Magnetic barcoded hydrogel microparticles for multiplexed detection.
ABSTRACT Magnetic polymer particles have been used in a wide variety of applications ranging from targeting and separation to diagnostics and imaging. Current synthesis methods have limited these particles to spherical or deformations of spherical morphologies. In this paper, we report the use of stop flow lithography to produce magnetic hydrogel microparticles with a graphical code region, a probe region, and a magnetic tail region. These anisotropic multifunctional magnetic polymer particles are an enhanced version of previously synthesized "barcoded" particles (Science, 2007, 315, 1393-1396) developed for the sensitive and rapid multiplexed sensing of nucleic acids. The newly added magnetic region has acquired dipole moments in the presence of weak homogeneous magnetic fields, allowing the particles to align along the applied field direction. The novel magnetic properties have led to practical applications in the efficient orientation and separation of the barcoded microparticles during biological assays without disrupting detection capabilities.
Article: Application of Flow Focusing to the Break-Up of a Magnetite Suspension Jet for the Production of Paramagnetic MicroparticlesJournal of Nanomaterials. 01/2011;
Article: Hydrogel microparticles from lithographic processes: novel materials for fundamental and applied colloid science.[show abstract] [hide abstract]
ABSTRACT: In recent years there has been a surge in methods to synthesize geometrically and chemically complex microparticles. Analogous to atoms, the concept of a "periodic table" of particles has emerged and continues to be expanded upon. Complementing the natural intellectual curiosity that drives the creation of increasingly intricate particles is the pull from applications that take advantage of such high-value materials. Complex particles are now being used in fields ranging from diagnostics and catalysis to self-assembly and rheology, where material composition and microstructure are closely linked with particle function. This is especially true of polymer hydrogels, which offer an attractive and broad class of base materials for synthesis. Lithography affords the ability to engineer particle properties a priori and leads to the production of homogenous ensembles of particles. This review summarizes recent advances in synthesizing hydrogel microparticles using lithographic processes and highlight a number of emerging applications. We discuss advantages and limitations of current strategies, and conclude with an outlook on future trends in the field.Current Opinion in Colloid & Interface Science 04/2011; 16(2):106-117. · 8.01 Impact Factor
[show abstract] [hide abstract]
ABSTRACT: This protocol describes the core methodology for the fabrication of bar-coded hydrogel microparticles, the capture and labeling of protein targets and the rapid microfluidic scanning of particles for multiplexed detection. Multifunctional hydrogel particles made from poly(ethylene glycol) serve as a sensitive, nonfouling and bio-inert suspension array for the multiplexed measurement of proteins. Each particle type bears a distinctive graphical code consisting of unpolymerized holes in the wafer structure of the microparticle; this code serves to identify the antibody probe covalently incorporated throughout a separate probe region of the particle. The protocol for protein detection can be separated into three steps: (i) synthesis of particles via microfluidic flow lithography at a rate of 16,000 particles per hour; (ii) a 3-4-h assay in which protein targets are captured and labeled within particles using an antibody sandwich technique; and (iii) a flow scanning procedure to detect bar codes and quantify corresponding targets at rates of 25 particles per s. By using the techniques described, single- or multiple-probe particles can be reproducibly synthesized and used in customizable multiplexed panels to measure protein targets over a three-log range and at concentrations as low as 1 pg ml(-1).Nature Protocol 11/2011; 6(11):1761-74. · 8.36 Impact Factor
DOI: 10.1021/la904903gLangmuir 2010, 26(11), 8008–8014Published on Web 02/23/2010
©2010 American Chemical Society
Magnetic Barcoded Hydrogel Microparticles for Multiplexed Detection
Ki Wan Bong, Stephen C. Chapin, and Patrick S. Doyle*
Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue,
Cambridge, Massachusetts 02139
Received December 29, 2009. Revised Manuscript Received February 10, 2010
Magnetic polymer particles have been used in a wide variety of applications ranging from targeting and separation to
diagnostics and imaging. Current synthesis methods have limited these particles to spherical or deformations of spherical
morphologies. In this paper, we report the use of stop flow lithography to produce magnetic hydrogel microparticles with a
graphical code region, a probe region, and a magnetic tail region. These anisotropic multifunctional magnetic polymer
particlesareanenhancedversionofpreviouslysynthesized“barcoded”particles( Science,2007,315,1393-1396) developed
for the sensitive and rapid multiplexed sensing of nucleic acids. The newly added magnetic region has acquired dipole
moments in the presence of weak homogeneous magnetic fields, allowing the particles to align along the applied field
direction. The novel magnetic properties have led to practical applications in the efficient orientation and separation of the
barcoded microparticles during biological assays without disrupting detection capabilities.
Magnetic polymer particles consist of magnetically addressable
components entrapped within or coated on a polymer matrix that
can be precisely tuned to exhibit a range of desired physical and
customization has enabled the use of such particles in biomedical
applications,1-4microscale assembly,5-8structural color printing,9
imaging,10and purification technology.11In addition, the particles
have been employed in microfluidic channels for bioassays,12-15
Recently, biological entities including cells and aptamers were
in a spatially addressable sorting manner by generating magnetic
field gradients in microfluidic channels.26,27
The enormous potential of magnetic polymer particles has
fueledthe development ofseveral distinct synthesis methods. The
conventional emulsification methods based on homogenization
use shear forces to encase superparamagnetic nanoparticles of
metal oxides within polymer droplets.28Unfortunately, these
approaches produce droplets with a wide size distribution and
consume large amounts of energy.28Membrane29and micro-
channel emulsifications30-32have been introduced as alternative
methods that can provide higher degrees of monodispersity for a
fraction of the energy cost. Microchannel emulsification in
particular has produced anisotropic magnetic gel particles using
channel geometries30or a double emulsion technique.31Janus
superparamagnetic gel particles have also been generated with
this approach.32However, the above methods have limited the
particle morphologies to spheres or deformed spheres.28-32A
more flexible synthesis system would expand the possible geome-
tries and thereby augment the applicability of the magnetic
polymer particles produced.
Encoded microparticles have been suggested as diagnostic
tools for the rapid, multiplexed screening of biomolecules
due to their advantages in detection and quantification.33-35
*Corresponding author. E-mail: email@example.com.
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Langmuir 2010, 26(11), 8008–8014
Bong et al.Article
easier probe-set modification, more efficient mixing steps, and
higher degrees of reproducibility. While polymer microspheres
doped with fluorescent dyes have been used most extensively,36
there are numerous systems under development that employ
chemical, graphical, electronic, or physical encoding schemes
for use in multiplexed detection.34Microcarriers fabricated from
a variety of advanced materials such as inverse-opaline photonic
beads37have the potential to transformthe biodiagnostic field by
enabling the analysis of complex sample media (such as serum),
and lowering limits of detection.
Barcoded hydrogels are an emerging subclass of encoded
particles that exhibit higher sensitivities and more favorable
hybridization kinetics than common metallic and polystyrene
microparticles that immobilize probe species on solid surfaces.38
multiplexed analysis, each anisotropic particle bears a probe
region and a corresponding graphical code region that identifies
the probe species. Production of these particles requires a novel
synthesis method called stop flow lithography (SFL),39which
affords precise control over morphology and functionality
through the semicontinuous photopolymerization across coflow-
ing laminar streams of various chemical compositions in micro-
fluidic channels. While the resulting gel-based particles have
proven to be effective tools in past multiplexed sensing of DNA
and RNA, their use in suspension assays and other screening
processes would be greatly simplified with the introduction of an
appropriate means for addressing and aligning the particles
during rinsing, mixing, and analysis procedures.
Magnetic barcoded particles are now introduced as an en-
hanced version of hydrogel microparticles for suspension assays
that can be manipulated using magnetic fields. Through a slight
modification of the SFL technique,39it is now possible to
incorporate magnetically addressable entities within a specific
the ability to sensitivity and specifically detect oligonucleotide
targets in solution. The advantages of the magnetic tail are
tion using a magnet.
Materials. All particles shown in this work were made from
poly(ethylene glycol) (700) diacrylate (PEG-DA 700, Sigma-
Aldrich). The code regions were synthesized using prepolymer
solutions of 35% (v/v) PEG-DA 700, 20% poly(ethylene glycol)
(200) (PEG 200, Sigma-Aldrich), 5% Darocur 1173 (Sigma-
Aldrich) initiator, and 40% 3? Tris-EDTA (pH = 8.0, EMD)
buffer. Rhodamine acrylate (Sigma-Aldrich) and food coloring
the code to give final concentrations of 0.4% and 2%, respec-
tively. The composition of prepolymer for the probe regions was
20% PEG-DA 700, 40% PEG 200, 5% Darocur 1173, and 35%
3? Tris-EDTA buffer. Oligonucleotide probes, no. 1 (50-ATA
GCA GAT CAG CAG CCA GA-30) and no. 2 (50-CAC TAT
GCG CAG GTT CTC AT-30), were purchased from IDT with
acrydite modifications on the 50end and mixed into the probe
prepolymer to give a final concentration of 50 μM. Lastly, the
magnetic region was prepared using solutions of 35% PEG-DA
700, 5% Darocur 1173, and 60% magnetic bead solutions
(Seradyn Inc., carboxylate-modified, 5% solids). Prior to being
incorporated into the particles, the commercial superparamag-
neticbeadsexhibitedashort responsetime uponthe introduction
of a magnetic field and had uniform size (779 nm (10%,
diameter).40Using alternating gradient magnetometry (AGM,
MicroMag 2900), the measured saturation magnetization values
particles were found to be 28 emu/g and 3 emu/g, respectively
(Supporting Information). As the mass of each barcoded micro-
particle varied depending on the code design, we polymerized
particles consisting of only a magnetic region and measured the
magnetization value for these simple hydrogels. A perfusion
solution consisting of PEG-DA 700 was also used to move
unincorporated magnetic beads into a waste reservoir to prevent
pouring PDMS (mixed at a base-to-curing agent ratio of 10:1)
over an SU-8 master and then curing 2 h at 60 ?C in an oven. In
each device, the particle synthesis chamber was 300 μm in width
and 20 μm in height, while the perfusion channel was 70 μm in
width and 110 μm inheight. Eachdevicewasplacedona PDMS-
coated glass slide and then sealed by curing overnight at 60 ?C in
an oven. For synthesis, devices were mounted on an inverted
microscope (Axiovert 200, Zeiss) equipped with a VS25 shutter
system (UniBlitz) to precisely control the UV exposure dose.39
A reservoir was cut into the PDMS to collect the particles.
Stop Flow Lithography Setup. We generated controlled
pressures in the range of 0-15 psia from house air using a Type
of the regulator, a 3-way solenoid valve (Burkert) was used to
switchrapidly between atmospheric pressure (stop) and theinput
pressure (flow). The output from the 3-way valve was connected
(Tygon). The pipet tips were filled with ∼100 μL of the desired
3-way valve and above shutter were controlled using a custom
written script in Labview 8.1 (National Instruments).
Photopolymerization Setup. Photomasks were designed in
AUTOCAD 2005 and printed using a high-resolution printer at
CAD Art Services (Bandon, OR). The mask was then inserted
into the field-stopofthemicroscope. A Lumen 200(Prior) served
as the source of UV light, and a filter set that allowed wide UV
of the desired wavelength for synthesis. The UV exposure time
was limited to 75 ms using the automated shutter system.
Magnetic Responsiveness. Toinvestigate theresponseofthe
magnetic barcoded particles in the presence of an external mag-
netic field, we fabricated analysis reservoirs by sealing a PDMS
rectangular frame (5 ? 5 ? 5 mm) onto a PDMS-coated glass
slide. Each reservoir was filled with the magnetic barcoded
NP-10 (Sigma-Aldrich, St. Louis, MO) (to prevent microparticle
aggregation) and then placed in a uniform magnetic field (planar
power supply (GPS-2303, GWInsteck). The magnetic fields were
calibrated using a Gauss meter (SYPRIS) with an axial probe
(forthe normalinducedmagneticfield) oratransverse probe(for
the planar induced field).
Hybridization and Labeling. Incubation mixtures were pre-
pared by adding ∼50 particles of each desired type to a 0.65 mL
Eppendorf tube containing a hybridization buffer of 0.5 M NaCl
in TET (1? Tris-EDTA with 0.05% Tween-20 (Sigma-Aldrich)).
biotinylated target oligonucleotides at 50 ?C for 90 min using
(36) Kellar, K. L.; Douglass, J. P. J. Immunol. Methods 2003, 279, 277–285.
(37) Zhao, Y. J.; Zhao, X. W.; Hu, J.; Xu, M.; Zhao, W. J.; Sun, L. G.; Zhu, C.;
Xu, H.; Gu, Z. Z. Adv. Mater. 2009, 21, 569–572.
(38) Pregibon, D. C.; Doyle, P. S. Anal. Chem. 2009, 81, 4873–4881.
Mater. 2006, 5, 365–369.
DOI: 10.1021/la904903gLangmuir 2010, 26(11), 8008–8014
ArticleBong et al.
Following hybridization, the samples were rinsed twice with
450 μL TET and then twice with 450 μL PBST (1? PBS
(Cellgro) with 0.05% Tween-20). Then, the probe-target com-
diluted 1:500 in TET to the Eppendorf tube. The labelingprocess
Multi-Therm shaker (Biomega). Before imaging, the particles
were rinsed three times with 450 μL TET and then twice with
450 μL PTET (5? Tris-EDTA buffer with 25% PEG 400 and
Imaging for Quantitative Analysis. A 15-μL droplet con-
taining ∼20 particles was pipetted onto a glass slide and sand-
wiched for analysis using an 18 ? 18 mm coverslip. The sample
UV Illumination source (X-Cite series 120, Exfo), and a custom
macro in NIH Image was used to capture 10 sequential frames
from an EB-CCD camera (C7190-20, Hamamatsu) mounted to
of 1/33 s, and the macro produced a final output image for
analysis by averaging over the 10 frames. Camera settings of 10,
1.6, and 9.9 for gain, offset, and sensitivity, respectively, were
used. Images were analyzed using Image J.
Results and Discussion
Figure 1A shows a schematic depicting the synthesis of
magnetic barcoded particles. Different prepolymer mixtures are
laminar flows. The middle stream is composed of poly(ethylene
glycol) diacrylate (PEG-DA) with an acrylate modified DNA
a fluorescent dye, rhodamine acrylate (rhodamine A), and with
magnetic beads, respectively. The flows can be stopped via
pressure release, during which an array of magnetic barcoded
particles are formedbya 75msUVexposurethrough a transpar-
ency mask using a standard fluorescence microscope. A pressure
pulse is then used to advect the polymerized particles into a
collection reservoir. This process is repeated using an automated
setup, allowing for the high-throughput synthesis of particles
(18000per hour) inasemicontinuousmanner.Prior tocollection
in the reservoir, a perfusion stream with flow perpendicular to
that in the synthesis chamber was used to move unincorporated
to simplify the rinsing procedures. While the excess beads flowed
into the perfusion line, the much larger encoded particles were
only collected in the reservoir of the synthesis chamber. The
commercially available superparamagnetic beads were well-
mixed with PEG monomer solutions and well-dispersed in
microfluidic channels (Figure 1B). Aside from the addition of
the simple perfusion stream, no special processing steps or
chemical treatments were required to integrate the magnetic
streams into the SFL process.
The magnetic barcoded particles were comprised of three
distinctregions:(1) coderegionfor identifyingparticleand probe
embedded within, (2) probe region for detecting target, and (3)
magnetic region for providing magnetic addressability. The
dimensions of each region were 105 ? 70 μm, 55 ? 70 μm, and
90? 70μm,successively(Figure1C). The size(0,1,2,and3) and
order of unpolymerized holes in the wafer structure were used to
construct a graphical code to distinguish particle types. The
number “0” was designed as a nonpunched area, while the
punched dimensions of numbers “1”, “2”, and “3” were 12 ?
15 μm, 12 ? 27.5 μm, and 12 ? 40 μm, respectively. Careful
focusing and inlet pressure control during the photopolymeriza-
tion process ensured a high degree of reproducibility in the
creation of the coding holes and the different chemical regions
on each microparticle.
particles. As seen in brightfield images (Figure 2, parts A, C, and
E), the brown magnetic regions are clearly separated from the
neighboring probe regions. Well-developed code regions are
shown in fluorescent images (Figure 2, parts B and D), with
sharp interfaces and feature resolution provided by the SFL
process. We prepared magnetic barcoded particles ∼16 μm in
height by using 20 μm-high channels (Figure 2C). The difference
between particle and channel heights can be attributed to the
∼2 μm-thick oxygen inhibition layer on both the top and bottom
channel surfaces.41Compared to code and probe regions, it was
observed thatthe magnetic regionwas slightly thinnerdue toUV
absorption by the iron oxide cores of the magnetic beads.
To investigate magnetic response, we exposed the magnetic
barcoded particles dispersed in a 0.005% (v/v) aqueous Tergitol
Figure 1. Production of magnetic barcoded particles. (A) Synthesis process of magnetic barcoded particles. Stop flow lithography (SFL) is
PEG-DA perfusionstream isusedtomoveunincorporatedmagneticbeadsintoawaste outlet.(B) Anexperimentalbrightfieldimage ofthe
three phases flowing in the channel. The magnetic beads in the bottom flow are seen to be well-dispersed. The scale bar is 50 μm. (C)
and “3” (12 ? 40 μm). The code in this illustration is “2333”.
(41) Dendukuri, D.; Gu, S. S.; Pregibon, D. C.; Hatton, T. A.; Doyle, P. S. Lab
Chip 2007, 7, 818–828.
Langmuir 2010, 26(11), 8008–8014
Bong et al.Article
(21.1 ( 0.1 mT) perpendicular to the reservoir substrate. Sus-
pended in a nonmagnetic medium, the particles acquired dipole
moments and flipped up perpendicular to the plane, forming
columnar structures along the applied field direction (Figure 3A
and Supporting Information). In the presence of a weak homo-
geneous field (14.7 ( 0.1 mT) parallel to the substrate plane,
attractive induced dipolar interactions lead to tail-to-tail self-
assembly of the particles (Figure 3B).
the barcoded particles as shown in Figure 3C-E and Supporting
Information. Using a hand magnet, it was possible to remotely
and precisely manipulate the orientation of magnetic barcoded
particles at the inlet of a microfluidic channel to aspirate all
particles such that they proceeded down the analysis chamber in
a “probe first” (versus “code first”) orientation. Figure 3C shows
the reorientation process of a barcoded particle from “code first”
to “probe first” within a microfluidic channel. By moving a more
transport this reoriented particle from the inlet to a more narrow
zone used for single-particle analysis (Figure 3D). Although the
transportation velocity was only 10 μm/s in this experiment, the
process was performed in a simple manner using a common
magnet. This pumpless method for orientation and movement
does not require the complex setup used in pressure-driven
alignment processes and does not subject the soft hydrogel
particles to the significant hydrodynamic forces that pressure-
driven processes can introduce in microchannels.42
This capacity to address the position and orientation of
of a magnetic aspiration column could be used to deliver all
particles to a flow-through scanning chamber42with the same
probe-first orientation. As existing high-throughput flow align-
ment methods cannot control which end of the particle leads in
the flow, decoding algorithms that determine probe identity and
amount of bound target must additionally ascertain the orienta-
be magnetically addressed to give the same orientation prior to
by a factor of 4. It should also be noted that the simultaneous
reorientation and transportation of multiple barcoded particles
was achieved in a large reservoir using a hand magnet (Figure 3E
and Supporting Information). This capability could potentially
be exploited for the ordered presentation of posthybridization
particles in a plate-based stationary scan.
The magnetic functionality also introduces a new means by
which the barcoded particles can be concentrated and subse-
quently separated from a carrier solution. In previous implemen-
tations of barcoded hydrogel particles for biomolecule detection,
10 centrifugal separations were required for the rinsing steps in a
typical assay. This density-based separation strategy tends to
concentrate fibers and other particulate matter along with the
encoded microparticles at the bottom of the sample tube. If these
contaminants then stick to the particles, they can interfere with
the analysis of the fluorescence emitted by the code and probe
regions. Magnetic force separation provides an alternative ap-
proach to segregating the barcoded particles for rinsing proce-
dures. Using a permanent magnet, we successfully separated the
particles on the side of a collection tube in 2 min (Figure 3F). In
further experiments, the 10 rinsing steps of a DNA hybridiza-
tion assay were carried out using magnetic barcoded hydrogel
Figure 2. Magnetic barcoded particles. (A) Bright field image (20? objective) of magnetic barcoded particles with code “2333”. (B)
B), 25 μm (C and D), and 100 μm (E).
(42) Chapin, S. C.; Pregibon, D. C.; Doyle, P. S. Lab Chip 2009, 9, 3100–3109.
DOI: 10.1021/la904903gLangmuir 2010, 26(11), 8008–8014
Article Bong et al.
of the particles, it was determined that the vast majority of
particles had been retained and, furthermore, a considerably
smaller amount of particulate matter was seen in the carrier
A wide variety of geometrically and chemically complex
the four particle types used in a multiplexed DNA sensing study,
illustrating the code, the identity of incorporated probe, and the
presence or absence of magnetic beads in the tail region. Types 1,
2, and 3 featured a magnetic tail and were incorporated with no
probe (type 1), probe no. 1 (type 2), or probe no. 2 (type 3) in the
central region. Type 4 featured a nonmagnetic tail, bore probe
with respect to target capture, the mean signals from the target
panels on types 2 and 4 should be the same when incubated with
target corresponding to probe no. 1.
The four particle types were hybridized with either 0 or
200 amol of two different biotinylated target oligonucleotides.
Following hybridization and labeling with SAPE, the fluorescent
were analyzed. An incubation matrix was prepared to compare
the performance of the various particles (Figure 4). Each plot in
type at the specified incubation condition. The mean fluorescent
intensity across the width of the particle (vertical axis, AU) was
calculated and then plotted at each lengthwise position
(horizontal axis, pixels) along the particle. The fluorescent in-
success of the detection and examining the effect of the magnetic
and 4 in Figure 4, the mean signals in these regions are similar
whether the tail region is magnetic or nonmagnetic, indicating
specific detection of the oligonucleotides.
It should be noted that target 1 generated a lower signal than
target 2 when incubations were performed with all four types
simultaneously in a single Eppendorf tube. The lower signal for
target 1 can be attributed to the presence of two particle types
(2 and 4) bearing probe 1 in the incubation mixture. Because of
incubation, whereas target 2 was spread over only ∼50 total
particles per incubation. When the same amount of target 1
Figure 3. Response of magnetic barcoded particles. (A) Response of magnetic barcoded particles to out-of-plane (21.1 ( 0.1mT) magnetic
field. (B) Response of magnetic barcoded particles to in-plane (14.7 ( 0.1mT) magnetic field. (C) Reorientation of a magnetic barcoded
particle in a microfluidic channel using a hand magnet. (D) Snapshots of magnetic transportation of a magnetic barcoded particle using a
handmagnet.Theparticlewas transportedtowardanarrowregioninthemicrofluidicchannelusedfor single-particlescanninganalysis.(E)
Image of reorientedmagnetic barcodedparticles movingtowarda handmagnet. (F) Bulk separationofmagnetic barcodedparticles using a
hand magnet. Scale bars are 50 μm (C and D), 100 μm (A and B), and 200 μm (E).
Table 1. Design of the Four Different Magnetic Barcoded Particle