temperature (25 1 C).

The gene-specic oligonucleotides for the dengue virus, DENV-1


(Probe and target) have as base sequences: DENV-1 (primer 1) 5-CAA
TAT GCT GAA ACG CGA GAG AAA CCG-3 and DENV-1 (primer 2) 5AGC AGC ATA AGG AGC ATG GTC AC-3. The DENV-1 (primer 1) was
used for Reverse Transcriptase-Polymerase Chain Reaction, RT-PCR,
and DENV-1 (primer 1 and primer 2) were used for Polymerase Chain
Reaction, PCR reaction.
2.2. Apparatus
All electrochemical experiments were carried out using a potentiostat CH Instruments, model 760 C connected to a serial output
program.
The electrochemical studies were carried using a graphite working
electrode of 6 mm diameter, cut from a graphite rod (99.9995%, Alfa
Aesar). Film morphology in absence or presence of biomolecules was
assessed by atomic force microscopy (AFM) (Nanoscope IIIa, Digital
Instruments). Polymerase chain reaction (PCR) was performed in a
thermocycler (Eppendorf Mastercycler).
2.3. Production of poly(4-hydroxyphenylacetic acid) [poly(4-HPA)]
The electrochemical studies were performed in a three-compartment
glass cell connected to a potentiostat. The graphite surface, prior to
electropolymerization, was mechanically polished with alumina
slurry (0.3 m diameter), ultrasonicated, washed with distilled
water and dried in the air. The monomer solutions were degassed
with N2 prior to electropolymerization. Poly(4-HPA) lms were
grown by means of potentiodynamic electropolymerization on
graphite electrodes from 4-hydroxyphenylacetic acid solution
(2.5 mmol L 1) in HClO4 solution (0.5 mol L 1). The potential cycling
was made between 0.70 V and + 1.20 V vs. SCE at 50 mV s 1. After
electropo1ymerization, the modied e1ectrode was rinsed in
deionized water to remove unreacted monomer. Preliminary studies
of the formation and characterization of poly(4-HPA) were described
previously by our group [18].
2.4. RT-PCR of dengue virus RNA, type 1, from human plasma
RNA from plasma specimens were isolated by using the Trizol
Reagent (Invitrogen), according to the manufactures' instructions.
First-strand cDNA was synthesized using a RT-PCR kit (Stratagene)
with a primer 1 and the RNA total as a template. The reaction was
carried out at 37 C for 1 h. Double strand DNA (dsDNA) was amplied
by PCR with the rst strand cDNA as a template and two primers
(primer 1 and primer 2).
PCR reactions contained 2 L of cDNA, 2 L forward and reverse
primers (nal concentration is 1 M for each primer), 2.5 L of PCR
buffer (100 mmol L 1 Tris HCl [pH 9.0], 0.75 L of 15 mmol L 1 MgCl2,
0.5 L of 10 mmol L 1 dNTP, 0.4 L of 2 U Platinum Taq DNA
polymerase (Invitrogen), and 13.85 L distilled water in a total volume
of 25 L.
PCR conditions were as follows: initial denaturation at 94 C for
1 min, followed by 35 cycles of denaturation at 94 C for 30 s,
annealing at 64 C for 30 s, and elongation at 72 C for 1 min, and nal
extension at 72 C for 3 min.
The PCR product was visualized in agarose gel stained with
ethidium bromide under UV light. The size of the PCR product was
288 bp. Subsequently, the concentration of dsDNA was measured by
the ultraviolet absorption at 260 nm ( = 6600 Lmol 1cm 1).
2.5. Oligonucleotide and DENV-1 probes immobilization on graphite
electrode modied with poly(4-HPA)
The immobilization of oligonucleotides was carried out by
applying 15 L of 6.4 10 2 mmol L 1 of poly(G), poly(A) or poly(GA).

T.A.R. Silva et al. / Materials Science and Engineering C 29 (2009) 539545

541

The amplicons obtained from PCR have a double helix structure


and the two strands should be separated (denatured) to allow the
hybridization with the probe immobilized on the sensor surface. To
DENV-1 immobilization, 15 L of 3.5 nmol L 1 dsDNA was rst
thermally denatured by using a dry-bath (5 min at +98 C). The
oligonucleotides or single-strand DNA (ssDNA) samples obtained
were immobilized by dropped on the modied electrodes and dried at
room temperature (25 1 C) in a dessicator for 5 min. The electrode
was immersed for 30 s in water. Differential pulse voltammetry
measurements were conducted using acetate buffer (0.1 mol L 1, pH
4.7) or phosphate buffer (0.1 mol L 1, pH 7.4) as electrolytes. All
potentials are referred to Ag/AgCl electrode. All voltammograms are
presented after baseline correction.
2.6. Hybridization detection of oligonucleotide or DENV-1 immobilized
on poly(4-HPA)
Hybridization experiments were carried out using both synthetic
oligonucleotides and amplied PCR target. After the immobilization of
the oligonucleotide probes, 15 L of 1.8 10 1 mmol L 1 poly(CT), poly
(T) or poly(C) targets were applied on the electrode modied.
Hybridization was carried out at 42 C for 20 min. The electrodes
were then rinsed by immersion in water, during 30 s, under agitation.
To DENV-1 detection, 15 L of 20 10 3 mol L 1 ethidium bromide was
added on the electrode surface. Another step of rinsing was carried out
by immersion in water during 30 s.
3. Results and discussion

Fig. 2. Differential pulse voltammograms of graphite electrode modied with poly(4HPA) prepared in pH 0.5 (baseline-corrected), 100 scans, containing poly(G) (Ia), poly(A)
(IIa), before hybridization and after 20 min incubation with non-complementary target:
poly(G) (Ib), poly(A) (IIb), or complementary target: poly(C) (Ic), poly(T) (IIc).
Electrolyte: 0.1 mol L 1 acetate buffer, pH 4.7. Modulation amplitude: 0.05 mV. Pulse
interval: 0.2 s; 5 mV s 1.

3.1. Electropolymerization of poly(4-HPA) lms


The electropolymerization of poly(4-HPA) was carried by potential
scanning (Fig. 1a). The electrochemical characterization was made in
HClO4 solution (Fig. 1b).
The rst cycle revealed the presence of an irreversible oxidation
process at ca. +0.95 V, attributed to the oxidation of the monomer.
Two redox peaks at ca. +0.63 V and +0.30 V increased with the
number of scans (Fig. 1a). These peaks are attributed to oxidation and

reduction processes of the poly(4-HPA) lm. During the rst scan, the
oxidation current peak dropped quickly, but after some cycles,
the current increased slowly. This effect was also observed to tyramine
[4-(2-aminoethyl)phenol], a similar monomer to HPA, seems to
indicate that the electrode is not passivated, because lms obtained
in acid aqueous medium allows to obtain thicker lms with improved
conductivity properties [19].
To electrodes modied with polymeric lm in perchloric acid
solution, oxidation/reduction waves were observed at +0.63 V / +0.30 V
for poly(4-HPA) (Fig. 1b). The anodic and cathodic branches of the CV
were integrated between the appropriated potentials furnishing,
respectively, the anodic Qa, and cathodic, Qc, charge spent in the
electrode process of the poly(4-HPA) lm. A Qa/Qc ratio close to one was
obtained supporting the lm electrochemistry behaves reversible, no
uncompensated process being involved in the electrode process.
3.2. Immobilization and detection of oligonucleotides on graphite
modied with poly(4-HPA)

Fig. 1. (a) Cyclic voltammograms for graphite electrode after successive potential scans,
100 scans, in 0.50 mol L 1 HClO4 + 2.5 10 3 mol L 1 4-HPA solution. (- - -) non-modied
and () modied with poly(4-HPA), 100 cycles, in 0.50 mol L 1 HClO4. 50 mV s 1 (b) The
arrows indicate the behavior of the current with consecutive potential scan.

Oligonucleotides immobilization at solid supports presents applications in detection of disease-causing and food-contaminating
organisms to the forensic and environmental research, clinical, as
well as others [20].
Homooligomers and heterooligomers of four DNA nucleobases
present a signicant electrochemical response. The immobilization of
a 16-mer DNA sequences on graphite electrode without lm and
modied with poly(4-HPA) acid is shown in Figs. 2 and 3.
Anodic peaks of purine oligonucleotides were observed at
potentials almost identical to those obtained at an oxidation of
mononucleotides, adenosine monophosphate and guanosine monophosphate, at modied graphite electrode with poly(4-HPA) [18]. The
presented data conrm again electroactivity of DNA nucleobases at
modied graphite electrode.
After the hybridization with the complementary target, we
observed a decrease of both guanosine and adenosine current peaks,

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T.A.R. Silva et al. / Materials Science and Engineering C 29 (2009) 539545

Fig. 3. Differential pulse voltammograms of graphite electrode modied with poly(4HPA) prepared in pH 0.5 (baseline-corrected), 100 scans, containing poly(GA) (a) before
hybridization and after 20 min incubation with non-complementary target: poly(GA)
(b), or complementary target: poly(CT) (c). Electrolyte: 0.1 mol L 1 phosphate buffer, pH
7.4. Modulation amplitude: 0.05 mV. Pulse interval: 0.2 s; 5 mV s 1.

when compared to the previously obtained voltammogram before the


hybridization. This fact is due to the hydrogen bonds formed between
complementary sequences leading to a duplex, inside which it is more
difcult to oxidize the bases, during the hybridization reaction, in
agreement with other results [21]. Another reason to the higher
current values obtained to ssDNA is that the last presents higher
proximity and higher adsorption onto the electrode surface, due to its
higher conformational exibility, facilitating the charge transfer
between the nitrogenated bases and the electrode [22,23].
Control experiments were performed with the probe immobilized
containing a non-complementary sequence. Since no hybridization
could have occurred during control experiments the increase of the
signals is due to non-specic adsorbed oligonucleotides molecules
onto the modied graphite electrode.
3.3. Immobilization and detection of DENV-1 gene on graphite modied
with poly(4-HPA)
A specic DNA fragment was immobilized on modied graphite
electrode. The gel electrophoresis detection of PCR products is shown
in Fig. 4.
The result of electrophoresis of the DENV-1 gene conrmed the
amplication of PCR products with the correct size, 288-bp, as well as
the DNA integrity.
The immobilization and detection of specic base sequences to
dengue virus type 1, DENV-1, PCR product (see Fig. 4) was carried out
using ethidium bromide (3,8-diamino-5-ethyl-6-phenyl phenanthridinium bromide), as intercalator. Ethidium bromide is known to bind
with polynucleotides by intercalation, with planar aromatic group,
into the base pair stakes of the DNA double helix structure.
Fig. 5 shows differential pulse voltammograms of ethidium
bromide as a redox intercalator at a modied graphite electrode,
when the immobilized probe was hybridized with different concen-

Fig. 4. Agarose gel electrophoresis to PCR-amplied DNA, DENV-1 gene. M, DNA marker,
100 pb; lane 1, 3 L of the PCR-amplied products from Aedes aegypti.

Fig. 5. (a) Differential pulse voltammograms of ethidium bromide as a redox intecalator


in 0.10 mol L 1 phosphate buffer, pH 7.4, onto graphite electrode modied with poly(4HPA) prepared in pH 0.5 (baseline-corrected), 100 scans, containing ssDNA before or
after hybridization with DNA target concentrations different. Modulation amplitude:
25 mV. Pulse interval: 0.2 s; 20 mV s 1. (b) Calibration data for the oxidation signal of
ethidium bromide obtained after hybridization of modied electrode containing the
probe with complementary target.

trations of the complementary target ssDNA and the linear dependence after hybridization with the complementary target.
From Fig. 5a, it can be seen that the oxidation potential of ethidium
bromide is about +0.63 V. We also observed a different afnity for
ethidium bromide by dsDNA when compared with the ssDNA. This
increase in the current values after incubation with the complementary target can be attributed to hybridization reaction, or be it, duplex
formation. This result indicates that it is possible to detect the
complementary target of the DENV-1. The Fig. 5b shows a linear range
from 12 to 42 nmol L 1 and a detection limit of 7.12 nmol L 1.
This approach may be used to detect each one of the others three
types of dengue sorotypes, or be it, DENV-2, DENV-3 and DENV-4 by
replacement of DNA probe on the modied graphite electrode with
poly(4-HPA).
3.4. AFM analysis
The AFM results after the immobilization and hybridization of the
probe and/or target on the modied electrode surface have strong
implications in the development of DNA electrochemical biosensors,
because they can show important morphological alterations on the
surface, in agreement with the electrochemical responses [24]. Experiments were carried out aiming at comparing the images of electrodes
before or after hybridization with the biomolecules in study (Fig. 6ae).
Topographical images of the graphite electrode modied by lm
with or without biomolecules show that the morphology is made up
of globular aggregates, randomly distributed on the graphite surface,
except to poly(4-HPA)oligo probe where the surface is more
homogeneous.
Spherical aggregates were observed, in the literature, by topographical images of the modied electrodes containing poly(G) or poly
(T) [24]. Analysis of the graphite surface without polymeric lm [25]

T.A.R. Silva et al. / Materials Science and Engineering C 29 (2009) 539545

shows that this surface is very different (rougher, containing more


pores) comparing with the surface containing polymeric lm with
poly(GA).
In all AFM experiments, we observed that the single stranded
oligonucleotide or DNA had lower roughness values than the double
stranded oligonucleotide or DNA, which suggests that the single
stranded biomolecules tend to fold back on themselves, and interact
more easily with each other. The occurrence of at surfaces, after
adsorption of poly(GA) suggests that its higher conformational exibility
facilitates the smoothness of the surface, in agreement with studies of
other modied electrode containing oligonucleotide-DNA [26].

543

Images and graphics of the section analysis obtained by AFM


analysis are represented in Fig. 7(aj).
Mode AFM images were used to demonstrate the surface
modication after immobilization and/or hybridization with the
complementary target. The immobilization of oligonucleotide or
DNA sequences was achieved by dropping and drying during 5 min,
as described in the Section 2.5.
After the introduction of probe biomolecules (oligonucleotide or
DNA), the surfaces present a more homogenous aspect in relation to the
modied electrode after hybridization. ssDNA molecules are rather
exible and aggregate into less folded structures on the surface of

Fig. 6. AFM topographical images of modied graphite electrode with poly(4-HPA): (a) without biomolecules; after immobilization and hybridization with biomolecules: (b) poly
(GA), before hybridization; (c) poly(GA): poly(CT), after hybridization; (d) DENV-1 ssDNA, before hybridization; (e) DENV-1 dsDNA, after hybridization.

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T.A.R. Silva et al. / Materials Science and Engineering C 29 (2009) 539545

Fig. 7. Images and graphics of section analysis to graphite electrodes modied with poly(4-HPA). (a, b) without biomolecules or after immobilization and hybridization with
biomolecules: (c, d) poly(GA), before hybridization; (e, f) poly(GA): poly(CT), after hybridization; (g, h) DENV-1 ssDNA, before hybridization; (i, j) DENV-1 dsDNA, after hybridization.

modied graphite electrode. After the introduction of complementary


targets, occurs a decrease in smoothness of the surface (Figs. 6ae
and 7aj).
The topographies of the modied electrode containing poly(4HPA)/ssDNA and poly(4-HPA)dsDNA have shown globular structure of

many different sizes, varying in height and diameter from 512 nm


and 70120 nm, and 2050 nm and 80150 nm, respectively.
Comparatively, the root-mean-square (r.m.s.) roughness values for
the graphite electrode modied with poly(4-HPA), poly(4-HPA)oligo
probe, poly(4-HPA)oligo probe:oligo target, poly(4-HPA)DENV-1

T.A.R. Silva et al. / Materials Science and Engineering C 29 (2009) 539545

probe, poly(4-HPA)DENV-1 probe:DENV-1 target were 22.1 nm,


1.2 nm, 27.4 nm, 6.6 nm and 53.2 nm, respectively.
Similar results have been found elsewhere [26,27], since an
increase in r.m.s after the hybridization is expected from the different
conguration of ssDNA and dsDNA, as mentioned earlier.
These alterations can be interpreted as a hybridization event,
since the dsDNA have also a rigid and elongated structure. According
to the literature [27], the dsDNA molecules are more resistant to the
AFM tip scanning the surface because of their more inexible
conformation.
It was demonstrated that AFM is an appropriate technique to
visualize differences between hybridized and non-hybridized surfaces.
4. Conclusions

Acknowledgements
The authors are grateful for the nancial support from Conselho
Nacional de Desenvolvimento Cientco e Tecnolgico (CNPq) and
Fundao de Amparo Pesquisa do Estado de Minas Gerais
(FAPEMIG). Also, we would like to thank teacher Ablio Borghi for
the review of the English manuscript.
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It was possible to modify the electrode surface with 4hydroxyphenylacetic acid by means of electropolymerization. Poly
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