SUPPLEMENTARY INFORMATION

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1 SUPPLEMENTARY INFORMATION Section S1: Methods Materials Supplementary Information M-ink is composed of superparamagnetic colloidal nanocrystal clusters (CNCs) and photocurable resin monomer solution (S1). Superparamagnetic CNCs with a core diameter of 110nm and silica shell thickness of 25nm were synthesized via a high temperature hydrolysis reaction followed by a modified Stöber process (S2) and dispersed in photocurable resin monomer solution at a concentration of 10mg superparamagnetic CNCs in 1ml photocurable resin. We used ethoxylated trimethylolpropane triacrylate (ETPTA, Sigma-Aldrich) as a photocurable resin with 10wt% of 2,2-dimethoxy-2- phenylacetophenone (DMPA, Sigma-Aldrich) as a photoinitiator for the magnetic actuation demonstration. In the DNA hybridization assay, superparamagnetic CNCs were dispersed in a monomer solution of 3:1 poly(ethylene glycol) diacrylate (PEG-DA, Sigma-Aldrich, M n =700) : deionized water with 10wt% DMPA and used for the code region. Probe oligomer solutions for the DNA oligomer probe region were prepared by adding DNA oligomer probes (12.5μM) into 3:1 PEG-DA:TE buffer (10mM Tris ph 8.0, 1mM EDTA) with 10wt% DMPA. Here we used arcylate-modified DNA oligomer probes with two different nucleotide sequences (Probe#1 : 5 -Acrydite-C9-ACA CTC TAC AAC TTC 3, Probe#2 : 5 -Acrydite-C9-ATC AGA TTG GTT AGT -3, IDT), so DNA oligomers could be incorporated into PEG-DA polymer network during photopolymerization (S3). Target oligomer solutions were prepared by adding Cy3-labelled DNA oligomer targets (Target#1 : 5 - Cy3 GAA GTT GTA GAG TGT -3, Target#2 : 5 Cy3 ACT AAC CAA TCT GAT 3, IDT) in TE buffer with 0.2M NaCl and 0.5% sodium dodecyl sulfate. The concentration of DNA oligomer target was 1μM in multiplexing demonstration and 100nM in reaction enhancement demonstration. We also used 3:1 PEG-DA:TE buffer as a wash buffer in every wash step unless otherwise specified. Microfluidic device fabrication The microfluidic device was fabricated using soft lithography. A microfluidic channel mold was prepared by patterning SU-8 photoresist (SU , MicroChem) on a silicon wafer using photolithography. Polydimethylsiloxane (PDMS) elastomer (Silgard 184, Dow Corning) with curing agent was poured onto the mold and thermally cured for 15min on a 150 C hot plate. The inlet and outlet of the channel were generated by punching holes in the PDMS. The replica of the mold was bonded to the PDMS-coated glass slide after oxygen plasma treatment with plasma cleaner (CUTE-MP, Femto Science). The bonded microfluidic device was heated for additional 10min on a 150 C hot plate for strong adhesion between the PDMS channel and PDMS-coated glass slide. A microfluidic channel with the height of 40µm was used for particle generation. nature materials 1

2 supplementary information Magnetic field generation and maskless lithography An electromagnet was obtained by wrapping copper wires around a cylindrical soft iron bar as a magnetic core. A current-amplifier circuit and control module were designed and constructed in order to control the electromagnet and generate constant current independent of temperature. The electromagnet was calibrated using a gaussmeter (455 DSP Gaussmeter, Lakeshore) and placed above the microfluidic device for magnetic field generation and corresponding colour tuning of M-ink. Colour barcoded magnetic microparticles were generated by photopolymerization. For dynamic maskless lithography, a digital micromirror device (DMD, Texas Instrument) and a 200W mercury-xenon lamp (LC8, Hamamatsu) were coupled to an inverted microscope (IX71, Olympus) to generate and expose a patterned UV light (S4). A self-designed computer program synchronizes magnetic field modulation, DMD pattern modulation, and UV illumination, enabling the generation of colour barcoded magnetic microparticles. The experimental setup is shown in Figure S1. DNA hybridization assay The colour barcoded magnetic microparticles for DNA hybridization assay were prepared through two synthesis steps: formation of a code region and followed by creation of the probe region. A code region was generated through the repetitive tuning and fixing of structural colour of M-ink as described in Section S3 in detail. After washing away residual M-ink with wash buffer, probe oligomer solution containing acrylate-modified DNA oligomer probes was introduced into the microfluidic channel. A UV mask pattern for the probe region was generated in order to form a probe region around the code region with precise alignment. UV light was then irradiated to induce both photopolymerization and incorporation of acrylate-modified DNA oligomers into the polymer network. For the multiplexed DNA hybridization assay, the colour barcoded magnetic microparticles were washed, incubated with Cy3-labelled target oligomer solutions for 10 min, and washed again with TE buffer for imaging. To demonstrate of reaction kinetics enhancement, the microparticles were collected from the microfluidic channel prior to washing. After washing steps, the colour barcoded magnetic microparticles were incubated with target oligomer solutions between two glass slides with a 2mm-thick PDMS spacer. Non-rotating control microparticles were magnetically forced to stand upright during the incubation, so the both faces of particles were maintained to be exposed to the three-dimensional reaction environments. All the microparticles were washed with TE buffer after incubation for imaging. All fluorescence micrographs were obtained using the same imaging conditions. Optical characterization Optical micrographs and fluorescence micrographs were acquired using a true-colour charge coupled device (CCD) camera (DP71, Olympus), which was equipped to an inverted microscope (IX71, Olympus). A 100W halogen lamp and a 250W metal-halide lamp were used to obtain transmission micrographs and reflection micrographs, respectively. For reflection micrographs, we used an off-axis illumination with a tilting angle of 30 from a 2 nature MATERIALS

3 supplementary information viewing axis. In the decoding process, we sampled RGB values of each code position from the reflection micrograph using image analysis software (DP manager, Olympus). The corresponding colour codes were then assigned based on the RGB values. To obtain transmission spectrum in Section S2, a CCD camera (idus, Andor) equipped with a spectrometer (DP320i, Dongwoo Optron) was coupled to an optical fiber with a lens at the other end. The lens collected light from M-ink solution and sent it to the spectrometer through the optical fiber for spectral analysis. Figure S1. Experimental setup. Instrumentation includes maskless lithography, electromagnet, and control unit. Maskless lithography produces dynamic UV patterns, the electromagnet generates a magnetic field, and the control unit synchronizes these two events. Section S2: Chain Formation Time of Superparamagnetic CNCs To monitor chain formation of superparamagnetic CNCs, we implemented a measurement setup as shown in Figure S2. Two electromagnets exert a magnetic field in the same direction to generate a perpendicular magnetic field with respect to the sample. The superparamagnetic CNCs/PEG-DA mixture was loaded between two coverslips with a 40μm-PDMS spacer. Transmitted light is sent to spectrometer through optical fiber and analyzed. Figure S3 shows the change of spectral transmittance under the on/off operation of the electromagnets. The sample starts to reflect light with a peak wavelength of 512nm under the constant magnetic field, and intensity of transmitted light decreases as a result. Approximately 70% of the transition was accomplished within 150ms. The sample goes back to its original state after turning off the electromagnets. nature materials 3

4 supplementary information Figure S2. Step response measurement setup. The system is composed of two coreless electromagnets, a fiber-coupled spectrometer and a collimated white light source. A thin layer of superparamagnetic CNCs/PEG-DA mixture is located between two electromagnets. Figure S3. Step response of spectral transmittance of superparamagnetic CNCs/PEG- DA mixture. Spectral transmittance was determined by dividing the spectrum of transmitted light by the spectrum of the light source. (a) Data set for a single on/off operation of the electromagnet. Each spectrum was acquired every 22ms. (b) Top-view of (a). On/off operation of the electromagnet is clearly shown. (c) Change of transmittance with respect to time at a wavelength of 512nm. (d) Close-up view of (c) during the transition period. 4 nature MATERIALS

5 supplementary information Section S3: Colour Barcoded Magnetic Microparticle Generation Colour barcode magnetic microparticles can be generated by the repetition of tuning and fixing of the structural colours of a M-ink material. When the external magnetic field is applied, the superparamagnetic CNCs form one-dimensional (1D) chains with an interparticle spacing diffracting a specific colour of light, and the inter-particle spacing of the CNCs is varied under the modulation of magnetic field (S1). Spatially patterned UV illumination on a specific area polymerizes the photocurable resin and fixes the arrangements of the CNCs. The cooperative actions of magnetic field modulation and spatially controlled UV exposure enable the multi-colour patterning in a single barcoded microparticle. The minimum size of a code element depends on the size of the CNCs (the width of a single CNC chain, ~160nm) and the resolution of optical lithography system. The chains show inter-chain distance of ~2μm under an external magnetic field (S5), making the minimum size of a code element larger than the resolution of our optical lithography system (~ 1μm). Currently, we routinely generate particles with a code element size of a few micrometers. The time required is typically 100ms for colour tuning and 50ms for fixation, so it takes approximately 1 second (1.2s) to produce barcoded particles with 8 different colour codes. The number of particles we can produce is dependent on the field of view of the lithography system. For instance, when we consider 1.4 cm x 1.0 cm DMD with 1x magnification for making 100 μm x 100 μm particles, we can make 1.4 x 10 4 particles in a single step. Figure S4. Step-wise view of colour barcoded magnetic microparticle generation nature materials 5

6 supplementary information Section S4: Magnetic Properties of Colour Barcoded Magnetic Microparticles Colour barcoded magnetic microparticles consist of multiple chains of superparamagnetic CNCs surrounded by a polymer matrix. Thus, magnetic properties of these two (superparamagnetic CNCs and polymer matrix) affect the overall magnetic properties of the colour barcode magnetic microparticles. Figure S5 shows magnetization (M-H) curves of the superparamagnetic CNCs, ETPTA polymer matrix, and ETPTA-based colour barcoded magnetic microparticles measured with superconducting quantum interference devices (SQUID). First, the superparamagnetic CNCs show superparamagnetic properties as shown in Figure S5-(a), and the measured data can be described and plotted as a Langevin function mh kt L= Ms coth kt mh where M s stands for saturation magnetization, m for magnetic moment, H for applied magnetic field, k for Boltzman constant, and T for temperature (S6). The saturation magnetization and the initial mass susceptibility were obtained from the M-H curves (Table S1). Second, the M-H curve from polymerized ETPTA with 10wt% DMPA photoinitiator has diamagnetic properties with diamagnetic susceptibility of emu/oe g. These two different magnetic properties are responsible for the magnetic characteristics of the microparticles as shown in figure S5-(c) and (d). A modified Langevin function was obtained from linear superposition of previously achieved functions, mh kt L ' = wm s coth + (1 w) χdia H kt mh, where w stands for percent weight of the superparamagnetic CNCs and χ dia for the diamagnetic susceptibility of the ETPTA polymer matrix. Optimal data fitting estimates a percent weight of 0.87%, which is almost the same as the initial composition of materials. The result does not show the constant saturation magnetization in a large magnetic field due to the contribution of diamagnetic materials. Superparamagnetic CNCs Colour barcoded magnetic microparticles Superparamagnetic CNC content (wt%) 0.87 Initial mass susceptibility (emu/oe g) Saturation magnetization (emu/g) (peak value) Table S1. Magnetic properties of superparamagnetic CNCs and colour barcoded magnetic microparticles. All values were obtained from the M-H curves in Figure S5. The saturation magnetization of the colour barcoded magnetic microparticles was selected as a peak value. 6 nature MATERIALS

7 supplementary information Figure S5. Magnetization curves (M-H curves) obtained by SQUID under the magnetic field variation of -30~+30kOe. (a) Superparamagnetic CNCs (b) ETPTA polymer matrix (c) ETPTA-based colour barcoded magnetic microparticles (d) Expanded curves of (c). nature materials 7

8 supplementary information Section S5: Magnetic Rotation of Colour Barcoded Magnetic Microparticles Experimental setup In order to manipulate particles precisely, we have developed a simple system that enables two axis rotation of an external permanent magnet. The system is composed of a permanent magnet, a DC motor to automate Z-axis rotation, power supply and extra components to join all parts (Figure S6). Manually controlled Y axis rotation determines whether the microparticles stick to the microchannel surface for barcode reading and solution exchange or stand upright perpendicular with respect to the flow to enhance reaction kinetics (Figure S7-(a) to Figure S7-(b)). Motorized Z-axis rotation makes the microparticles tumble around the Z-axis thereby increasing the effective reaction area (Figure S7-(c)). Figure S6. Motorized magnet rotation setup implanted on the microscope. (a) Magnet rotation on the Z axis for particle rotation is motorized by a DC motor which is connected to the magnet holder with a flexible tube. (b) Magnet rotation on Y axis for particle flipping is manually controlled using a handle attached to the magnet holder. Figure S7. Magnetic manipulation of microparticles with a magnet rotation setup (a) For barcode reading or solution exchange the microparticles are attached on the upper side of the microchannel or vial horizontally. (b) Flipping of microparticles. Rotation of the magnet on the Y axis changes the direction of the magnetic field line horizontally across the microparticles. (c) Reaction enhancement by rotation. Microparticles are rotated by magnet rotation on the Z axis. 8 nature MATERIALS

9 supplementary information Theoretical model of colour barcoded magnetic microparticle rotation Colour barcoded magnetic microparticles are hexagonal shaped microparticles in which superparamagnetic CNCs are embedded. The superparamagnetic CNCs are arranged into one-dimensional chain-like structures, and the chains are distributed with constant interchain distances under an external magnetic field (S5). These arrangements of superparamagnetic CNCs and their chains are fixed in the microparticles through a photopolymerization process, enabling the magnetic microparticles to rotate and align along the external magnetic field line. To analyze the angular dynamics of the magnetic microparticles with fixed arrangements of superparamagnetic CNCs, the magnetic torque applied to a single chain was calculated first. All the torque exerted on individual CNCs from the magnetic interaction of the CNCs with their near neighbors is summed with the assumption that superparamagnetic CNCs behave as point-like induced magnetic dipoles. We approximate that only the nearest CNCs affect the torque as the dipolar interaction is a function of jk4 r ( = j kd), where j and k are indices of individual CNCs, and d is inter-particle distance. The magnetic torque applied to a single chain is [ n] /2 r θ τ i = ( idf j + rf j j ) j= [ n] /2 3μ 1 1 3μ 1 = id + 4 r r 4 r 2 [ n] /2 [ ]/2 2 j 1 n [ n] /2 [ n] /2 0m 2 0m (1 3cos α) ( ) sin 2 α j [ n] /2 k [ n] /2 4 k j 1 4 r j j [ n] /2 k [ n] /2 4 π = = = + jk jk π = = jk 2 3 [ n] /2 [ n] /2 μ 0m 1 sin 2 α r j [ ]/2 [ ]/2 4 4π j= n k= n jk = r 2 2 3μ 0m sin 2α n, 3 4π d where n is the number of superparamagnetic CNCs in a single chain, D is inter-chain distance, m is the magnetic moment, and α is the angle between the magnetic field and the chain (S7). The total magnetic torque on the microparticle is 2 2 3μ0m n τtotal = Nτi = N sin(2 α) 3 4π d μ0n χ R π 2 = N H sin(2 α ), 3 3d where N is the number of chains inside a single microparticle, n is the number of superparamagnetic CNCs in a single chain, R is the radius of a superparamagnetic CNC and χ is the initial mass susceptibility of superparamagnetic CNCs. Here, the total magnetic torque is simply N times the torque on a single chain since inter-chain interactions are ignored in the microparticles. This result implies that the motion of microparticles is easily controlled by changing the structural geometry or inter-particle distance in the chain structures. The maximum total magnetic torque is obtained as 4 μ 0n χ R π when α is N 3d 3 H nature materials 9

10 supplementary information To obtain an approximated maximum magnetic torque, the inter-particle distance and the inter-chain distance are assumed as 60nm and 2μm, respectively (S5). We also considered a thin disk with a length 30μm and a diameter 250μm. In this condition, the maximum total magnetic torque is 1.34nNm when the external magnetic field is 500Oe. Figure S8. A schematic diagram of chain rotation embedded inside a magnetic microparticle. Section S6: Supplementary Movies Movie S1: Free-floating colour barcoded magnetic microparticles This movie shows free floating colour barcoded magnetic microparticles in a PDMS microfluidic channel. Since an oxygen inhibition layer near PDMS walls inhibits the photopolymerization, free-floating microparticles are generated. Movie S2: Flipping motion of the colour barcoded magnetic microparticles This movie shows repetitive flipping of the colour barcoded magnetic microparticles. Colour barcodes in the microparticles are clearly shown when the microparticles lie on the surface of the vial. The particles can be stood upright perpendicular to the surface of the vial for further magnetic modulation such as rotation. Movie S3: Rotation of the colour barcoded magnetic microparticles This movie demonstrates a rotational motion of the colour barcoded magnetic microparticles. A motorized magnet rotation system enables microparticles to rotate with controlled angular frequency. All the microparticles rotate under magnetic field modulation except for one microparticle, which was intentionally made to have randomly distributed superparamagnetic CNCs in order to show that chain formation of superparamagnetic CNCs is a critical factor for rotational motion. 10 nature MATERIALS

11 supplementary information References S1. Kim, H., Ge, J., Kim, J., Choi, S. E., Lee, H., Lee, H., Park, W., Yin, Y., Kwon, S., Structural colour printing using a magnetically tunable and lithographically fixable photonic crystal. Nature Photonics 3, (2009). S2. Ge, J., Yin, Y., Magnetically tunable colloidal photonic structures in alkanol solutions. Adv. Mater. 20, (2008). S3. Pregibon, D. C., Toner, M., Doyle, P. S., Multifunctional encoded particles for highthroughput biomolecule analysis. Science 315, (2007). S4. Chung, S. E., Park, W., Park, H., Yu, K., Park, N., Kwon, S., Optofluidic maskless lithography system for real-time synthesis of photopolymerized microstructures in microfluidic channels. Appl. Phys. Lett. 91, (2007). S5. Ge, J., Hu, Y., Zhang, T., Huynh, T., Yin, Y., Self-assembly and field-responsive optical diffractions of superparamagnetic colloids. Langmuir 24, (2008). S6. Rosensweig, R. E. Ferrohydrodynamics, (Cambridge Univ. Press, New York, 1985). S7. Melle, S., Fuller, G. G., Rubio, M. A., Structure and dynamics of magnetorheological fluids in rotating magnetic fields. Phys. Rev. E 61, (2000). nature materials 11