Alexander James
Wright‡
ab,
Hashem Hassan
Nasralla‡
a,
Rahul
Deshmukh
ab,
Moeid
Jamalzadeh
b,
Matthew
Hannigan
c,
Andrew
Patera
de,
Yanxiao
Li
a,
Miguel
Manzo-Perez
b,
Nitika
Parashar
a,
Zhujun
Huang
b,
Thanuka
Udumulla
e,
Weiqiang
Chen
f,
Davide
De Forni
g,
Marcus
Weck
c,
Giuseppe Maria
de Peppo
e,
Elisa
Riedo
*a and
Davood
Shahrjerdi
*b
aDepartment of Chemical and Biomolecular Engineering, Tandon School of Engineering, New York University, Brooklyn, NY 11201, USA. E-mail: elisa.riedo@nyu.edu
bDepartment of Electrical and Computer Engineering, Tandon School of Engineering, New York University, Brooklyn, NY 11201, USA. E-mail: davood@nyu.edu
cDepartment of Chemistry, New York University, New York, NY 10003, USA
dDepartment of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY 11203, USA
eMirimus, Inc, 760 Parkside Ave, Brooklyn, NY 11226, USA
fDepartment of Biomedical Engineering, Tandon School of Engineering, New York University, Brooklyn, NY 11201, USA
gViroStatics S.r.l., Viale Umberto I, 46, 07100 Sassari, Italy
First published on 24th September 2024
The rise in antibiotic-resistant pathogens, highly infectious viruses, and chronic diseases has prompted the search for rapid and versatile medical tests that can be performed by the patient. Field-effect transistor (FET)-based electronic biosensing platforms are particularly attractive due to their sensitivity, fast turn-around time, potential for parallel detection of multiple pathogens, and compatibility with semiconductor manufacturing. However, an unmet critical need is a scalable, site-selective multiplexed biofunctionalization method with nanoscale precision for immobilizing different types of pathogen-specific bioreceptors on individual FETs, preventing parallel detection of multiple targets. Here, we propose a paradigm shift in FET biofunctionalization using thermal scanning probe lithography (tSPL) with a thermochemically sensitive polymer. This polymer can be spin-coated on fully-fabricated FET chips, making this approach applicable to any FET sensor material and technology. Crucially, we demonstrate the spatially selective multiplexed functionalization capability of this method by immobilizing different types of bioreceptors at prescribed locations on a chip with sub-20 nm resolution, paving the way for massively parallel FET detection of multiple pathogens. Antibody- and aptamer-modified graphene FET sensors are then realized, achieving ultra-sensitive detection of a minimum measured concentrations of 3 aM of SARS-CoV-2 spike proteins and 10 human SARS-CoV-2 infectious live virus particles per ml, and selectivity against human influenza A (H1N1) live virus.
Furthermore, the detection limits of FET-based sensors have been pushed to ultralow concentrations (i.e., femto-molar or less) by adapting nanoscale materials such as nanowires,6,7 In2O3,8 and graphene.9–11 The progress in this direction promises new applications for FET-based sensor technologies in drug discovery12,13 and clinical diagnostics.14–17
Despite continuous progress, the application of FET-based sensors for highly parallel detection of multiple distinct pathogens or biomarkers remains elusive. At present, functionalization of FET biosensors commonly involves the drop casting method without any or limited spatial selectivity, which must be specialized for a given FET material. Therefore an unmet critical need is a FET material independent and scalable surface chemistry fabrication strategy that can allow modification of each FET on a chip on-demand with distinct pathogen/biomarker-specific bioreceptors, such as antibodies18–20 and aptamers.8,21,22 Overcoming this challenge will enable portable and wearable rapid diagnostic tests with unprecedented capabilities.
Several key limitations of existing surface functionalization strategies present barriers to realizing a highly parallel multiplexed FET sensor chip. A primary limitation is the lack of a scalable spatially selective methodology that provides nanoscale precision. Indeed, significant research is ongoing to implement multiplexed FET biosensors, highlighting the need for site-selective functionalization. Recent examples include electrografting-enabled site-selective functionalization of graphene FETs,23 application of bioactive hydrogel as local gates on graphene FETs,24 and implementation of physical macroscopic barriers for separating FETs8,10,25,26 (see ESI Table 1† for a review). Despite progress on site-selective functionalization, no methodology yet offers scalable biochemical multiplexing for biosensing (i.e., several different bioreceptors on different FETs) and nanoscale precision in modifying the surface chemistry of the FET sensors. Modern semiconductor manufacturing can integrate billions of sub-100 nm size FETs into functional microchip products. Therefore, a paradigm shift in biofunctionalization that enables scalable site-selective multiplexed chemical modifications with nanoscale precision has the potential to transform modern chips into advanced sensing platforms by configuring each individual nanoscale FET into a distinct pathogen/biomarker-specific biosensor.
Surface functionalization with nanoscale precision capability could significantly enhance the robustness, reproducibility, and uniformity of the functionalization outcome across an array of FETs as well as among different chips. Existing functionalization methodologies are largely vulnerable to microscopic and nanoscopic surface non-idealities such as contaminations and variations in defect species of the surface.
Another limitation of existing functionalization approaches pertains to the development of surface chemistry processes that are FET-material independent. For instance, attaching a given antibody or aptamer to a graphene film will involve different processing steps compared to an oxide film. Functionalizing graphene requires, for example, creating either ester or vinyl sulfone groups on the surface,27 which react with the primary amine groups of the receptor-antibodies. On the other hand, a different approach is needed for functionalizing In2O3 FETs sensors with aptamers, involving the covalent modification of In2O3 with dopamine or serotonin aptamers using silane chemistry.8 Therefore, as FET sensor technologies evolve, for example to achieve higher sensitivity or improved manufacturability, their adaptation into a biosensing platform may require development of new surface chemistry processes. Therefore, a FET material independent chemical modification process facilitates the adaptation of different FET technologies.
To address the above-mentioned limitations, here, we introduce a scalable, FET material independent functionalization strategy that permit local bioreceptor functionalization of individual FETs on the same chip with nanoscale spatial precision. Our strategy involves the use of thermal scanning probe lithography (tSPL) with a thermochemically sensitive polymer. This tSPL method is capable of chemically patterning a polymer-coated chip surface at prescribed locations, enabling multiplexed functionalization of different bioreceptors from antibodies to aptamers, at sub-20 nm resolution and 200 nm pitch, a distance comparable to the pitch of modern FETs array in CMOS chips. In a typical FET biosensor, the trapping of a target analyte by a specific bioreceptor results in the change of electronic charge at the channel region, generating a measurable electronic signal. We show that the capture of the target analytes at the surface of the polymer-coated FET sensors in our experiments equally gives rise to detectable electronic signals due to the effective capacitive behavior of the polymer film. Furthermore, patterning individual FETs allows for in situ differential sensing, a key ingredient to ensure signal fidelity. The feasibility of this platform is established through the detection of a single pathogen type using both antibody- and aptamer-modified FET sensors. Specifically, the tSPL-functionalized FET sensors achieve an ultra-sensitive detection of a minimum measured concentration of 3 aM of SARS-CoV-2 spike proteins and 10 human SARS-CoV-2 infectious virus particles per ml, and selectivity against human influenza A (H1N1) live virus.
All solvents are acquired from Sigma-Aldritch, unless stated otherwise. The (+)-biotin N-hydroxysuccinimide (NHS) ester, DyLight™-conjugated esters, streptavidin are acquired from ThermoFisher Scientific. Biotinylated Anti-SARS-CoV-2 Spike RBD Neutralizing Antibody (S1N-VM226), as well as SARS-CoV-2 spike proteins for detection are purchased from ACRO Biosystems. Aptamers are synthesized per order from Integrated DNA Technologies (IDT) using the following sequences from previous studies:38,39 Anti-SARS-CoV-2 Aptamer-6C3 5′-CGCAGCAC CCAAGAAC AAGGACTG CTTAGGAT TGCGATAG GTTCGG-3′ (see Fig. S6†).38 Anti-hemagglutinin (HA) aptamer-RHA-0006 (Integrated DNA Technologies, 5′-GGGTTTGG GTTGGGTT GGGTTTTT GGGTTTGG GTTGGGTT GGGAAAAA-3′, see Fig. S7†).39 Aptamers are modified with biotin on the 5′ end and tagged with TYE™ 665 (Aptamer-6C3) or 6-carboxyfluorescein (Aptamer-RHA-0006) fluorescent dye on the 3′ end, formulated by Integrated DNA Technologies, Inc.8,9 and purified using high performance liquid chromatography (HPLC).38 See ESI Note 4† for further details on the functionalization, incubation process and aptamers.
Similarly, a high titer (>10 × 106 TCID50 per mL) viral suspension of H1N1 (A/PR/8/34) was produced from infected cultured of MDCK (Madin-Darby canine kidney). DMEM 2% FBS was used to store the virus at −80 °C. Live virus suspensions for the gFETs experiments are prepared using a buffer containing 1 mM HEPES and 0.6 mM NaCl.
The implementation of the NanoBioFET platform begins by fabricating a FET array. As shown in Fig. 1b, we adopt monolayer graphene for realizing the FET-based sensors (see Experimental methods), due to its potential for ultrahigh sensitivity.41,42 We then cover the fully fabricated graphene FETs (gFETs) by spin coating two thermally sensitive polymer resist films (see Experimental methods). The stack comprises a first film of about 70 nm-thick polymethacrylate–carbamate–cinnamate copolymer (PMCC),31–33 which provides amine groups on demand in designated FET regions upon local heating by tSPL. PMCC can be locally patterned through local heat-induced deprotection of amine groups from tetrahydropyranyl carbamates in the carbamate block of PMCC30–34 (see Experimental methods). The second film is poly(phthalaldehyde) (PPA)36,43 which serves as a top layer resist (10–20 nm thick) to reduce non-specific binding outside the FET channel region (see ESI Note 1†).
After forming the bilayer polymer resist stack, we proceed with the localized functionalization of individual FETs with desired bioreceptors. Employing tSPL, we modify the bilayer polymer resist stack atop the channel region of each target gFET with amine groups. This process utilizes a hot nano-tip in a commercial tSPL system (see Experimental methods), which removes PPA completely above the channel region, while simultaneously applying heat to the PMCC polymer surface above the amine deprotection temperature (∼120 °C), exposing amine groups in the desired area (Fig. 1b). For differential sensing, we pattern only the FET used as a sensor, while leaving the un-patterned FET as a control device. Ensuring signal fidelity is a key challenge for commercialization of FET-based biosensors. Hence, providing a platform that allows for in situ differential sensing is a key milestone. Using standard conjugation strategies, the amine groups in the channel region can subsequentially be functionalized with ad-hoc bioreceptors such as antibodies or aptamers (see Experimental methods for details). At this point, the sensor/control FETs are ready for biodetection of a specific target, such as SARS-CoV-2 virus. As discussed later, when the FET sensor is exposed to a specific target, the target is immobilized by the bioreceptor near the polymer surface, giving rise to a change in the electronic signal of FET-based sensors.
In Fig. 1c, we demonstrate the resolution of the NanoBioFET fabrication method. Specifically, Fig. 1c shows an in situ tSPL topographical image (see Experimental methods) of an amine pattern produced by tSPL in a PPA/PMCC bilayer polymer resist stack deposited on a blank SiO2/Si substrate (i.e., without gFETs). The pattern consists of a 10 × 10 matrix of 15 nm-diameter amine circles with 40 nm pitch, comparable to that of an advanced-node silicon FET technology. Importantly, this image is taken in situ during the tSPL patterning process, since thermal probes can also allow local nanoscale imaging (Experimental methods). This feature enables localization of target regions on a chip with nanoscale precision without requiring sophisticated and costly pattern alignment procedures.
To demonstrate the ability of the NanoBioFET fabrication method to pattern relevant biomarkers with high reproducibility and precision, Fig. 1d and e present two fluorescence optical microscopy images of one-hundred squares (with 5 μm and 500 nm sides, respectively) of biotinylated anti-SARS-CoV-2 aptamers, which have been fluorescently tagged with a red dye (see Experimental methods for details on the aptamers used here). These aptamer patterns have been produced first by exposing amine groups by tSPL on the surface of the PPA/PMCC polymer resist, and then by conjugating the amine groups to NHS–biotin, followed by streptavidin, and biotinylated aptamers (the details of the chemical functionalization steps are reported in the Experimental methods). Note that the PPA/PMCC double polymer stack in these experiments is spin-coated on a on a blank SiO2/Si substrate (i.e., without gFETs).
In Fig. 1f and g, we show how the NanoBioFET fabrication process is implemented on a gFET array chip. For this purpose, we fabricate an array of four gFETs with a channel length of 1 μm, where each sensor FET is adjacent to a control FET. The PPA and PMCC resists are then spin-coated on the gFETs, and tSPL is used to remove PPA and pattern amine groups in the channel region of the two gFET sensors, leaving the FET controls un-patterned. In Fig. 1f and g we show, respectively, an in situ tSPL topographical image, and an ex situ friction atomic force microscopy (AFM) image of the resulting gFET sensors and controls after tSPL patterning. The graphene region underneath the polymer is indicated with a dashed red rectangle. In Fig. 1f, the tSPL topography image shows that the patterns above the channel region of the gFET sensors are at a depth of approximately 10 nm, corresponding to the thickness of the PPA film, which is sublimated during tSPL patterning. It is important to note that since tSPL allows in situ imaging of the FET underneath the dual polymer stack, we are able to locate the channel region of each FET and pattern where required without the need of markers. The AFM friction image in Fig. 1g is particularly revealing since it shows clear friction contrast in the sensor area due to the change in hydrophilicity upon the thermal deprotection of the amine moiety. This agrees with a more hydrophilic surface where the amine groups have been exposed, and the consequent presence of larger friction forces at the nanoscale due to larger capillary forces.40,44
In Fig. 2b we present a fluorescence optical microscopy image of biochemical patterns generated by four sequential rounds of the site-selective functionalization process as depicted in Fig. 2a. In particular, Fig. 2b shows the fluorescence of four types of NHS-esters terminated dyes (red, yellow, green and sky-blue) attached directly to the amine moieties exposed during the tSPL process on the surface of the PPA/PMCC polymer resist deposited on a blank SiO2/Si substrate (i.e., without gFETs). Fig. 2c shows the implementation of the multiplexed chemical patterning in an array of gFETs. Specifically, the channel regions of four representative gFETs have been functionalized with four different types of NHS-esters terminated dyes (red, yellow, green, and sky-blue) attached directly to the amine moieties exposed by tSPL on the surface of a PPA/PMCC polymer resist spin-coated on a gFET chip.
Fig. 2d and e demonstrate the capability of this fabrication method to produce independent patterns of different types of bioreceptors (here aptamers) sensitive to different types of target molecules, e.g., different viruses. In particular, here we show a fluorescence image of patterns of two types of fluorescently labelled aptamers, influenza A anti-hemagglutinin (HA) aptamer tagged with a green fluorophore, and anti-SARS-CoV-2 aptamer (tagged with a red fluorophore). The patterns are created by exposing amine groups by tSPL, and subsequently by attaching NHS–ester biotin to the amine patterns. Biotin patterns are then exposed to streptavidin, and finally to the biotinylated HA aptamer (green). A second identical round of site-selective functionalization is performed to attach the biotinylated CoV-2 aptamer (red) to the desired area on the surface. The details are reported in the Experimental methods.
Fig. 2e and f demonstrate the high spatial resolution with which patterns/bits of different bioreceptors can be fabricated, demonstrating the potential of this approach for site-selective functionalization of nanoscale FETs. In particular, following the same process as in Fig. 2d and e, we produce patterns of two types of aptamers (HA and CoV-2 aptamers) on a blank SiO2/Si substrate. The fluorescence image in Fig. 2e shows green-aptamer and red-aptamer patterns with a “bit” dimension of 500 nm. Because of the limited resolution offered by optical microscopy, we also fabricate two-aptamer circle/dash patterns with a 20 nm width and a minimum 200 nm pitch, i.e., minimum distance between circle (HA aptamer) and dash (CoV-2 aptamer) pattern centers. We then image them in situ by tSPL imaging (Fig. 2f). We perform three measurements on the PPA/PMCC surface. First, we image pattern type-circle after a first round of tSPL. Second, we functionalize pattern type-circle with NHS–biotin/streptavidin/HA aptamer and image the pattern region after a second round of tSPL to produce pattern type-dash. Third, we image the polymer surface after functionalization of pattern type-dash with NHS–biotin/streptavidin/CoV-2 aptamer. The cross-sections show the high registry and robustness of the fabrication process and the change in depth of the patterns after functionalization due to the filling of each pattern with the NHS–biotin/streptavidin/aptamer molecules (approximately 10–15 nm). The two types of patterns have been produced with different shapes to add clarity to the image and show that tSPL can also produce patterns at different depths and shape. See also ESI Fig. S9.† We remark that the same platform can be adapted to be used with different chemical bioconjugation strategies to link the biomarkers on the surface, such as click-chemistry conjugation.
Fig. 3a shows the schematic illustration of an antibody-modified gFET, where the graphene channel is separated from the bioreceptor by the PMMC polymer (the blue rectangle). The sensor is solution-gated, where a fixed bias gate voltage (Vgs) is applied to the solution (300 mV in our experiments) using an external Ag/AgCl reference electrode. A small bias voltage (Vds = 50 mV) is simultaneously applied between the source and drain electrodes, generating a current flow (Ids) in the gFET, which is monitored in real time.
Fig. 3 Spike protein–antibody capture on the NanoBioFET platform. (a) Schematic of a gFET functionalized with SARS-CoV-2 antibody using the NanoBioFET platform. The device structure, electrical measurement setup and Debye length at 1 mM HEPES buffer are indicated. (b) Simplified capacitor circuit model of the sensing platform for detection of a charge ΔQ, demonstrating capacitive coupling through the polymer (with capacitance Cpol). Double-layer capacitance (CDL) and quantum capacitance (Cq) are shown. (c) SPR measurement at 1 mM HEPES buffer, demonstrating successful interaction between the antibody and spike protein. (d) Transfer characteristics of the gFET device. The p-branch and n-branch are indicated. The current and voltage range used in the transient measurement in panel d is indicated by the dashed box. (e) Calibrated transient response of the antibody-modified gFET in 1 mM HEPES. Black circle and red diamond symbols denote, respectively, injections of buffer and spike protein of increasing concentrations. The measurement is split across two panels with different vertical scales. Dashed lines are a guide-to-the-eye of the measured signal. (f) Sensitivity plot of the gFET, obtained from a Hill fit to the calibrated sensor response data at different spike protein concentrations. The gray rectangle represents the limit of detection based on noise analysis (see ESI†). |
Fig. 3b illustrates the simplified capacitor circuit model of the bioreceptor-modified gFET in our experiment. The conjugation of target analytes (e.g., spike protein or virus) with bioreceptors results in the change of charge (denoted as ΔQ in Fig. 3b) on the surface of the polymer. As shown in this circuit model, the PMCC capacitance (Cpol) allows the compensation of charged carriers in the graphene channel due to ΔQ, thereby resulting in a measurable change in Ids (i.e., ΔIds) due to the biochemical reaction. This recorded Ids signal can be used to quantify the concentration of target analytes through creation of a sensitivity calibration curve, as we explain later. We note that the PMCC polymer in the hydrated state (i.e., exposed to the buffer solution) provides a high capacitance (μF cm−2 range, see ESI Fig. S12†), which is consistent with the previous reports on the significant increase in the relative permittivity of other polymers in hydrated states.45
A key experimental challenge in FET-based biosensing is the electronic screening of charges with increasing distance from the surface, characterized by the Debye length λDebye, with multiple mitigation strategies proposed in the literature.8,46–49 A common approach for overcoming this limitation is to adjust the ionic strength of the buffer environment,46,50 thereby increasing λDebye. In the experiments below, we adopt a similar strategy, modifying the buffer solution and its ionic strength based on the choice of the bioreceptor (i.e., antibody or aptamer).
We select biotinylated anti-SARS-CoV-2 spike RBD neutralizing antibody (see Experimental methods) for these electronic sensing experiments. The feasibility of its binding affinity to SARS CoV-2 spike protein at 1 mM HEPES buffer, which provides λDebye = 10 nm, is validated by surface plasmon resonance (SPR) measurements (Fig. 3c). In these SPR experiments, the concentration of spike proteins is limited to a low nanomolar range, which is the typical sensitivity of this type of measurements.51,52 Although the SPR traces for the spike protein against the antibody probe confirm affinity, they also indicate a lower response compared to typical buffers with physiological salinity levels (e.g., 1× PBS). Furthermore, the SPR data indicate a deviation from the ideal curve shape expected for the interactions, which we attribute to the low ionic strength of the buffer used. Therefore, we use the SPR data only as qualitative indication of the viability of the affinity at 1 mM HEPES. However, detailed kinetic analysis may not be reliable because the very low ionic strength causes some artifacts producing poor curve fitting to the kinetic data (see ESI Fig. S13†).
We then proceed to perform the electronic sensing measurements. In all sensing experiments, the bioreceptor-modified gFETs are placed in a microfluidic chamber (see Experimental methods). We then perform an initial screening of a gFET sensor quality by measuring its transfer characteristics (Idsvs. Vgs) using a buffer solution gate. In Fig. 3d, we show the typical transfer characteristics of an antibody-modified gFET, obtained by sweeping the solution gate voltage, Vgs, and recording Ids at a fixed Vds of 50 mV. Vgs modulates the gFET charge carrier concentration and carrier type, from holes in the p-branch, to electrons in the n-branch, passing through the charge neutrality point (at VCNP). For simplicity the data are centered around VCNP. When an analyte is captured by the bioreceptor in the channel region, the local change in charge produces a shift of the Idsvs. Vgs characteristics and therefore a change in Ids is measured at fixed Vg.
We next monitor the real-time electronic response of a SARS-CoV-2 antibody-modified gFET sensor to different concentrations of spike protein. The experiment involves recording Ids continuously in time at a fixed Vgs of 300 mV while injecting analytes at different times into the microfluidic chamber. The objective of this experiment is to quantify the sensitivity of this antibody-modified gFET and evaluate its limit of detection. In Fig. 3e, we show the corresponding transient response of the gFET. To account for device-to-device variation, we normalize the change in Ids by the device transconductance to obtain a calibrated signal, tracking the change in VCNP (see ESI Note 6† for more details). We monitor the transient sensor response due to injections of the spike protein (see Experimental methods for discussion on the concentrations). Upon each spike injection, we observe a strong decrease in the sensor signal that follows an apparent exponential behavior (marked with dashed exponential fits). The subsequent spike injection occurs once the sensor signal establishes a new steady-state baseline. Each of the spike protein injections generates a qualitatively similar response, with decreasing magnitude as the sensor starts to saturate.
Fig. 3f shows the sensitivity plot of the antibody-modified gFET, plotting the cumulative sensor response against its corresponding spike concentration (on a log-scale). Also included in the plot are data points from a second measurement on a different device, demonstrating reproducibility of our measurements (see ESI Fig. S10†). To evaluate the sensor limits of detection and saturation, we fit the calibrated signal response to a Hill model of the form V = Vmax[A]n/(Knd + [A]n), where V is the signal strength, saturating at value Vmax, [A] is the analyte (spike protein) concentration, Kd is the equilibrium dissociation rate of the receptor–analyte pair, and n is the Hill coefficient, limited to a maximum value of 2 (for two receptor sites per antibody). We obtain an excellent fit to the data with, with the sensor response starting to saturate near 100 aM (Vmax = 16 mV), and n = 1.5 indicating cooperative binding of spike proteins to antibodies. Analysis of the electronic noise in these measurements reveals a 1.8 mVrms input-referred noise, corresponding to an estimated limit of detection of 1 aM based on the Hill fit (see ESI Note 2†). The excellent sensitivity of these gFETs, which could be further optimized in terms of electrical characteristics, reinforces the prospects of NanoBioFETs platform for site-selective functionalization of FET sensors.
We implement aptamer-modified gFETs following an identical tSPL fabrication and biofunctionalization procedure as in the experiments in Fig. 1 and 2, and we use a biotinylated anti-SARS-CoV-2 aptamer as bioreceptor (see Experimental methods for details). Before the electrical sensing experiments, we employ fluorescent microscopy to confirm the aptamer attachment in the channel region of the gFETs designated as biosensors. Indeed, the strong fluorescence in the channel region (20 × 50 μm2) of an aptamer-modified gFET (see left panel in Fig. 4b) confirms the effectiveness of our procedure in locally attaching aptamers. In this experiment, we also demonstrate the versatility of this approach in implementing control gFETs on the same chip by leveraging the spatial-selective biofunctionalization capability of tSPL. Control devices are produced simply by skipping the tSPL step in the channel region of a few select gFETs, while subjecting these gFETs to the same subsequent surface chemistry treatments as sensor gFETs. The fluorescent microscopy results for the control gFET (see right panel in Fig. 4b) confirm the chemical inactivity of the channel region in the control gFET with minimal non-specific binding.
In Fig. 4c, similarly to experiments of antibody in Fig. 3, we perform SPR experiments for validation of the binding between the anti-SARS-CoV-2 aptamer and spike protein in 0.1× PBS (λDebye of 2 nm). The subsequent electronic sensing experiments in a microfluidic chamber demonstrate the ability of aptamer-modified gFETs in generating detectable electronic signals in response to spike protein injections in the same buffer concentrations (see Fig. 4d). The simultaneous monitoring of an adjacent control device in this experiment provides confidence about the fidelity of the electronic signals generated by the gFET biosensor. This key feature of the NanoBioFET platform in enabling differential detection and simultaneous monitoring of non-specific binding is an important step toward achieving robust analyte detection using FET-based biosensors.
A closer look at the results in Fig. 4d reveals two important observations. The first observation is the significantly weaker signal amplitude of the aptamer-modified gFET compared to its antibody-modified counterpart in Fig. 3e. Whereas the antibody-modified gFET generates a 4 mV signal in response to 3 aM of spike concentration, the aptamer-modified counterpart produces only a 1.3 mV signal when exposed to 500 aM of spike protein. We attribute this characteristic primarily to the significantly smaller λDebye at 0.1× PBS. We expect that ongoing research in the field, focused on increasing the λDebye at a given ionic strength46 and developing alternative chemical conjugation strategies beyond biotin–streptavidin will directly benefit future experiments utilizing aptamer-modified gFETs. The second observation pertains to the relationship between the signal amplitude and the spike protein concentration. The data indicate a nearly diminishing response with the subsequent spike protein injections at higher concentrations. This observation suggests that the capturing aptamers on the gFET are reaching full occupancy, wherein the captured surface proteins block the interactions of incoming proteins with the surface probes. To quantify this, we plot the calibrated signal responses as a function of the analyte concentration (log-scale) in Fig. 4e, and fit the data with a Hill model as before. From the fit we estimate Vmax = 6 ± 2 mV, indicating a lower sensitivity of the aptamer-modified gFET in 0.1× PBS. The fit also returns a Hill coefficient of 0.38, indicating negative cooperativity. A full understanding of the nature of observed binding interactions in these experiments is a focus of future studies.
The measurement setup and procedure are nearly identical to that for the antibody–spike protein measurements earlier, with a 1 mM HEPES buffer (see Fig. 5a and Experimental methods for details). We monitor the temporal changes in Ids during the course of the sensing experiment. The experimental sensing procedure involves injection of the blank virus medium at the beginning of the experiments, followed by a few alternating injections of SARS-CoV-2 virus and the human H1N1 influenza virus (see Experimental methods for details on these viruses). Fig. 5b shows the transient response of the antibody-modified gFET with live virus injections in 1 mM HEPES. Injections of virus medium (black circle), SARS-CoV-2 virus (red diamond), and H1N1 virus (green star) are marked in Fig. 5b. The data demonstrate the sensitive and selective detection by the SARS-CoV-2 antibody-modified gFET. The SARS-CoV-2 virus (red diamond) and H1N1 virus (green star) in Fig. 5 show that the SARS-CoV-2 virus repeatedly produces an exponential-like response in the sensor, whereas the H1N1 virus (which we use as a negative control) or buffer produce no response. The first four virus injections are at a concentration of 20 TCID50 per ml and the last at 200 TCID50 per ml, estimated to be about 10 infectious virus particles per ml, demonstrating ultra-sensitive detection of the live virus. The insensitivity of the sensor to H1N1 injections highlights the selectivity of the gFET sensor.
The successful electronic sensing experiments for detection of CoV-2 targets confirm the feasibility of integration of the proposed functionalization strategy with FET biosensors. The key to this advance is the effective function of the polymer as a capacitor between the surface-anchored bioreceptors and the buried FET sensors, allowing the electronic detection of interactions between target analytes and specific bioreceptors. The electronic sensing experiments reveal ultrasensitive and selective sensing performance of the gFETs functionalized using the NanoBioFET platform. We achieve detection for 3 aM of SARS-CoV-2 spike proteins and 10 human SARS-CoV-2 infectious live virus particles per mL, as well as selectivity against human influenza A (H1N1) live virus. While this study confirms the feasibility of the NanoBioFET platform, future studies will focus on enabling multiplexed FET sensing using this methodology.
Lastly, we remark on the nanomanufacturing prospects of the proposed NanoBioFET platform. A key asset of this functionalization strategy is its generalizability to various FET materials from silicon to graphene. Indeed, the polymer stack is spin coated atop the fully fabricated chips, a process scalable to commercial silicon and other types of substrates with up to 300 mm diameter. Therefore, the NanoBioFET platform is compatible with commercial semiconductor manufacturing for producing CMOS chips that can contain many FETs (thousands to millions), where each FET or a group of FETs can be modified for detecting a specific target pathogen. To this end, we note that the tSPL process could be parallelized with the use of hot probes arrays, while the scanner head could work in parallel with picoliter piezo-type printing, decreasing the nanopatterning times, which are at present about 10 minutes per FET. Furthermore, tSPL is a flexible and sustainable nanofabrication method that does not require vacuum or high energy or alignment marks since each FET can be imaged in situ during patterning. Finally, we remark that the here-proposed biotin–streptavidin strategy to anchor the biomarkers to the surface can be easily changed with different amine-bioconjugation approaches to meet different device requirements.
All experimental data are available from the corresponding author upon reasonable request.
Footnotes |
† Electronic supplementary information (ESI) available. See DOI: https://doi.org/10.1039/d4nr02535k |
‡ These authors contributed equally to this work. |
This journal is © The Royal Society of Chemistry 2024 |