Porous Protein-Based Nanoparticle Hydrogel for Protein Chips with Improved Sensitivity
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Transcript of Porous Protein-Based Nanoparticle Hydrogel for Protein Chips with Improved Sensitivity
Communication
Porous Protein-Based Nanoparticle Hydrogelfor Protein Chips with Improved Sensitivity
Hiroyuki Tanaka, Tatsushi Isojima, Minako Hanasaki, Yasuo Ifuku,Hisao Takeuchi, Haruma Kawaguchi, Toshifumi Shiroya*
We have discovered a novel method to prepare a protein-based hydrogel, that is, a ‘three-dimensional nanostructured protein hydrogel’ (3D NPH), which is composed of looselyinter-connected protein–polymer hybrid nanoparticles. The 3D NPH can be easily preparedby spotting a protein/polymer mixture on asubstrate. Surprisingly, gold nanoparticlescarrying protein molecules easily diffuse intothe 3D NPH through pores and spaces. Wehave shown that the protein chip made byour 3D NPH method has tremendouslyimproved sensitivity in detecting protein–protein interactions compared with that bydirect protein immobilization methods.
Introduction
Protein chips are important tools for high-throughput
analysis of biological events.[1–7] Recently, a number of
spots, each containing an immobilized protein, have been
placed on a chip surface. The number of spots, i.e., the
surface density of spots, has been increasing dramatically,
and this trend towards a high surface density results in the
reduction of immobilized protein amount per one spotted
area. As a general rule, however, a lower immobilized
H. Tanaka, T. Isojima, M. Hanasaki, H. Takeuchi, T. ShiroyaMitsubishi Chemical Group Science and Technology ResearchCenter, INC., 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-8502,JapanFax: þ81-45-963-3741; E-mail: [email protected]. IfukuMitsubishi Chemical Medience Corporation, 1144 Ohwadashin-den, Yachiyo, Chiba 276-0046, JapanH. Tanaka, H. KawaguchiGraduate School of Science and Technology, Keio University,3-14-1, Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
Macromol. Rapid Commun. 2008, 29, 1287–1292
� 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
protein amount has resulted in lower sensitivity in protein
chips. This trade-off between the surface density and the
sensitivity requires a new method to increase the binding
capacity per unit area and to improve the sensitivity of
protein chips for detecting protein–protein interactions.
One such method can be found in protein immobilization
using hydrogels: proteins are immobilized in a three-
dimensional (3D) matrix of a hydrogel. There have been
various reports about hydrogel surfaces. For example,
carboxymethyl dextran (CMD),[8,9] polyacrylamide
gel,[10–14] agarose thin film,[15] poly(acrylic acid)
brushes,[16] supramolecular hydrogel,[17] and others,[18–20]
have been used to immobilize proteins. By using these
kinds of hydrogel, the immobilized amount of ligand
proteins can be increased with a reduction in non-specific
protein adsorption to the surfaces.
However, the increase in the amount of immobilized
ligand proteins has not necessarily achieved an increase
in the amount of analyte proteins bound to ligand
proteins.[9,16] These results could be explained by mass
transfer limitation and a reduced accessibility of the
DOI: 10.1002/marc.200800090 1287
H. Tanaka et al.
1288
hydrogels for analyte proteins. To improve the accessibility
of analytes to the ligands immobilized in the hydrogel
matrices, highly porous hydrogels have been made.[14]
However, since the mechanical stabilities of hydrogels
could be incompatible with high porosities, there are
limitations to the porosity of hydrogels.
From a different view for practical use, preparation
processes are required to be easy and well suited to mass
production. For example, recently, a hydrogel composed of
multi-functionalized polymers and proteins were formed
in situ using a one-step process.[21]
Here we report a novel method to prepare a protein-
based hydrogel, i.e., a ‘three-dimensional nanostructured
protein hydrogel’ (3D NPH), which is composed of loosely
inter-connected protein–polymer hybrid nanoparticles.
The 3D NPH can be easily prepared by spotting a protein/
polymer mixture on substrates. The morphology, physical
properties, and bio-functions of the resulting 3D NPH are
studied. In particular, the use of the 3D NPH as a substrate
for an affinity assay is focused on and carefully examined.
Experimental Part
Polymerization and Characterization of
Poly(NAM-co-NAS)
Poly[(N-acryloylmorpholine)-co-(N-acryloxysuccinimide)] [poly-
(NAM-co-NAS)] was prepared by free-radical polymerization
of N-acryloylmorpholine (Sigma-Aldrich, MO, U.S.A.) and
N-acryloxysuccinimide (Acros Organics, NJ, U.S.A.) at an 80:20
molar ratio in anhydrous dioxane (Wako Pure Chemicals
Industries, Ltd., Osaka, Japan) as a solvent according to previous
reports.[22,23] The concentration of all of the monomers was
0.5 mol � L�1. The copolymerization was performed at 60 8C for 4 h
using azoisobutyronitrile (Wako Pure Chemicals Industries, Ltd.,
Osaka, Japan) as a polymerization initiator (1 mol-% of the
monomers). Poly(NAM-co-NAS) was precipitated into a large
volume of ethylic ether, recovered by filtration, and dried under
vacuum. The molecular weight was determined by size exclusion
chromatography (SEC) analysis: HLC-8220 GPC(L) (TOSOH, Japan),
using a TSK gel GMPW�1 column (TOSOH, Japan). The eluent
used was dimethylformamide (DMF) with 50� 10�3M LiBr (Wako
Pure Chemicals Industries, Ltd., Osaka, Japan) at a flow rate of
0.5 mL �min�1. The average copolymer composition was deter-
mined from 1H NMR spectra (Avance 500, Bruker, Germany) of the
copolymer according to a previous report.[22] Poly(NAM-co-NAS),
NAM/NAS¼ 65/35 (mol/mol), Mw ¼ 86 000) was prepared.
Preparation of 3D NPH on Substrates
An Au-coated plastic substrate was treated with a 10�10�3M
solution of 16-mercaptohexadecanoic acid (Sigma-Aldrich, MO,
U.S.A.) in ethanol (Junsei chemical, Tokyo, Japan) for 12 h. The
introduced carboxy groups on Au were activated to form
reactive succinimide esters using a solution of 0.1 mol � L�1
N-ethyl-N0-(3-dimethylaminopropyl) carbodiimide hydrochloride
Macromol. Rapid Commun. 2008, 29, 1287–1292
� 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
(EDC, Dojindo corporate, Kumamoto, Japan) and 0.4 mol � L�1
N-hydroxysuccinimide (NHS, Pierce Biotechnology, Rockford,
U.S.A.) in water. After the activation reaction, one micro-liter of
a protein and poly(NAM-co-NAS) mixture (protein/polymer¼10/
1 (w/w) in buffer solution) was deposited by a pipette on the
substrates which have the succinimide groups, and subsequently
reacted by concentration of the mixture by a drying process. After
about 1 h reaction, the remaining succinimide groups were
masked using 1 M ethanolamine solution (pH 8.5) and the
substrates were washed with PBS 0.01 vol.-% Tween 20 (PBST)
buffer solutions five times.
Characterization of 3D NPH
The composition (protein/polymer weight ratio) of 3D NPH–IgG
was determined by amino acid analysis (amino acid analyzer
L8500, Hitachi, Japan) and pyrolysis gas chromatography mass
spectrometry (HP5973MSD, Agilent, USA) of polyacrylic acids after
the hydrolysis of 3D NPH–IgG by 6 N HCl. For the analysis, 100 mL
of 3D NPH–IgG ([protein]/[polymer]¼ 10/1, [protein]¼1.0 wt.-%)
was hydrolyzed by 6 N HCl into amino acids and polyacrylic acids,
the amounts of which were determined.
SEM measurements for the cross section of 3D NPH were carried
out using a JEOL JSM-6320F. 3D NPH–IgG was stained by osmium
tetroxide vapor at room temperature for 2 h and embedded in
Epon 812 epoxy resin (Polysciences, Inc., Pennsylvania, U.S.A.) at
60 8C for 48 h. The sample was etched by glow discharge at 400 V.
Atomic force microscopy (AFM) observations were performed
at room temperature under dry and wet conditions with a Multi
mode AFM (Digital Instrument USA) over a 5 mm�5 mm area in
tapping mode and the raw data was analyzed using the
Nanoscope III software package provided by the manufacturer.
Under dry conditions, the probe of SSS-NCH SUPERSHARPSILICON
(Nanoworld, L¼128 mm, R<5 nm) was used. The spring constant
was 25 N �m�1, and the frequency was 263 kHz. Under wet
(phosphate-buffered saline, PBS) conditions the probe of
OMCL-TR400PSA (OLYMPUS, L¼200 mm) was used. The spring
constant was 0.02 N �m�1, and the frequency was 7.62 kHz.
Transmission electron microscopy (TEM) measurements were
carried out using a JEOL LEM 1200 EX to examine a cross section of
3D NPH–IgG reacted with protein A–Au colloid particles. The
sample was fixed in 2 wt.-% glutaraldehyde in 0.1 M cacodylate
buffer (pH 7.4) at room temperature for 2 h; then it was
dehydrated in ethanol at room temperature for 30 min and
embedded in Epon 812 epoxy resin at 60 8C for 48 h. The sample
was etched by an ultramicrotome.
Cy3-Labeled Anti-Mouse IgG F(ab’)2 Binding
Experiments
Three kinds of 3D NPH (Streptavidin, MW 60 kDa, Wako Pure
Chemicals Industries, Ltd., Osaka, Japan, Protein A, MW 60 kDa,
Sigma-Aldrich, MO, U.S.A., and Mouse IgG, MW 150 kDa, LAMPIRE
Lab. PA, U.S.A.) were prepared using one micro-liter of a protein
and poly(NAM-co-NAS) mixture ([protein]/[polymer]¼10/1,
[protein]¼1.0 wt.-%) according to the method described above.
In the case of 2D surfaces, proteins were directly immobilized on a
substrate. The patterned 2D and 3D NPH surfaces were treated for
DOI: 10.1002/marc.200800090
Porous Protein-Based Nanoparticle Hydrogel for . . .
30 min with Cy3–anti-mouse IgG F(ab’)2 (10 mg �mL�1, MW 100
kDa, Sigma-Aldrich, MO, U.S.A.) prepared in phosphate-buffered
saline (PBS), at pH 7.4 after being blocked for 1 h with a 3 wt.-%
solution of bovine serum albumin (BSA, MW 60 kDa, Sigma-
Aldrich, MO, U.S.A.) prepared in PBS, at pH 7.4. All the 3D NPH and
2D surfaces were post-washed with PBST five times. The
fluorescence signals were detected using genepix 4000B (Axon
instrument). To examine the relation of the protein/polymer
concentrations in the feed to the analyte binding, three 3D
NPH–Mouse IgG solutions were prepared by changing the
protein/polymer total concentrations ([protein]/[polymer]¼10/
1, [protein]¼ 0.13, 0.25, and 0.50 wt.-%) in the feed. An Anti Biotin
IgG (MW 150 kDa, Sigma-Aldrich, MO, U.S.A.) solution of 3D NPH
was prepared using one micro-liter of protein and poly(NAM-co-
NAS) mixtures ([protein]/[polymer]¼ 10/1, [protein]¼ 1.0 wt.-%).
In the case of 2D surfaces, proteins were directly immobilized on a
substrate. The analyte concentration of Cy3–Biotin-HRP applied to
the 3D NPH–anti Biotin IgG and 2D surface was 10 mg �mL�1.
Cy3–Biotin-HRP was prepared with Biotin-HRP (MW 45 kDa,
Pierce Biotechnology, Rockford, U.S.A.) and Cy3 dye reagent (GE
Healthcare, Uppsala, Sweden).
Results and Discussion
Polymers contribute to the assembly protein molecules to
form nanoparticles, the assembly of nanoparticles to form
Figure 1. Schematic representation of the 3D NPH preparation proce
Macromol. Rapid Commun. 2008, 29, 1287–1292
� 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
aggregates, and to connect the aggregates. The preparation
procedure of 3D NPH is shown in Figure 1. One micro-liter
of a protein/poly(NAM-co-NAS) mixture (protein/poly-
mer¼ 10/1 (w/w) in buffer solution) were deposited on
substrates which have succinimide groups, and amino
groups of the proteins reacted with the succinimide groups
of the poly(NAM-co-NAS) and/or substrates while the
mixed solution was concentrated through a drying
process. After 1 h of reaction, the remaining succinimide
groups were masked by 1 M ethanolamine solution (pH 8.5)
and the substrates were washed with buffer solutions five
times to remove unreacted proteins and polymers. This
preparation method of 3D NPH includes a gelation process
between proteins and the reactive polymers on substrates
upon concentrating the mixture. The hydrogel could be
made on the limited areas of the substrates by this
method. It has been pointed out that cross-contamination
and overflow during microdrop depositing may occur
because of an overall coverage of the substrate by a
hydrophilic hydrogel.[24] By using this 3D NPH method, we
can make a protein array with high surface densities
without cross-contamination among neighboring spots
and overflow.
The results of amino acid analysis and pyrolysis gas
chromatography mass spectrometry showed that 3D
ss and analyte interaction with 3D NPH.
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H. Tanaka et al.
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NPH-IgG, which was prepared from a mixture of IgG/
poly(NAM-co-NAS) of 10/1(w/w) in the feed, had an IgG/
poly(NAM-co-NAS) ratio of 96/4 (w/w). This shows that the
composition of 3D NPH–IgG almost coincides with that in
the feed, and this means that the 3D NPH is a
protein-based hydrogel. Hereafter, in this study, the
composition of 3D NPH was fixed at 10/1 (w/w).
The surface concentration of IgG immobilized in the 3D
NPH–IgG was 26 mg � cm�2, and this value shows that
about 80 wt.-% of the amount of protein deposited on the
substrate remains as a hydrogel. The surface concentration
of the IgG monolayer in an end-on or side-on orientation
was reported as 1.85 and 0.27 mg � cm�2, respectively.[25]
Therefore, the surface concentration of 3D NPH–IgG is
equivalent to about 14–93 layers.
Figure 2. Structure analyses of the 3-D NPH. a) SEM image of a croscross-section of 3-NPH-IgG reacted with protein A Au colloid particles.Au colloid particles. d) AFM image of a surface of 3-D NPH-IgG in dry coNPH-IgG in wet condition; AFM image of a surface of 3-D NPH-strepimmobilized with gulteraldehyde.
Macromol. Rapid Commun. 2008, 29, 1287–1292
� 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
Next, the structures of the 3D NPH were analyzed by
several microscopic observations such as scanning elec-
tron microscopy (SEM), TEM, and AFM. Figure 2(a) shows
an SEM image of a cross-section of 3D NPH–IgG which was
prepared by a 1 mL deposition of a protein/polymer
mixture ([protein]/[polymer]¼ 10/1, [protein]¼ 1.0 wt.-%)
in PBS, on a gold-coated plastic substrate, followed by
being embedded in epoxy and cut by a glow discharge. It is
clear from this image that the 3D NPH–IgG consists of
nanoparticles. These nanoparticles are presumed to be
conjugates composed of IgG and poly(NAM-co-NAS)
molecules.
Figure 2(b) and (c) show SEM and TEM images of the 3D
NPH–IgG after being stained with protein A–gold particles.
The rims surrounding the ellipsoidal aggregate are protein
s-section of 3-D NPH-IgG on the solid substrate. b) SEM image of ac) TEM image of a cross-section of 3-NPH-IgG reacted with protein Andition. e) The zoomed image of (d). f) AFM image of a surface of 3-D
tavidin, (g) and -BSA (h). i) AFM image of a surface of BSA hydrogel
DOI: 10.1002/marc.200800090
Porous Protein-Based Nanoparticle Hydrogel for . . .
Figure 3. a) Fluorescent image of three kinds of 3D NPH after probing withCy3–anti-Mouse IgG F(ab’)2 (Proteins: streptavidin, protein A, and Mouse IgG). b) Fluo-rescent image of the 3D NPH–Mouse IgG ([protein]/[polymer]¼ 10/1, [protein]¼0.13, 0.25,and 0.50 wt.-% in the feed) and of the 2D surface ([protein]¼0.13, 0.25, and 0.50 wt.-% inthe feed) after probing with Cy3–anti-Mouse IgG F(ab’)2. c) Line plot of fluorescentintensity vs. Mouse IgG concentrations in the feed. d) Fluorescent image of 3D NPH–antiBiotin IgG after probing with Cy3–Biotin-HRP.
A–gold particles (diameter: about 10
nm). These SEM and TEM images show
that actually 3D NPH consists of aggre-
gates that are micrometer in size, which
are composed of nanoparticles. The SEM
and TEM images reveal that protein
A–gold particles could diffuse into 3D
NPH–IgG and bind the Fc regions of the
IgG molecules immobilized in the 3D
NPH–IgG. This finding indicates that the
3D NPH–IgG has sufficient space in
water through which large molecules
such as analyte protein molecules can
diffuse. The protein A–gold particles
adsorbed on the vicinity of the aggre-
gate surfaces and did not penetrate into
them (Figure 2(c)). The degree of cross-
linking in the aggregates might be so
high that the protein A–gold particles
could not penetrate into the aggregates,
whereas the lower cross-linking degree
among the aggregates might enable the
protein A–gold particles to diffuse into
the 3D NPH–IgG through the voids between the aggre-
gates.
AFM images with a lower magnification of 3D NPH–IgG
surfaces are shown in Figure 2(d) and (f), which were
observed under dry and wet conditions, respectively.
Aggregates and voids are observed all over the 3D
NPH–IgG surface. The aggregates are about a micrometer
size, and there are voids around them. The aggregate sizes
almost coincided with the aggregate sizes shown in
Figure 2(c) and, on the surface of these aggregates,
nanoparticles could be recognized (Figure 2(e)). In water,
3D NPH–IgG swells and almost retains the original size of
the aggregates (Figure 2(f)). This finding indicates that 3D
NPH mainly swells between the aggregates. The reason
for this heterogeneous swelling behavior might also be
that the degree of the cross-linking in aggregates is higher
than that between the aggregates. We are currently trying
to control the size of the aggregates by changing the
preparation conditions such as polymer species, and
composition and concentration of the protein/polymer
mixtures in the feed.
Figure 2(g) and (h) show AFM images of 3D NPH surfaces
made by other kinds of proteins (streptavidin, albumin).
Nanoparticles and their aggregates could be also con-
firmed in these AFM images, whereas the distinctive
structure could not be recognized in the AFM image of the
albumin hydrogel made by glutaraldehyde (Figure 2(i)).
Since a large amount of ligand proteins could be
immobilized on the substrate and the analyte proteins
could diffuse into the 3D NPH smoothly, it is highly
expected that 3D NPH can be applied for protein arrays
Macromol. Rapid Commun. 2008, 29, 1287–1292
� 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
with high sensitivity to detect specific protein–protein
interactions.
First, to examine specific and non-specific bindings to
the 3D NPH, the 3D NPH of several proteins (Streptavidin,
Protein A, Mouse IgG) were probed with Cy3–anti-Mouse
IgG F(ab’)2 (10 mg �mL�1) (Figure 3(a)) The increase in
fluorescence was only observed for the 3D NPH–Mouse
IgG, which indicates that specific protein–protein recogni-
tion occurred, and the analyte protein did not bind to the
other 3D NPH–Streptavidin and 3D NPH–Protein A
non-specifically.
Next we spotted four 3D NPH–Mouse IgG with different
protein/polymer total concentrations ([protein]/[poly-
mer]¼ 10/1, [protein]¼ 0.13, 0.25, and 0.50 wt.-%) in the
feed to test the capacity of the 3D NPH–Mouse IgG to bind
analyte proteins (Cy3–anti-Mouse IgG F(ab’)2). In addition,
to compare the analyte protein binding capacity, Mouse-
IgG molecules were immobilized directly on an Au
substrate that had succinimide groups (2D surface). The
fluorescence intensity of the 2-D-Mouse IgG was saturated
above 0.25 wt.%, however, the fluorescence intensity of the
3-D NPH–Mouse IgG increased almost linearly with
increasing the concentrations of the Mouse IgG/polymer
mixtures over the examined range (Figure 3(b)). The
fluorescence intensity of the 3D NPH–Mouse IgG
(0.50 wt.-%) was about 50-fold greater in fluorescence
signal than that of the Mouse IgG immobilized on a 2D
substrate (Figure 3(c)). This result showed that the binding
capacity of the 3D NPH could be controlled by the
concentrations of the protein/polymer mixtures in the
feed with good reproducibility. The significant increase
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H. Tanaka et al.
1292
in the fluorescence intensity of the 3D NPH could be
attributed to the large amount of immobilized Mouse IgG
molecules and the unique porous structure of the 3D NPH.
In the case of conventional 3D methods using poly-
acrylamide or a poly(ethylene glycol) (PEG) cross-linker,
the 3D hydrogels were two to three fold greater in
fluorescence signal than the 2D surface.[10,13,21] Some
researchers controlled the porosity of polyacrylamide or
modified polyacrylamide gel to improve the diffusion of
analyte proteins into the hydrogel and completed the
assay within several hours.[10,26] In our case, owing to
the highly porous and hydrophilic matrix of 3D NPH,
analyte proteins can easily diffuse into the pores and
the analyte proteins can interact with ligand proteins
therein in assay times shorter than 30 min. It is difficult to
compare these results rigorously because of the difference
of the kind of proteins and hydrogels. However, we believe
that the 3D NPH method is superior to conventional 3D
methods and 2D methods in terms of the sensitivity and
speed of analysis.
Furthermore, to confirm whether the proteins immobi-
lized in 3D NPH retain their activities, we made 3D
NPH using anti-Biotin IgG ([protein]/[polymer]¼ 10/1,
[protein]¼ 1.0 wt.-%) in the feed and examined whether
they can capture Cy3–Biotin-HRP as the analyte protein
(Figure 3(d)). IgG molecules immobilized in the 3D NPH
maintained their activity to interact with the analytes, and
could capture a much larger amount of analyte compared
with the 2D surface.
Conclusion
We have demonstrated that a ‘3D nanostructured protein
hydrogel’ (3D NPH) composed of protein–polymer nano-
particles can be successfully prepared by condensing a
protein/polymer mixture on substrates. The 3D NPH could
immobilize a large mount of proteins and has novel porous
structures through which the analyte proteins may diffuse
into it. Therefore, the ability of the ligand proteins in the
3D NPH to capture the analyte proteins is remarkably high
compared with a 2D surface, and thus a highly sensitive
protein chip could be made by the 3D NPH method.
Acknowledgements: The authors thank Prof. Kenji Kubota ofGunma University and Dr. Hisashi Koga of Kazusa DNA
Macromol. Rapid Commun. 2008, 29, 1287–1292
� 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
Research Institute for their helpful suggestions. They also thankDr. Takamasa Hanaichi for the TEM measurements.
Received: February 11, 2008 Revised: April 9, 2008; Accepted:April 14, 2008; DOI: 10.1002/marc.200800090
Keywords: biomaterials; hydrogels; nanoparticles; proteins
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DOI: 10.1002/marc.200800090