K. K.
Sriram†
a,
Simantini
Nayak‡†
b,
Stefanie
Pengel†
b,
Chia-Fu
Chou
*acd and
Andreas
Erbe
*be
aInstitute of Physics, Academia Sinica, Taiwan. E-mail: cfchou@phys.sinica.edu.tw
bMax-Planck-Institut für Eisenforschung GmbH, Max-Planck Str. 1, 40237 Düsseldorf, Germany. E-mail: a.erbe@mpie.de
cResearch Centre for Applied Sciences, Academia Sinica, Taiwan
dGenomics Research Centre, Academia Sinica, 128, Sec.2 Academia Road, Taipei, Taiwan 11529
eDepartment of Materials Science and Engineering, NTNU, Norwegian University of Science and Technology, 7491 Trondheim, Norway
First published on 14th November 2016
The fabrication of sub-nanoliter fluidic channels is demonstrated, with merely 10 nm depth on germanium, using conventional semiconductor device fabrication methods and a polymer assisted room-temperature sealing method. As a first application, an ultralow volume (650 pL) was studied by ATR-IR spectroscopy. A detection limit of ∼7.9 × 1010 molecules of human serum albumin (HSA) (∼0.2 mM) in D2O was achieved with highly specific ATR-IR spectroscopy.
Attenuated total reflection (ATR) IR spectroscopy is a variant of IR spectroscopy, in which the absorption of an evanescent IR wave, generated at a high refractive-index medium's interface with a low refractive index liquid, solid or gaseous sample medium may be quantitatively analysed. The high refractive index internal reflection element (IRE) needs to be transparent in the IR range, and chemically resistant to the sample environment. Popular IRE materials are semiconductors with a low or medium band gap, such as Si, Ge, ZnSe or ZnS.4 An evanescent wave, with a penetration depth dp, is generated at the IRE/sample medium interface at an angle of incidence above the critical angle θc of the total internal reflection. One crucial advantage when using ATR as a sampling technique in routine analysis is the possibility to use multiple reflections to enhance the sensitivity,3 wherein such an approach enables, e.g., the detection of reaction intermediates.5,6 As dp is typically a few hundred nanometres, the sample needs to be in close contact with the IRE. Along with the advantage of reduction in sample volume, these factors have led to the development of combining ATR-IR spectroscopy with micro- and nanofluidics to study molecular systems.7 Initial efforts using ATR-IR coupled microfluidic devices showed that these devices can be used to study chemical reaction kinetics8 and microfluidic flows,9 with the latest reports on the adsorption of polymers in flow.10 The demonstration of a portable microsystem with an integrated waveguide for IR spectroscopy of quantitative chemical detection in human saliva opens up the possibility of using these devices for point-of-care analysis.11 A recent study also showed the possibility of combining ATR-IR spectroscopy and microfluidics to image the release of pharmaceutical ingredients, aiming towards high-throughput analysis of drug delivery.12 There is a recent tendency to shrink the channel size down to the nanoscale, as nanochannels have a much larger surface-to-volume ratio than microchannels, thus all molecules can be confined closely to volumes near the surface where the probing evanescent waves are the strongest. Examples are the use of ATR-IR coupled nanochannel devices to understand the behaviour of fluidic field effect transistors13 and to study the native pH shift analogous to fluorescence spectroscopy.14 In these previous cases, the minimum depth of the ATR-IR detection devices was 400 nm,13,14i.e. the depth was larger than dp, which gives rise to higher background and the devices were manufactured in silicon with typically a limited transmission in the IR fingerprint region.15 A review from Karabudak neatly summarizes earlier studies involving silicon micro- and nanofluidic devices for ATR-IR spectroscopy, discussing potential applications, advantages and drawbacks of the method.16
Germanium (Ge) is a semiconductor material suitable for the fabrication of micro- and nanofluidic devices and has the highest refractive index (n = 4) among commonly used IREs. Various groups demonstrated the use of chemically modified Ge to effectively immobilize proteins on substrate surfaces, for ATR-FTIR studies.17 Notable studies are on the use of different organic molecules grafted onto the substrate surface18,19 or through silanization.20 In some cases, the surface modification seems to minimize the sensitivity of the device.21 In this work, we demonstrate the fabrication of a Ge nanofluidic device, integrated with multi-reflection ATR-IR spectroscopy for molecular analysis (Fig. 1). The advantage of Ge optical elements is exploited in combination with a polysilsesquioxane (PSQ) assisted room temperature bonding process.22,23 The successful fabrication is shown for a 10 nm deep Ge nanofluidic channel. The nano-confinement helps to keep the protein molecules very close to the surface, thus eliminating the need for chemical modification. The ATR-IR spectrum of human serum albumin (HSA) in D2O is obtained as a first application of the device using sub-nanoliters of the sample solution.
First, ATR-IR optical elements were obtained by dicing 0.5 mm thick 4-inch Ge (100) wafers (University Wafer, Boston) to a size of 52(L) × 20(W) mm2. Diced substrates were polished to an angle of 30° along the short edges on both sides of the Ge substrates, to facilitate 60° angle of incidence. After polishing, substrates were immersed in 2% Extran neutral solution (VWR, Germany) for 1 h, followed by iso-propanol immersion for 1 h to remove all impurities from polishing, rinsed thoroughly with ultrapure deionized water and blow dried with N2. Before the fabrication process, substrates were further cleaned using acetone and iso-propanol by ultra-sonication for 2 minutes, rinsed using ultrapure deionized water and dried with N2 to ensure a clean surface. A photoresist (S1813, Shipley Inc.) was spin-coated on Ge substrates at 4000 rpm for 25 s and baked at 90 °C for 1.5 min. Fluidic channel patterns were transferred from a chromium photomask to the photoresist using a one-step photolithography (EVG620 mask aligner) process. After UV exposure (8.5 s at 10 mW cm−2), the photoresist was developed using MF 319 (Shipley Inc.) for 35 s. Photoresist patterns were transferred to a Ge substrate using reactive ion etching (RIE Plasmalab 80+, Oxford Instruments). An initial de-scum process using 100 sccm O2, 300 mTorr pressure and 150 W RF power for 2 min to remove any residual photoresist in the region of interest was followed by etching using 10 sccm CHF3, 3 mTorr pressure and 100 W power for 1 min. Surface profiler measurements (Alpha step IQ, KLA Tencor) and atomic force microscopy (AFM Nanoscope III, Veeco) measurements confirmed that the depths were around 10 nm with the average surface roughness in etched and un-etched regions less than 0.5 nm (Fig. 2).
Through holes (1 mm diameter) were drilled using a sand-blaster on glass coverslides (no. 1, gold seal, 25 × 25 mm) to form the inlet/outlet of the loading reservoirs. Then the coverslides were cleaned with a piranha solution (98% H2SO4 and 30% H2O2 in 1:1 ratio) for 15 min, rinsed thoroughly in deionized water and dried in a N2 stream. Cleaned glass coverslides were then dehydration baked at 200 °C for 3 min before spin-coating PSQ on the coverslide at 3000 rpm for 30 s. PSQ was freshly prepared before coating by mixing 2 parts of xylene and 1 part of Hardsil (AP grade, Gelest Inc.) and filtered using a 0.45 μm PTFE membrane (Basic Life Inc.). Coverslides with spun-on PSQ were then baked at 240 °C for 30 min.
Hydrogen peroxide (H2O2) etches Ge vigorously and thus cannot be used to clean the substrates.24,25 Alternatively, UV-ozone cleaning was used for 15 min to render the Ge surface clean and hydrophilic, important for good bonding and effective filling of channels. Cleaned Ge substrates and PSQ coated coverslides were exposed to O2 plasma (17 sccm O2, 50 W RF power, 0.18 mbar, 1 min) in a RIE chamber. The plasma treated PSQ surface was brought into contact and aligned to overlap loading holes with fluidic patterns on the Ge substrate, then pressed gently with tweezers to enable effective bonding. Silanol (Si–OH) groups on PSQ react with germanol (Ge–OH) groups on the Ge substrates, forming Si–O–Ge bonds through a condensation reaction.26 The presence of an –OH surface termination on Ge was previously confirmed by angle resolved X-ray photoelectron spectroscopy (ARXPS).27 Finally, silica reservoirs were bonded over the loading-hole regions using a UV-curable glue (no. 108, Norland optical adhesives). With this step, fabrication was complete and devices were ready for experiments (Fig. 3a).
Fig. 3 (a) PSQ-bonded serpentine nanochannel device. (b) Optical micrograph showing the filling of channels by means of capillary flow. White arrow indicates the flow direction. |
ATR-IR spectra of HSA protein in D2O were recorded with a FTS 3000 Fourier Transform IR spectrometer (Bio-Rad, Palo Alto, CA) using a liquid N2 cooled mercury cadmium telluride (MCT) detector. The spectrometer was purged with N2 before and during experiments in order to minimize the content of atmospheric water vapour. For multiple reflection ATR-IR measurements, a horizontal ATR mirror unit (Spectra Tech 0001-100, Stamford, CT) was used. The built-in crystal plate of the ATR mirror unit was replaced by a PTFE plate, on which the Ge substrate with nanochannels was placed during IR measurements. Details on the experimental setup have been described before.4,5 250 scans were co-added for each IR spectrum with a spectral resolution of 4 cm−1. IR spectra were recorded in both s- and p-polarizations. In this work, each IR spectrum is displayed as absorbance, defined as A = −log10(Isam/Iref), where Isam and Iref are the IR light intensity of sample and background measurements, respectively, with the latter carried out at the Ge–air interface before nanochannels were filled with any solution. For comparison, the spectra of D2O were recorded by placing a drop (20 μL) of D2O on a plain Ge IRE without nanochannels.
Absorptions between 1500–1600 cm−1 correspond to the amide II bands of the proteins and peptides in H2O.29 Upon deuteration, the amide II mode shifts from ∼1550 cm−1 to 1450–1490 cm−1.29 In the ATR-IR spectrum of HSA in D2O, bands are visible both at 1450 cm−1 and 1560 cm−1. The peak centred around 1560 cm−1 that contains at least three main contributions at 1538 cm−1, 1552 cm−1 and 1571 cm−1 closely resembles the amide II mode of a polypeptide chain with incomplete H/D exchange. The weak association mode of D2O, which is centred around 1555 cm−1,31 contributes only in negligible amounts to the observed absorption, as is shown by the small contribution (compared to the O–D stretching mode) in the D2O spectrum. Amino acid side chains, which may contribute to the spectrum in this region, are aspartic acid and glutamic acid, with their respective COO− stretching modes at 1584 cm−1 and 1565 cm−1.29 HSA contains 6.7% aspartic acid and 10.3% glutamic acid,29 likely to have some contribution to the peaks at ∼1560 cm−1. The other possible contribution to this peak is from the incomplete H/D exchange in the protein.
In order to test the sensitivity of our device, we performed a second experiment with one order of magnitude lower HSA concentration in D2O, 30 g L−1 (0.45 mM). Although the absorbance peaks are not as prominent as in the 300 g L−1 experiment, the amide I and II peaks can still be clearly distinguished. A small peak is also observed in the D2O spectrum without HSA around 1450 cm−1, which is assigned to the H–O–D bending vibration. Hence the absorption at 1450 cm−1 can be assigned to a superposition of the H–O–D bending mode with the amide II mode of HSA in D2O.17,18 In comparison with the amide I peak height, the amide II peak is not so prominent for 30 g L−1, but it is clear from the experiment with higher HSA concentration that the peak at 1450 cm−1 is indeed a mixture of H–O–D and amide II components.
The presence of an amide II mode of the H-form of a protein in D2O solution may stem from two different causes. If the peptide chain contains hydrophobic portions that are inaccessible to water, residual H remains on the chains. For HSA, however, 1 h after sample preparation, almost complete H exchange was reported previously.26 In contrast, kinetic exchange experiments at 25 °C show still a considerable fraction of H-form amide II after >4 h of HSA exposure to D2O. In the spectra observed here for 300 g L−1 and 30 g L−1 HSA in D2O too, residual OH stretching modes are observed around 3400 cm−1, indicating that indeed H is still present as a minor (20% fraction for 300 g L−1 and 3% for 30 g L−1 from estimating peak areas), but detectable, fraction. In the total system, there are about 5% H compared to D (one order smaller for the 30 g L−1 case), so residual contributions of OH or non-exchanged amide are to be expected. The small bulge observed at 1644 cm−1 can be assigned to amide I vibrations in random coil conformation, but in the case of the incomplete H–D exchange, the 1644 cm−1 peak could most likely be from H–O–H bending. In both D2O and HSA in D2O solutions, 2 more bands are observed. The band at 2488 cm−1 is assigned to the O–D stretching mode of the D2O solvent and the one at 1224 cm−1 to a D–O–D bending mode.29 Hence our results indicate the presence of globular HSA proteins under partially deuterated conditions.
The peak absorbance of the amide I mode increases linearly with the protein concentration. Because the peak positions of deuterated and non-deuterated forms are similar, the area in the amide I mode can still be used for concentration determination. The slope of the line of best fit provides the sensitivity of our device as 6.7 × 10−4 g L−1, i.e. 0.1 mM (6.1 × 1015 molecules per L, Fig. 4c). Furthermore, the limit of detection of our device could be obtained from the plot, by analyzing the signal corresponding to three times the signal of the blank measurement. With an intercept error of 3 × 10−3, this will be an absorbance of 9 × 10−3, which corresponds to a concentration of 13.4 g L−1 (corresponding to 7.9 × 1010 molecules in the device, with a HSA molecular weight of 66478 g mol−1). This corresponds to a detection limit of 0.2 mM.
Footnotes |
† Joint first authors. |
‡ Present address: Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QR, UK. |
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