Regular Papers

First Steps towards the Development of a New Bio-optoelectronic
Device with a Functioning Protein on a Silicon Substrate
Koji Sumitomo†, Hiroshi Nakashima, Mime Kobayashi,
Keiichi Torimitsu, Chandra Ramanujan, and John F. Ryan
Abstract
The combination of biological systems with artificially fabricated nanoscale structures offers thepotential for developing new electronic, photonic, and biosensing molecular-scale devices. In this study,
we investigated the use of bacteriorhodopsin (bR), the photoreceptor protein in purple membrane, toform the basis of new optoelectronic devices using nanofabricated silicon structures. The periodicalhexagonal shape of bR was observed in liquid by atomic force microscopy. Imaging the suspended purple membrane over artificially fabricated cells is an essential first step in developing a device with afunctioning protein. We found that slight modification of the silicon surface or difference in the salt concentration of the buffer affected how the bR attached to the surface. We are still at a very early stage on
the road toward optoelectronic devices on a silicon surface.

1. Introduction
Molecular and biomolecular electronics have beenstudied extensively in the last decade because they
promise better performance at a lower production
cost than conventional silicon-based integrated circuits [1]. The combination of biological systems andsemiconductor nanotechnology has great potential
for device applications [2].
Initially, at least, we are investigating the photoreceptor bacteriorhodopsin (bR) because it has wellcharacterized optical and electrical properties. It is arobust protein found in the purple membrane of thes a l t - l o v i n g m i c r o o rg a n i s m H a l o b a c t e r i u msalinarum, which was discovered more than three
decades ago in the extreme environment of salt
marshes [3]. It is typical of the class of photochromic
proteins, and it functions as a light-driven proton
pump and enables the organism to survive at extremely high salt concentrations using sunlight as the sole
† NTT Basic Research Laboratories
Atsugi-shi, 243-0198 Japan
E-mail: sumitomo@will.brl.ntt.co.jp

40source of energy (Fig. 1) [4]. Two important properties have driven enormous interest in device applications of bR. First, it serves as a simple model for cellmembrane photoreceptors: the photosensitivity andability to switch functions in response to illuminationof this biological photochromophore are far superior
to those of synthetic materials. Second, it serves as aprototype of a membrane transporter: it transports
ions against an electrochemical potential [5]. Unveiling the mechanisms behind the physical functions ofbR is an appealing way to learn from biological molecules in order to develop new electronic devices.
A lot of studies have been conducted to analyze andunderstand its structure and biological functions [3][17]. Purple membrane consists of two-dimensional(2D) crystals of 75% bR protein and 25% lipid derivatives [6], [7]. Trimers of bR are regularly arranged in
the purple membrane to form a hexagonal lattice(Fig. 2). The bR protein consists of seven transmembrane alpha-helical*1 structures (A to G), linked by*1 Alpha helix: A common structure found in proteins, characterized
by a single, spiral chain of amino acids (polypeptide) stabilized byhydrogen bonding.

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Purple membrane

O=

Halobacterium
salinarium
m cell

+

C

H

O–

Inside
B
A

C
G

D
E
F

Retinal

H3N+

Outside+Photon of light

H

Bacteriorhodopsin proteinin the lipid membrane

Fig. 1. Schematic illustration of bacteriorhodopsin (bR) protein in purple membrane.

short loops on either side of the membrane [8], [9].
The chromophore*2 retinal is connected via a Schiff
base*3 to the nitrogen atom of a lysine*4 –216 residue
in helix G [10]. Upon absorption of light in the visible spectral region, retinal changes its configurationfrom the all-trans form to the 13-cis form, whichtakes about one picosecond. The photoisomerization*5 triggers the transport of a proton from the cytoplasmic to the extracellular side, and an electrochemical potential of up to 250 mV is thus generated
across the membrane. This potential translates into a
10,000-fold difference in proton concentration. The
resulting proton gradient is used to synthesize ATP*6,
which is the universal energy source of living organisms. The bR undergoes structural changes during theunidirectional proton pumping: a series of intermediates, referred to as K, L, M, N, and O states that havedifferent colors, have been well characterized by
optical absorption spectroscopy [11]. Since the mid1980s, the photoinduced electrical effects arisingfrom the proton transport have been studied in an artificial cell using metal electrodes and electrolytic
medium [12]. Sensory aspects of the bR molecule
have also been demonstrated in a completely solidVol. 4 No. 9 Sep. 2006

device [11], [13].
In this paper we describe a model device with biomolecular function obtained from electrically contacted artificially fabricated cells, as shown in Fig. 3.
The device consists of a purple membrane (bR protein and lipid) covering a small cell (submicrometer
dimensions) fabricated on a Si substrate and electrodes attached to them. These cells can contain proteins that are chosen or modified according to the*2 Chromophore: The part of a molecule responsible for its color. In
biological molecules that serve to capture or detect light energy,
the chromophore is the moiety that causes a conformationalchange of the molecule when exposed to light.
*3 Schiff base: A base structure containing R 1 N=CHR 2 or
R1N=CR3R4 chemical bonds, which are obtained by the reaction
between primary amine (R1N-H2) and aldehyde (R2CHO) or
ketone (R3COR4).
*4 Lysine: One of the essential amino acids. Lysin-216 indicates the216th amino acid from the NH3+-end of successively connectedamino acids (polypeptide).
*5 Photoisomerization: Structural change of a molecule between isomers (e.g., retinal: from the all-trans to the 13-cis form) caused byphotoexcitation.
*6 ATP: Adenosine triphosphate (ATP) is synthesized from adenosine diphosphate (ADP) and inorganic phosphate using the electrochemical potential of protons.

41Regular Papers

E

F G A
C B
D

Fig. 2. Schematic illustration of 2D crystal of bR in purple membrane (cytoplasmic side).
Photon of light
Counter electrode
H+
Lipid

channel in a purple membrane and it is expected toact as a transistor by utilizing the gating function of
the membrane protein. The integration of a number ofdifferent proteins on such a multi-cell substrate could
provide novel functionality.
2. Results and discussion+

H

Solution
Electrode
Substrate

Fig. 3. Schematic drawing of a purple membrane-Si
optoelectronic device.

functional needs of the device. For example, if a photoreactive membrane protein such as bR is used tocover cells, the flow of ions through the membrane
could be controlled by photons of light. The cell mustbe filled with electrochemical buffer solution such as
KCl. Photons of light control the gating of the ion
42

2.1 AFM images of purple membranes on mica
In order to utilize membrane proteins like bR in the
fabrication of nanoscale devices, as shown in Fig. 3,
functional or structural changes of the protein should
be monitored at the nanoscale, i.e., on the molecularscale, and under physiological conditions, i.e., in liquid. To confirm the exact location of membrane protein on the optoelectronic device, we decided to use acommercial atomic force microscope (AFM: Dimension 3100, Veeco Instruments Inc., USA). Althoughelectron microscopy, nuclear magnetic resonance(NMR), and X-ray diffraction techniques with highspatial resolution have been used with great successfor structural analysis of biological molecules, thesetechniques require samples to be in a static condition(low temperature) or in vacuum. On the other hand,
AFM has been widely used for imaging biologicalmolecules in liquid with nanometer resolution [18].
In AFM measurements, the very weak atomic force
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(a)

(c)

(d)

100 nmEC
patch
CP patch
A
B

(b)
B

A

5 nm

10 nm

Fig. 4. (a) Topographic AFM image of purple membrane on mica surface. (b) Cross-sectional image along the line
indicated in (a). (c) Trimers of bR on cytoplasmic patch can be clearly distinguished. (d) 3D reconstructed image of(c). (EC: extracellular, CP: cytoplasmic)(<1 nN) acting between the probe and the sample isdetected and a topographic image is obtained [19].
The “tapping mode” AFM operation drasticallyshortens the interaction time between the probe andsample, so it substantially reduces frictional forcesand damage to the sample during imaging [20]. Thismethod is particularly effective for imaging soft
materials such as proteins, DNA, and other biologicalmolecules. The morphology of purple membrane surfaces and the mechanical properties of bR have previously been measured with high resolution in aqueous conditions [14]. Physical manipulation of theprotein using the tip of an AFM probe has also beenreported [15], [16].
First, we performed AFM imaging of purple membrane on mica, which is the established substrate for
AFM of biomaterials [14], [15], [17]. Purple membranes of Halobacterium salinarium strain S9 (>99%pure) were obtained from Sigma-Aldrich Corp.
(USA). A lyophilized powder*7 of the purple membrane was diluted in buffer solution (100 mM KCl, 10mM tris-HCl, pH 8.0) to the final concentration of
5–50 µg/ml and adsorbed onto a freshly cleaved micaplate. After incubation for 20 to 30 minutes, 0.2 ml ofbuffer solution was added and imaging was per*7 Lyophilized powder: Freeze-dried powder of biological substances

Vol. 4 No. 9 Sep. 2006

formed in liquid at room temperature. Membranepatches about 5 nm thick and from 0.5 µm to several
micrometers wide were observed, as shown in Figs.
4(a) and (b). Judging from the surface morphology(Fig. 4(a)), two types of patch were present: one witha smooth surface and the other with a relatively roughsurface. On the basis of previous work by one of theauthors (J.F.R) and his coworkers [17], we considered the former to be the extracellular side and thepatch with the relatively rough surface to be the cytoplasmic side. For molecular-level studies of mechanical or electrostatic properties, it is important to know
which side is present on the device.
Figures 4(c) and (d) show high-resolution imagesof the cytoplasmic patch obtained by very soft tapping following the conditions used in ref. [17]. A
hexagonal network originating from the 2D crystal ofbR can be seen. High-resolution imaging and Fourier
analysis enabled us to resolve the trimer shape of bR,
with a size of about 2 nm. The results indicate thatmolecular-scale imaging in physiological conditions
is readily obtained and that we can locate the protein
structures precisely.
2.2 AFM images of purple membranes on thesilicon hole pattern
The test device structure we chose to evaluate consisted of an array of electrochemical cells, each 1
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attoliter in volume, fabricated in silicon by a photolithographic technique using synchrotron orbitalradiation and dry etching. Each cell was 100 nm ×
100 nm square and 100 nm deep, and the pitch of thepattern was 500 nm. Electrodes were not connected tothe sample device, but the nano-bio device was in thegeometry shown in Fig. 3. A hydrophobic surface,which is essential for strong membrane adhesion, wasobtained by HF treatment to produce hydrogen-terminated silicon. This surface was imaged with thetapping-mode AFM in air, as shown in Figs. 5(a) and(b). The cross-sectional profile along the line indicated in Fig. 5(b) was analyzed to confirm the shape ofthe cell (Fig. 5(c)). The measured cell shape waswithin expectations given the convolution of the celland AFM tip.
Purple membrane was deposited on the silicon surface in the same manner as for mica and imaged withthe tapping-mode AFM in liquid, as shown in Fig.
5(d). Some of the cells were covered by patches ofthe membrane, which extended from about 500 nm toseveral micrometers in width. A high-magnification

image of the suspended membrane over the cell isshown in Fig. 5(e). The cross sectional line-profile
between A and B, shown in Fig. 5(f), clearly showsthat the membrane sagged slightly over the cell, as
shown by the blue arrow, while a relatively deep holeremained in the area where the membrane incompletely covered the cell (indicated by the red arrow).
The depression, which was estimated to be 5–10 nm
deep, could be due to the interaction between the
AFM probe and the membrane during tapping-mode
imaging. However, rupture of the membrane by the
AFM probe was never observed. Protein suspended
over the cell was free from interactions with the substrate, so it should retain its original configurationand function. This structure could therefore provide
an ideal electrical platform for observing a functioning membrane protein [2].
2.3 Effects of modified silicon surface on thedeposition of purple membrane
In the next stage of the fabrication of the proposed
device (shown in Fig. 3), the cells filled with buffer

(a)

(d)

(e)

(b)
A

Membrane

B

1 µm

1 µm

(c)

Substrate

B

A

B

(f)
Membrane

A
A

5 nm

Substrate

B

20 nm

Hole
Hole

Fig. 5. Topographic AFM image (5 × 5 µm2) of the cell pattern on H-terminated silicon measured in air (a) and purple
membrane on the pattern surface measured in buffer solution (100 mM KCl) (d). Here, (b) and (e) are magnified
images (800 × 800 nm2) of (a) and (d), respectively, and (c) and (f) are cross-sectional images along the lines
indicated in (b) and (e), respectively.

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solution should be isolated from the outside by forming a highly resistive seal between the bio-membraneand silicon surface [21]. From the viewpoint of semiconductor device processing, insulators such as silicon dioxide and silicon nitride are the preferred materials for the top-most surface to electrically separate
the electrodes in different cells and separate themfrom the counter electrodes. They form flat, stablesurfaces and their manufacturing processes are wellestablished. For these reasons we evaluated both silicon dioxide and silicon nitride in the present device
configuration.
AFM topographic images of silicon nitride, silicon
dioxide, and hydrogen-terminated silicon substrates
are shown in Figs. 6(a), (b), and (c), respectively. The
insets show magnified images and their line-profiles(Figs. 6(d), (e), and (f)) and indicate that their surfaces provide a flat profile for the attachment of biomembranes. The measured root-mean-square roughnesses were 0.42, 0.41, and 0.15 nm, respectively. To
determine the degree of hydrophilicity/hydrophobicSiN(a)ity, the contact angles were measured to be 17.8°,
28.6°, and 73.8°, respectively. Hydrophilicity/hydrophobicity may be one of the important factors
determining the strength of the interaction between
membrane and substrate. As expected, silicon nitride
and silicon dioxide surfaces were hydrophilic.
Purple membrane was deposited on each substrate,in the same manner as described before and imaged
in liquid with 0 to 500 mM of salt, as shown in Figs.
6(g)–(l). The interaction between the membrane andsubstrate was influenced by the salt concentration of
the buffer solution. On hydrogen-terminated silicon,
the attachment of purple membrane was good, andthere was little difference between 250 mM (Fig. 6(i))
and 500 mM (Fig. 6(l)). In contrast, on silicon nitride
and silicon dioxide, the attachment of purple membrane was not good enough. In the case of 250 mM
KCl, as shown in Figs. 6(g) and (h), only a few patches of purple membrane attached. The straight edge ofthe membrane (blue arrows) along the scanning
direction indicates that the deposited membrane
SiO2

H-Si

(b)

(c)

(e)

(f)

500 0
(h)

500 0
(i)

(k)

(l)

5 nm

Roughness
(nm)

1µm
0 nm
(d)
0.5
0
–0.5
0
(g)

500

30 nm

250 mM KCl

1µm
(j)

0 nm
30 nm

500 mM KCl

1µm
0 nm

Fig. 6. Topographic AFM images (5 × 5 µm2) of silicon nitride surface (a), silicon dioxide surface (b), and hydrogenterminated silicon surface (c) before deposition of purple membrane measured in air. Insets show magnified
images (500 × 500 nm2). (d)–(f) Cross-sections of the magnified images. (g)–(l) Topographic AFM images (5 × 5µm2) of purple membrane deposited on each surface.

Vol. 4 No. 9 Sep. 200645

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peeled off during AFM imaging. In subsequent scansof the same area, no membrane was visible, probably
because it peeled off. We found that a salt concentration higher than 500 mM was required (Figs. 6(j) and(k)). Therefore, this preliminary study showed that it
will be important to optimize the salt concentrationand the surface properties in order to provide a goodseal between the bio-membrane and the lip of the fabricated cell.
3. Summary
We described a way of using biological materials todevelop a new type of electronic device. Using AFM,
we observed the periodical hexagonal shape of bR on
mica. We succeeded in imaging a membrane protein
suspended over artificially fabricated cells preparedon a silicon substrate with submicrometer dimensions. Molecular-scale imaging was readily obtained
and the structure of the protein being used for thedevice could be located precisely. The results showthat an electrical platform with a functioning membrane protein was provided. We also found that surface modification and the salt concentration of thebuffer solution affected the attachment of the membrane protein to form a highly resistive seal with thefabricated cell.
Before we can make a new device using functional
biomolecules, we need to improve the fabrication
techniques and understand the mechanisms of proteins. We must also learn how to place proteins in
specific locations accurately. In the final stage of
device fabrication, electrodes will be incorporated
into the individual cells to permit discrete electricalmeasurements. The functional modification of proteins is also something that we will pursue. Imaging
with molecular-scale resolution will help clarify themechanism governing the appearance of biomolecular functions. Molecular-level studies on mechanicaland electrical/electronic analysis are also in progress.
We also hope to elucidate the conformational change
by real-time imaging, leading to an investigation of
the dynamics of proteins function. The results willcontribute to the integration of biomolecular functions into new devices.
Acknowledgments
We thank Kislon Voïtchovsky (Univ. of Oxford),
Sonia A. Contera (Univ. of Oxford), and Kazuaki
Furukawa (NTT BRL) for fruitful discussions, suggestions, and assistance. We also thank Masahiro
46

Uchibatake (NTT-AT) and Miho Kanazawa (NTTAT) for their excellent technical assistance. This
work was conducted as part of the joint bionanoscience collaboration between NTT Basic
Research Laboratories and the University of Oxford.
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R. R. Birge, N. B. Gillespie, E. W. Izaguirre, A. Kusnetzow, A. F.
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Koji Sumitomo

Keiichi Torimitsu

Senior Research Scientist, NTT Basic
Research Laboratories.
He received the B.E., M.E., and Ph.D. degrees
in electronics from Osaka University, Osaka, in
1986, 1988, and 1991, respectively. He joined
NTT Basic Research Laboratories in 1991. Since
then, he has been engaged in research on thecharacterization and control of nanostructures on
semiconductor surfaces. His current work
includes research on nano-bio technologies. He
is a member of the Physical Society of Japan, theJapan Society of Applied Physics (JSAP), theSurface Science Society of Japan, the American
Vacuum Society, and the Materials ResearchSociety.

Executive Manager, Materials Science Laboratory, Group Leader, Molecular and Bio Science
Research Group, NTT Basic Research Laboratories.
He received the B.E., M.E., and Ph.D. degrees
in instrumentation engineering from Keio University, Kanagawa, in 1980, 1982, and 1986,
respectively. In 1986, he joined NTT Basic
Research Laboratories and worked in the biocomputer project. He is currently focusing on
nano-bio science and nano-bio device fabrication. He is a member of the Society for Neuroscience, International Brain Research Organization, Japan Neuroscience Society, JSAP, and theJapanese Pharmacological Society.

Hiroshi Nakashima

Chandra Ramanujan

Research Scientist, NTT Basic Research Laboratories.
He received the B.E., M.E., and Ph.D. degrees
in applied chemistry from Waseda University,
Tokyo, in 1995, 1997, and 2002, respectively. He
joined NTT Basic Research Laboratories in
1997. Since then, he has been engaged inresearch on the synthesis and control of optoelectrical properties of (semi)conductive polymers. His current work includes research on
nano-bio technologies. He is a member of the
Chemical Society of Japan, the Society of Polymer Science, Japan, and the Society of Silicon
Chemistry, Japan.

NTT Bionanoscience Research Fellow,
Department of Physics, University of Oxford.
He received the Ph.D. degree in atomic force
microscopy and nanomechanics from the University of Oxford and is currently a member ofthe joint bionanoscience collaboration between
NTT Basic Research Laboratories and Oxford
University.

Mime Kobayashi

John F. Ryan

Research Associate, NTT Basic Research Laboratories.
He received the B.S. degree in agriculturalchemistry from Kyoto University, Kyoto, and the
M.S. and Ph.D. degrees in biological sciencesfrom Nara Institute of Science and Technology,
Nara, in 1994, 1996, and 1999, respectively. He
was a post-doctoral associate in the departmentof Pharmacology at Weill Medical College ofCornell University before joining NTT Basic
Research Laboratories in 2004. His current work
includes research on nano-bio technologies. He
is a member of the Biophysical Society (USA)and the Molecular Biology Society of Japan.

Professor of Physics and Director of the Bionanotechnology Interdisciplinary Research Collaboration, University of Oxford.
He is a graduate of Edinburgh University. His
research has focused on quantum optoelectronics
and semiconductor nanostructures, and his current interests include bionanostructures anddevices, membrane proteins, and scanning probe
microscopy.

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47