Surface & Coatings Technology 194 (2005) 244 – 250

www.elsevier.com/locate/surfcoat

Adhesive behavior of DNA molecules on silicon wafers treated

by argon and oxygen plasma
Jianxia Gao, Mary B. Chan-Park*
The Biological and Chemical Process Engineering Laboratory, School of Mechanical Engineering, Nanyang Technological University,
50 Nanyang Avenue, Singapore 639798, Singapore

Received 21 December 2003; accepted in revised form 19 August 2004

Available online 1 October 2004

Abstract

The adhesion of Deoxyribose Nuclei Acid (DNA) on an electrode surface such as silicon is a key issue in the sensitivity of DNA chips, in
order to maximize the DNA concentration on the electrodes of DNA chips and increase the detected signal, the chip should have good
adhesion of DNA to its electrodes. In our study, several pieces of silicon wafer were treated by argon and oxygen plasma, respectively. We
analyzed the DNA content on the different silicon surfaces using the X-ray photoelectron spectroscopy (XPS). The results indicate that the
content of DNA molecules adhered on the silicon surface treated with an oxygen plasma is higher than that on the surface treated with an Ar
plasma. This can be interpreted in terms of the interaction of parasitic charges and van der Waals forces on silicon oxide surfaces.
D 2004 Elsevier B.V. All rights reserved.

PACS: 34.20.Gj; 52.27.
h; 33.60.Fy

Keywords: DNA; Adhesion; Plasma; XPS

1. Introduction developed [7] as they offer many more possibilities than

Nucleic acid detection and analysis in Deoxyribose
Nuclei Acid (DNA) chips are key challenges of biotechnol-
ogy and medical diagnostics. Moreover, the recent require-
ment of total genome determination of various living
organisms and human beings has spurred the development
of ultra-rapid and sensitive DNA chips [1]. DNA chips
allow massively parallel on-chip DNA hybridization [2,3]
and significant improvements over traditional DNA ana-
lytical procedures in terms of speed and cost. Initially, DNA
chips were developed by chemists and other nonsilicon-
processing related engineering communities [4,5], and this
led to the proliferation of small complementary DNA
microarrays [6] based on glass, plastic and ceramic
substrates. With the onset of the race for faster and smaller
DNA chips, silicon substrates have been tested and
* Corresponding author. Tel.: +65 6790 6064; fax: +65 6792 4062.
E-mail address: mbechan@ntu.edu.sg (M.B. Chan-Park).
0257-8972/$ - see front matter D 2004 Elsevier B.V. All rights reserved.
doi:10.1016/j.surfcoat.2004.08.189
their glass or plastic counterparts for integrated control and
detection circuitry.
It is well known that interactions between DNA
molecules and surfaces involve electrostatic forces as well
as long-range van der Waals forces and dipole–dipole
interactions [8], so the selection of substrates used for
DNA chips is very important for the adhesion of DNA on
substrates during experiment. An ideal DNA chip should
possess two somewhat contradictory properties. First, the
chip should have good adhesion of DNA to its electrodes in
order to maximize the DNA concentration on the electrodes
and, consequently, the detected signal. Second, to reduce the
costs of DNA analysis, it should be possible to completely
remove the DNA after detection without damaging the chip
in order to permit reuse. The achievement of this balance
between good DNA adhesion to and reusability of silicon-
based DNA chips calls for the development of techniques by
which to finely adjust the surface mechanical, chemical and
electrical properties of the silicon substrate. Plasma surface
treatment with nonreactive or reactive gases offers a set of
 J. Gao, M.B. Chan-Park / Surface & Coatings Technology 194 (2005) 244–250
techniques which may be useful for the achievement of the
desired properties in DNA chips. Till now, few reports
showed the adhesion behavior of DNA molecules to silicon
surfaces that have been treated with Ar and O2 plasmas,
respectively.
The Radio-Frequency (RF) generated glow discharge
employed in plasma etching/sputtering machines has found
a variety of uses in the manufacture of semiconductor
devices, including surface cleaning, surface modification
and etching [9]. Plasma etching has at least three different
modes: conventional plasma etching (neutral chemical
reaction only), reactive ion etching (RIE), and high-density
plasma etching [10]. In the plasma-etching mode, the
electrons accelerated by the applied RF field in the plasma
sheath collide with gas atoms and molecules. Some atoms
and molecules are ionized or dissociated to form ions,
radicals, and atoms during these collisions. Some of the
active species (radicals, ions, etc.) collide with the surface of
the etching target, where they may chemically or mechan-
ically react with target atoms. The etching products are
volatile and desorb from the sample. In conventional plasma
etching, the gas pressure is usually 100–300 mTorr and the
sample is grounded during etching. The main etching
mechanism in this case is radical chemical etching. For
RIE, the gas pressure is less than 100 mTorr, and the sample
potential is floating or biased. In this case, both chemical
etching by radicals and physical bombardment by ions
contribute to the etching. For high-density plasma etching,
such as by inductively coupled plasma systems, the ratio of
the ion flux to the reactive neutral flux is larger and ion
bombardment etching is dominant.
In plasma etching, the particle flux impacts the etched
surface from all directions (unless the substrate is strongly
biased) and has a broad energy distribution and angular
distribution of momentum. The etching dynamics are
governed mainly by the dynamics of the gas transport
process as demonstrated by trench evolution during plasma
etching [11–13].
Argon plasma etching involves the physical removal of
substrate atoms and molecules by energetic Ar+ ions
accelerated toward the substrate, which is electrically biased
to serve as a cathode; such etching will clean the substrate
surface, for example to remove a thin layer of SiO2 from Si
surface [9,14]. Another widely used plasma etching gas, O2,
is chemically reactive and oxidizes as well as etches
exposed surfaces. The etching of silicon substrates with
O2 plasma consequently generates a surface oxide layer
[15]. The generation of insulating oxide layers on the
surface of semiconducting silicon is an important process
and is widely used in microelectronic and optical device
fabrication. However, oxidation at an elevated temperature
can generate dislocations and stacking faults in the silicon.
High-temperature oxidation also changes the distribution of
dopant atoms in silicon and the p/n junction depth in
electronic, it means high temperature is harmful for
reliability of electronic devices [16].
245
Plasma oxidation is promising as a low-temperature
process [16,17]. Low-temperature plasma-grown silicon
dioxide layers represent a good alternative to thermally
grown layers. It has been shown that, following plasma
oxidation, dopant redistribution in silicon material is
negligible [18]. It means the plasma oxidation process is
compatible with current process for making semiconductor
devices. One of the main advantages of plasma-grown
layers is that silicon oxide is formed by chemical reaction of
substrate silicon with oxygen atoms during the process. By
contrast with high-temperature thermal deposition, plasma-
grown silicon oxide layer can be obtained at relatively lower
process temperatures. So the plasma treatment is a very
convenient method for modification of silicon surface.
In our present work, DNA was immobilized on silicon
substrates prepared with a variety of surface treatments and
X-ray photoelectron spectroscopy (XPS) technique was
used to detect the amount of DNA molecules adhered to
the substrates. Argon and oxygen plasma treatments were
used to modify the silicon surfaces and these were found to
affect the amount of DNA adhered. Plasma treatment of
silicon is easily performed and offers a convenient method
by which to modify the adhesion of DNA to silicon.
2. Experimental
2.1. Preparation of silicon wafers
p-type (100) silicon wafers with a resistivity of 0.07 V
cm were used as substrates for DNA coatings. Firstly, they
were cleaned with a standard silicon cleaning solution, a
Piranha solution comprising 15:1 (v/v) 96 wt.% H2SO4/
H2O2 for 20 min at 120 8C. The wafers were then cleaned
with distilled water for 10 min and then dried by baking at
150 8C for 1 h. The wafers were then treated with argon or
oxygen plasma for 30 min. The plasma treatment was
carried out in a plasma etching System (Technics/Micro-RIE
series 800-II, manufacturer: Technics/Micro, Princeton
University) with a 300-mm diameter stainless steel chamber
and a 230-mm diameter electrode. The plasma system has a
350-W solid state radio frequency generator operating at
13.56 MHz. In our experiments, a RF power of 300 W was
used as working power without considering DC offset, the
oxygen and argon gas flow rates were 19 sccm (standard
cubic centimeters per second) and 17 sccm, respectively.
The pressure of oxygen or argon in the chamber was kept at
approximately 165 mTorr. After the completion of the
plasma treatment, the RF was turned off and the wafers were
left in the plasma chamber for a further 10 min, exposed to
the oxygen or argon gas.
2.2. Immobilization of DNA oligonucleotides
The single-stranded (ss) DNA molecules with 22 bases
were purchased from Proligo in Singapore. A buffer
246 J. Gao, M.B. Chan-Park / Surface & Coatings Technology 194 (2005) 244–250
solution containing 200 mM NaCl, 20 mM Tris–HCl, 5
mM EDTA and 95% ethanol with 28.6% (v/v) was
prepared and adjusted to pH 7.5 with NaOH or HCl. For
preparation of ssDNA layers, 1 AM ssDNA in the buffer
solution was stored at room temperature overnight. The
ssDNA solution was dispensed onto the surface of the
silicon wafers and then spin-coated onto the wafers at
1000 rpm for 2 min. Each wafer was then cut into several
pieces, one of which was washed with doubly distilled
(DD) water, one of which was washed with ethanol, and
one of which was not washed.
2.3. X-ray photoelectron spectroscopy (XPS) and atomic
force microscopy (AFM) measurements
The XPS measurements were performed in the ultrahigh
vacuum chamber of a Kratos Ultra XPS system (Kratos
Analytical, Surface Analysis Product Group, Manchester,
England). The chamber contained a dual anode (Al or Mg
Ka1,2) and a monochromatic Al Ka1,2 X-ray source and was
connected to a hemispherical electron energy analyzer. The
base pressure of the chambers was 2.510
9 Torr. During
measurement, samples were exposed to X-ray irradiation
from the monochromated Al Ka1,2 X-ray source
(hm=1486.6 eV) operated at 150 W (15 kV, 10 mA). The
photoelectrons induced by the X-ray bombardment were
filtered by the hemispherical analyzer, and finally recorded
by multi-channel detectors.
Fig. 1. AFM image of the chip surface. (a) Cleaned silicon surface; (b) DNA-coated silicon surface; (c) buffer solution coated silicon surface; (d) DNA washed
from silicon surface.
Silicon samples with and without coated DNA were
characterized by atomic force microscopy (AFM) in tapping
mode in air. A scan size of 2 Am was used.
3. Results and discussion
3.1. Oxygen plasma physics
When argon plasma etches a silicon surface, there is no
chemical reaction between argon and silicon atoms and only
physical bombardment takes place. Therefore, only the
oxygen plasma etch mechanism needs to be discussed.
The kinetics of the oxide growth during the oxygen
plasma process was well described by the linear-parabolic
growth law with an initial rapid growth in the following
equation [16]:
x2 =kP þ x=kL ¼ t þ s ð1Þ
where x is the oxide thickness, t is the oxidation time, k P
and k L are the parabolic-rate and linear-rate constants, and s
is a time constant. k P and k L are activation energies for the
reaction taking place between silicon and oxygen atoms.
It can be considered that the oxide consists of two layers
on a silicon surface: a surface layer with low density and a
bulk layer with high density. The thickness and diffusion
coefficient of the surface layer are x s and D s, respectively,
and those of the bulk layer are x b and D b, respectively. So
 J. Gao, M.B. Chan-Park / Surface & Coatings Technology 194 (2005) 244–250
Fig. 2. Chemical structure of a single-stranded DNA.
Fig. 3. XPS spectra of silicon wafers treated with non-oxidizing and
oxidizing plasma. (a) Argon plasma, Si0: 2185; Si+2: 388; Si+4: 805. (b)
Oxygen plasma, Si0: 775; Si+2: 2124; Si+4: 2670.
247
the parabolic-rate constant k P and the linear-rate constant k L
can be expressed as follows [16]:
kP ¼ 2Db C0 X; ð2Þ
kL ¼
kP =½2xs ð1
Db =Ds Þ; ð3Þ
where C 0 is the concentration of oxidant at the oxide
surface, and V is the oxide volume per unit. The activation
energies k P and k L can be determined from an Arrhenius
plot of k P and k L, it shows that the value of the k P is 0.37
eV, which is much smaller than that of the thermal
oxidation (1.23 eV) and indicates that the diffusing oxidant
is not molecular oxygen. The activation energy k L is about
0.35 eV, which is also much smaller than that of the
thermal oxidation (2.0 eV). This is why the silicon oxide
can be formed at lower temperature in an oxygen plasma
environment.
AFM was used to characterize the effect of DNA
solution, buffer solution and washing on the silicon surface.
Fig. 1a is the AFM image of a h100i silicon substrate
Fig. 4. XPS spectra of a silicon wafer treated with argon plasma. (a) Survey
scanning spectrum; (b) N (1s) spectrum.
248 J. Gao, M.B. Chan-Park / Surface & Coatings Technology 194 (2005) 244–250

The silicon substrates were cleaned by standard silicon

cleaning procedure followed by argon or oxygen plasma
treatment, respectively. The electronic states of the Ar and
O2-treated DNA-free control silicon surfaces were obtained
by XPS (Fig. 3). The deconvolution analysis of the Si(2p)
peak in Fig. 3a shows the content of Si0/Si+2/Si+4 to have
the atomic ratio of 2185:388:805. The Si0 signal is due to
pure silicon while Si+2 and Si+4 are due to SiO and SiO2,
respectively. It is apparent that the Ar-treated surface is
predominantly unoxidized silicon. Fig. 3b shows the ratio of
Si0/Si+2/Si+4 to be 775:2124:2670. As expected, the oxide
content of the O2-treated surface is much higher than for the
Ar-treated surface; both contents of SiO and SiO2 are
enhanced.
Fig. 4a shows the wide energy XPS spectrum of a silicon
substrate treated by argon plasma. The presence of oxygen
and carbon peaks indicates carbonaceous contamination of
the silicon surface by the environment. However, there is no
significant nitrogen peak in the spectrum (Fig. 4b),
indicating the absence of nitrogen-containing contamina-
tion. Consequently, the N(1s) peak was employed to
quantify the DNA content of the sample surfaces.

Fig. 5. XPS spectra of DNA coated on silicon surface which was treated
with Ar plasma. (a) Survey scan; (b) N (1s) spectrum.

cleaned with the standard washing procedure. Fig. 1b is that

of a DNA-coated silicon surface. The DNA molecules
appeared to have agglomerated in circular patches on the
surface. Fig. 1c shows the buffer-coated silicon surface; this
surface has no DNA on it and appears similar to that of the
cleaned silicon surface. Fig. 1d shows the DNA-coated
silicon surface which was washed with DD water. Washing
with DD water appears to have removed almost all of the
DNA from the surface.
DNA is composed of the bases adenine, cytosine,
guanine and thymine joined by a phosphate backbone
(Fig. 2). The atomic content of DNA is limited to carbon,
oxygen, nitrogen, hydrogen and phosphorus. The quantity
of DNA adhered to a silicon surface can in principle be
measured via XPS from the surface atomic content of
carbon, oxygen, nitrogen or phosphorus. In practice,
contamination by environmental carbon or oxygen is
common, rendering these species unsuitable as proxies for
DNA content. The amount of phosphate is low in DNA
molecules, so the nitrogen can be used to trace the content Fig. 6. XPS spectra of DNA coated on silicon surface which was immersed
of DNA. into oxygen plasma. (a) Survey scan; (b) N(1s) spectrum.
 J. Gao, M.B. Chan-Park / Surface & Coatings Technology 194 (2005) 244–250 249

The wide XPS spectrum of the silicon surface which

was treated with Ar plasma and coated with the DNA
solution is shown in Fig. 5. The N(1s) and P(2p) peaks
in Fig. 5a are indicative of DNA molecules. The
phosphorus peak is smaller than the nitrogen peak,
expected from the relative content of N and P in DNA
structure showed in Fig. 2. The narrow N(1s) XPS peak
(Fig. 5b) was used to quantify the DNA content.
Similarly, Fig. 6 shows the wide XPS spectrum of the
DNA-coated, oxygen plasma-treated silicon surface. The
content of DNA on this surface was also calculated from
the N(1s) peak (Fig. 6b).
The DNA solution coating on the silicon surface treated
by oxygen was washed by ethanol and DD water,
respectively. The wide XPS spectrum of the ethanol-washed
surface is shown in Fig. 7a; the N(1s) peak is much
diminished with respect to the unwashed surface. The actual
content of nitrogen was calculated from N(1s) peak (Fig.
7b). The XPS spectrum of the oxygen plasma-treated
surface coated with DNA and washed by DD water is

Fig. 8. XPS spectra of DNA coated on silicon surface washed by DD water.

(a) Survey scan; (b) N (1s) spectrum.

shown in Fig. 8; the content of nitrogen was obtained from

the narrow N(1s) peak area (Fig. 8b).
The content of nitrogen on the variously prepared
silicon surfaces is compared in Fig. 9. Prior to application

Fig. 7. XPS spectra of DNA coated on silicon surface washed by ethanol.

(a) Survey scan; (b) N (1s) spectrum. Fig. 9. Effect of surface treatment on relative nitrogen content.
250 J. Gao, M.B. Chan-Park / Surface & Coatings Technology 194 (2005) 244–250
of the DNA coating, the nitrogen content of the silicon
surface is very low. After the silicon surface was treated
with Ar plasma, the DNA solution was put on the surface.
The XPS analysis shows the content of nitrogen, and
hence, DNA on the silicon surface increased rapidly.
Further, the amount of DNA detected on the silicon
surface treated with oxygen plasma is about two times
greater than that of a silicon surface treated with Ar
plasma. After washing, the content of nitrogen, and hence
DNA, on the surface is significantly reduced. Water was
found to be a better solvent than ethanol. Using water,
most of the DNA molecules were removed.
Our experiment shows that there is a layer of SiO2 on
the silicon surface after treatment with oxygen plasma.
There are four kinds of parasitic charges in the SiO2
layer or at Si/SiO2 interface [19]. The first kind is fixed
oxide charges which exist close to the Si/SiO2 interface.
Their generation is related to the defects in the oxide
layer. The second kind is the trapped oxide charges
which are induced by ions. They exist throughout the
whole SiO2 layer. As the silicon wafers were cleaned
with oxygen plasma, oxygen ions reacted with silicon
and formed a silicon oxide layer. This layer is not
stoichiometric SiO2 because of the growth method; rather
it is SiOx (0bxb2), so the fixed oxide charges are
generated during formation of the SiO2 layer. In addition,
after the oxide layer is formed, oxygen ions in plasma
inject into the oxide layer and induce trapped oxide
positive charges. The third kind is the trapped interface
charges which lie at the Si/SiO2 interface. In general,
these four kinds of parasitic charges can affect the
electric property of the bulk silicon, and have the
characteristics of donors or acceptors. For p-type Si, they
act as acceptors while for n-type Si they act as donors.
P-type silicon wafers were used in our experiment, so
their behavior is acceptor and similar to positive charges.
The last kind is the mobile ions which exist within the
oxide layer and arise from contamination with alkaline
ions, if present. These can move in an external electric
field. There is no alkaline element in our experiment, so
it can be considered that mobile ions do not exist in our
oxide layers. Generally, these parasitic charges are
positive charges and they will induce a polarity in the
DNA and then attract the nearer negative pole.
There is thus an electrostatic force that holds DNA
molecules to the O2 plasma-treated silicon surface. In
addition, van der Waals interactions are always present
between substrate surface and DNA. However, for the
silicon surface which was cleaned with Ar plasma, there
is no oxide layer on the surface, we postulate that only
van der Waals forces exist between the silicon surface
and DNA. This would explain the reduced content of
DNA on the Ar plasma-treated surface compared to the
surface treated with O2 plasma.
4. Conclusions
The content of DNA molecules on silicon surfaces
treated with a variety of plasma treatments and washing
solvents was measured with the XPS technique. It is found
that oxygen plasma treatment leads to superior DNA
adhesion to silicon than non-reactive Ar plasma treatment.
The improved adhesion with oxygen plasma treatment can
be understood on the basis of the generation of parasitic
charges in the oxidized surface which interact electrostati-
cally with the DNA molecules. Doubly deionized water, a
polar solvent, was found to be highly effective in removing
DNA from the oxygen plasma-treated silicon surface.
Acknowledgements
This research was supported by a Start-up grant (SUG
10/02) from the Nanyang Technological University and an
A-STAR (Singapore) grant (Project No. 022 107 0004).
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