Fabrication of Carbon Nanotube High-Frequency Nanoelectronic Biosensor for Sensing in High Ionic Strength Solutions

Summary

We describe the device fabrication and measurement protocol for carbon nanotube based high frequency biosensors. The high frequency sensing technique mitigates the fundamental ionic (Debye) screening effect and allows nanotube biosensor to be operated in high ionic strength solutions where conventional electronic biosensors fail. Our technology provides a unique platform for point-of-care (POC) electronic biosensors operating in physiologically relevant conditions.

Abstract

The unique electronic properties and high surface-to-volume ratios of single-walled carbon nanotubes (SWNT) and semiconductor nanowires (NW) ^1-4 make them good candidates for high sensitivity biosensors. When a charged molecule binds to such a sensor surface, it alters the carrier density⁵ in the sensor, resulting in changes in its DC conductance. However, in an ionic solution a charged surface also attracts counter-ions from the solution, forming an electrical double layer (EDL). This EDL effectively screens off the charge, and in physiologically relevant conditions ~100 millimolar (mM), the characteristic charge screening length (Debye length) is less than a nanometer (nm). Thus, in high ionic strength solutions, charge based (DC) detection is fundamentally impeded^6-8.

We overcome charge screening effects by detecting molecular dipoles rather than charges at high frequency, by operating carbon nanotube field effect transistors as high frequency mixers^9-11. At high frequencies, the AC drive force can no longer overcome the solution drag and the ions in solution do not have sufficient time to form the EDL. Further, frequency mixing technique allows us to operate at frequencies high enough to overcome ionic screening, and yet detect the sensing signals at lower frequencies^11-12. Also, the high transconductance of SWNT transistors provides an internal gain for the sensing signal, which obviates the need for external signal amplifier.

Here, we describe the protocol to (a) fabricate SWNT transistors, (b) functionalize biomolecules to the nanotube¹³, (c) design and stamp a poly-dimethylsiloxane (PDMS) micro-fluidic chamber¹⁴ onto the device, and (d) carry out high frequency sensing in different ionic strength solutions¹¹.

Introduction

When a charged molecule binds to a SWNT or NW electronic sensor, it can either donate/accept electrons or act as a local electrostatic gate. In either case, the bound molecule can alter the charge density in the SWNT or NW channel, leading to a change in the measured DC conductance of the sensor. A large variety of molecules^15-20 have been successfully detected by studying DC characteristics of the nanosensors during such binding events. Even though charge-detection based sensing mechanism has many advantages including label-free detection²¹, femto-molar sensitivity²², and electronic read out capability¹⁵; it is effective only in low ionic strength solutions. In high ionic strength solutions, DC detection is impeded by ionic screening^6-8. A charged surface attracts counter-ions from the solution which forms an electrical double layer (EDL) near the surface. The EDL effectively screens off these charges. As the ionic strength of the solution increases, the EDL becomes narrower and the screening increases. This screening effect is characterized by the Debye screening length λ_D,

, where ε is the dielectric permittivity of the media, k_B is the Boltzmann's constant, T is the temperature, q is the electron charge, and c is the ionic strength of the electrolyte solution. For a typical 100 mM buffer solution, λ_D is around 1 nm and the surface potential will be completely screened at a distance of a few nm. As the result, most of nanoelectronic sensors based on SWNTs or NWs operate either in dry state²⁰ or in low ionic strength solutions^{5,15,17,21-22} (c ~ 1 nM - 10 mM); otherwise the sample needs to undergo desalting steps^15,23. Point-of-care diagnostic devices need to operate in physiologically relevant ionic strengths at patient site with limited sample processing capability. Hence, mitigating ionic screening effect is critical for development and implementation of POC nanoelectronic biosensors.

We mitigate the ionic screening effect by operating SWNT based nanoelectronic sensor at megahertz frequency range. The protocol provided here details the fabrication of a SWNT transistor based nanoelectronic sensing platform and high frequency mixing measurement for biomolecular detection. The single-walled carbon nanotubes are grown by chemical vapor deposition on substrates patterned with Fe catalysts²⁴. For our SWNT transistors, we incorporate a suspended top-gate²⁵ placed 500 nm above the nanotube, which helps enhance high frequency sensor response and also allows for a compact micro-fluidic chamber to seal the device. The SWNT transistors are operated as high frequency mixers^9-11 in order to overcome the background ionic screening effects. At high frequencies, the mobile ions in solution do not have sufficient time to form the EDL and the fluctuating biomolecular dipoles can still gate the SWNT to generate a mixing current, which is our sensing signal. The frequency mixing arises due to the nonlinear I-V characteristics of a nanotube FET. Our detection technique differs from the conventional techniques of charge based detection and impedance spectroscopy^26-27. Firstly, we detect biomolecular dipoles at high frequency rather than the associated charges. Secondly, the high transconductance of SWNT transistor provides an internal gain for the sensing signal. This obviates the need for external amplification as in case of high frequency impedance measurements. Recently, other groups have also addressed biomolecular detection in high background concentrations^23,28. However, these methods are more involved, requiring complex fabrication or careful chemical engineering of receptor molecules. Our high frequency SWNT sensor incorporates a simpler design and utilizes the inherent frequency mixing property of a nanotube transistor. We are able to mitigate the ionic screening effects, thus promising a new biosensing platform for real-time point-of-care detection, where biosensors functioning directly in physiologically relevant condition are desired.

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Protocol

1. Catalyst Patterning for SWNT Growth

1. Begin with a silicon wafer with a low pressure chemical vapor deposition (CVD) grown 500 nm Si₃N₄/ 500 nm SiO₂ film on top.
2. Spin coat a layer of photoresist (PR) at 500 rpm for 5 sec and then 4,000 rpm for 40 sec.
3. Bake the wafer at 115 °C for 90 sec.
4. Use a photomask with rectangular pits for catalysts (Figure 1) and expose the wafer in UV (365 nm) irradiance of 300 mJ/cm² for 0.3 sec. After exposure bake the wafer at 115 °C for 90 sec.

Tip: Design pits of different sizes e.g. 5 micron x 5 micron, 10 micron x 5 micron etc. to account for the variability in SWNT chemical vapor deposition (CVD) growth process.

5. Develop the wafer in developer for 70 sec gently shaking the wafer through the process.
6. Rinse the wafer with DI water for 2 min and then blow dry with a nitrogen (N₂) gun.
7. Load the developed wafer into e-beam evaporator chamber and deposit 0.5 nm iron (Fe) at a chamber pressure of 10^-6 torr.
8. Dice the wafer into smaller dies 1.5 cm x 1.5 cm.
9. Remove the photoresist by dipping in warm acetone and isopropanol (IPA) for 10 min each. This leaves behind Fe catalyst in the rectangular pits for nanotube growth.

2. CVD Growth of Carbon Nanotubes

1. Place the catalyst coated dies in the quartz tube of the CVD growth furnace.

Tip: Determine sweet spot for nanotube growth. Growth is uniform over an area of 2inch x 2inch downstream for our furnace (Figure 2c).

2. Anneal the substrate in air at 880 °C for one hour to remove photoresist residue (Figure 2a). Allow to cool down.
3. Purge the chamber with Argon for 5 min at 3 SLM (standard liter per minute).
4. Ramp up the furnace to 800 °C at the center of the tube, while maintaining a flow of 1 SLM of argon (Figure 2b).
5. Flow 0.2 SLM of hydrogen for 5 min to reduce the catalyst particles i.e. convert iron oxide to iron.
6. Introduce 5.5 sccm (standard cubic centimeter per minute) of ethylene (C₂H₄) for 35 min to grow SWNTs. Maintain a H₂ flow of 0.2 SLM throughout the process. The length of SWNTs obtained from this recipe is > 20 micron (μm).
7. Allow the furnace to cool down to room temperature with a small argon flow.

3. SWNT FET Transistor Fabrication

1. Design a photomask (Figure 1) for defining source-drain electrodes for current-voltage (I-V) characterization of carbon nanotubes.

Tip: Extend electrode contact pads far apart on the die so that they remain accessible even after putting down a micro-fluidic stamp on the active nanotube region.

2. Follow steps 1.2 -1.6 to define area for metal deposition for contacts.
3. Deposit Ti/Au 0.5 nm/50 nm for source-drain contacts in an e-beam evaporator chamber at 10^-6 torr.
4. Leave the die in acetone overnight for metal liftoff. After liftoff, dip the die in IPA for 10 min and then blow dry using N₂ gun.
5. Do a blanket deposition of 500 nm e-beam evaporated SiO₂ for gate dielectric at 10^-6 torr.
6. Design a photomask (Figure 1) for defining the gate electrode.
7. Follow steps 1.2-1.6 to define region for gate metal deposition.
8. Evaporate 50 nm/50 nm Cr/Au as the top gate electrode in e-beam evaporator. Follow step 3.4 for metal liftoff.

Tip: Use thick chrome layer to increase strength of suspended top gate. Gate dimensions are also critical for successful suspension.

9. Blanket deposit a thin layer (20 nm) of SiO₂ for top electrode passivation.
10. Design a photomask (Figure 1) to open a trench in SiO₂ to access the carbon nanotube channel. Design pad-etch area in the same mask to open up region for accessing source, drain and gate electrodes far away from the SWNT channel.
11. Follow steps 1.2-1.6 to pattern the PR to open up the trench for wet etch of SiO₂.
12. Wet etch the evaporated SiO₂ using 1:20 BHF solution for 3 min and 30 sec. Si₃N₄ provides a etch stop layer to prevent further penetration of BHF.

Tip: Etch time calibration is recommended.

13. Thoroughly rinse the device in DI water, and then dip it in IPA for 5 min. Blow dry using a N₂ gun. The device structure remains intact due to the thick chrome layer.

4. Chemical Functionalization of Carbon Nanotube Sidewalls

1. Prepare a solution of 6 mM 1-pyrenebutanoic acid succinimidyl ester (PBSE) in dimethylformamide (DMF).
2. Incubate the SWNT FET die in this linker molecular solution for 1 hr at room temperature.
3. Thoroughly rinse the die in DMF to wash away the excess reagent. Blow-dry the device.
4. Prepare a 20mg/ml solution of biotinyl-3, 6-dioxaoctanediamine (biotin PEO amine -BPA) in DI water for biotinylation of SWNTs.
5. Incubate the die in this solution for 18 hr after which thoroughly rinse the die in DI water and blow dry. BPA attaches to the PBSE linker molecule.
6. Prepare a solution of 1mg/ml streptavidin in 7.2 pH PBS solution for streptavidin binding.
7. For static measurements, incubate the die in streptavidin solution for 20 min to completely functionalize the biotinylated SWNT. Thoroughly rinse and blow dry the die. For real time sensing, stamp the PDMS flow channel (step 6) first and then flow the streptavidin solution in high ionic strength background for streptavidin binding (Figure 3).

Note: We rinse the die by dispensing DI water (~50 ml) over the die using a squeeze bottle. Then we move the die to another Petri dish containing DI water and move the die around for 1 min. We repeat the two steps a total of 8-10 times.

5. Preparation of Polydimethylsiloxane (PDMS) Mold for Fluid Chamber

1. In a weighing cup, pour 9 parts by weight of PDMS monomer and add 1 part by weight of curing agent and thoroughly mix the two.
2. Degas the mixture in a desiccator for 25 min. The bubbles will rise through the mixture and leave.

Tip: If the mixture starts foaming, vent the chamber and let it settle down for a few seconds before degassing again.

3. Place a new silicon wafer in a Petri dish. Pour the degassed PDMS mixture on top of it to have a PDMS layer of 5 mm above the wafer.
4. Place the Petri dish in an oven at 70 °C for 1 hr.
5. Remove the Petri dish and let it cool down. Use a scalpel to cut out a rectangular piece of PDMS and pull it out using a tweezer.

Tip: The PDMS side directly in contact with the silicon wafer is clean and extremely flat. This side will be in contact with the SWNT FET die. Be careful not to contaminate it.

6. Place the rectangular die upside down and drill a hole in it using a biopsy punch (3 mm diameter) from the flat side to the other. This ensures no rough edges on the flat side of PDMS (Figure 4a).
7. Place the PDMS chamber on top of the device carefully by aligning it on top of the active area of the fabricated SWNT FET dies (Figure 4a, b). Tap it gently to secure the stamp on die. The flat side bonds to the die to provide a leak-tight chamber.

Tip: This can be done with the naked eye or using an optical microscope with enough working space. If the PDMS does not stick well (generally if the die and/or the PDMS stamp is not clean), do oxygen plasma (20 watts, 15 sec) on PDMS to assist bonding. Using plasma powers higher than this leads to stronger bonding, however, we have seen ripping of electrodes while removing the PDMS in such case.

8. Remove the PDMS stamp after electrical testing and before next chemical functionalization step by dipping the die in DI water and gently lifting the stamp.

6. Preparation of Microfluidic Flow Channel

1. Take a clean silicon wafer and place it on hot plate at 200 °C for 5 min to remove any moisture.
2. Spin coat SU-8 2015 at 500 rpm (100 rpm/sec ramp rate) for 5 sec and then 1,250 rpm for 30 sec at 300 rpm/sec ramp rate. This gives a 30 μm thick SU-8 layer on silicon wafer.
3. Soft bake the wafer at 95 °C for 5 min.
4. Design a photomask (Figure 4c) to define the 300 μm wide flow channel pattern on top of the SWNT area.

Tip: To avoid collapse of structure a channel width: height ratio of 10:1 is sufficient (300 μm: 30 μm in this case).

5. Using 365-nm UV photolithography define the flow channel with a UV exposure time of 0.9 sec.
6. Post bake the die at 95 °C for 5 min.
7. Develop the pattern in SU-8 developer for 5 min accompanied by gentle shaking.
8. Rinse the wafer in IPA and blow dry with N₂ gun.
9. Follow steps 5.1-5.2 to prepare a PDMS mixture.
10. Place the wafer with SU-8 mold in a desiccator along with a 2-3 drop of silanizing agent trichloro(3, 3, 3-trifluoropropyl)silane in a Petri dish. Turn on the vacuum pump let the wafer sit in vacuum for 1 hr.
11. Pour the degassed PDMS mixture onto the wafer and heat it in an oven at 70 °C for 1 hr.
12. Cut the PDMS mold (negative of SU-8) using a scalpel.
13. Place the PDMS stamp upside down and using a biopsy punch (0.75 mm diameter) to drill a hole at each end of the flow channel. Make sure to drill the hole from the flat side (the side in contact with the silicon wafer) to the other to avoid rough edges (Figure 4e).
14. Place the PDMS flow chamber on top of the device carefully by aligning it on top of the active area of the fabricated SWNT FET dies under a microscope. Tap it gently to secure the stamp on die. The flat side bonds to the die to provide a leak-tight chamber. (Figure 4c and 4d)
15. Push a polyethylene tube into the holes and connect the other end to a fluid source and drain syringe (Figure 4e).
16. Attach the syringe to a syringe pump system to maintain a controlled flow of the fluid through the channel (Figure 6).

7. DC Electrical Measurement Setup

1. Connect the source and gate contacts of SWNT FET to voltage ports of a DAQ card.
2. Connect the drain contact to input port of DAQ card through a current pre-amplifier.
3. Apply 30 millivolt (mV) to source contact, sweep the gate voltage and record the current from the drain (Figure 5a).

Tip: For measurements in solution, keep gate voltage sweep parameter within |0.7 volts| to avoid leakage and reaction between the gate metal electrode and solution.

8. AC Electrical Measurement Setup

1. Connect the Ref-out signal from lock-in amplifier to the external modulation signal port on frequency generator to setup AM modulated frequency output.
2. Connect source contact of SWNT FET to the AM-modulated RF output port of frequency generator and dc voltage from DAQ card using a bias tee (Figure 5b and 5c).
3. Connect gate contact to voltage port of DAQ card.
4. Connect the drain contact to a lock-in amplifier to read the ac current through the nanotube. Read the amplitude and phase of current through the DAQ input ports.
5. Hold source dc voltage at 0 volt and AM signal frequency at 200 kilohertz (kHz).
6. Sweep the gate voltage and measure the current from the drain.
7. Increase frequency and repeat step 8.6 for I_mix-V_g sweeps at different frequencies.

9. Electrical Measurements in Solution (No Flow)

1. Prepare 1 mM NaCl, 10 mM NaCl and 100 mM NaCl salt solutions starting from 5M NaCl stock solution.
2. Take the SWNT device from step 3.13. Carry out steps 4.1-4.5 to obtain a biotinylated device.
3. Follow step 5 to put a PDMS chamber on top of the device.
4. Fill the chamber with DI water using a pipette.
5. Follow step 8 for frequency mixing measurements for different frequencies.
6. Repeat 9.4 for the three different salt solutions 1 mM NaCl, 10 mM NaCl and 100 mM NaCl.

Tip: Use pipette to withdraw previous solution and then flush the chamber multiple times with the new solution. Always switch from the low to high concentration solutions.

7. Remove the PDMS stamp by gently lifting the stamp with a tweezer.
8. Thoroughly rinse the device with DI water.
9. Carry out streptavidin binding as explained in 4.6-4.7.
10. Repeat steps 9.3-9.6.

10. Electrical Measurement in Solution (Real Time Flow)

1. Prepare 100 mM NaCl salt solution starting from 5 M NaCl stock solution.
2. Take the SWNT device from step 3.13. Carry out steps 4.1-4.5 to obtain a biotinylated device.
3. Place the micro-fluidic flow channel on the device following step 6.. Connect an empty syringe to one end of the micro-fluidic channel for withdrawal mode operation. At the other end attach a syringe with background solution of 100 mM NaCl.
4. Set up the electrical measurement as detailed in step 8. Fix the frequency (f = 10 MHz) and gate voltage bias (V = 0).
5. Start syringe pump in withdrawal mode (flow rate = 0.4 ml hour^-1) and monitor the current signal with time. Switch the solution to 1mg/ml streptavidin in 100 mM NaCl and monitor signal change for streptavidin-biotin binding (Figure 6).

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Results

A scanning electron microscope image of SWNT transistor with a suspended top gate is shown in Figure 7a. The gate dimensions are critical for suspension²⁵. The current design dimensions are (length x width x thickness = 25 μm x 1 μm x 100 nm). The gate electrode consists of 50 nm Cr/50 nm Au; a thick chrome layer adds more strength to suspended structure. The suspended structure is confirmed by absence of leakage current between top gate and drain (Figure 7b).

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Discussion

The growth of carbon nanotubes depends not only on furnace conditions but also substrate cleanliness. The optimal gas flow rate, temperature and pressure for growth have to carefully calibrated and once fixed they are more or less stable. Even with these conditions being met, we found that growth depends on the patterned catalyst area, amount of catalyst and substrate cleanliness. Hence, we incorporated multiple catalyst pit sizes to account for the variability in growth. A one hour high temperature anneal step helped re...

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Materials

Name	Company	Catalog Number	Comments
REAGENTS
Reagents which were provided within Lurie Nanofabrication Facility (University of Michigan) are marked as LNF in the catalogue column. Chemicals which require protective equipment (gloves, safety goggles, face mask, apron) and/or fume hood are denoted with PPE in comments section.
Silicon wafers (P-type, <100>, 500-550 μm thick)	Silicon Valley Microelectronics
SPR 220 3.0	Dow (Rohm and Haas)	Megaposit SPR	PPE
AZ 300MIF	AZ Electronic Material Corporation		PPE
Acetone	J T Baker	9005-05	PPE
Isopropanol (IPA)	J T Baker	9079-05
Buffered Hydrofluoric Acid	Transene		PPE
1-Pyrene Butanoic Acid, succinimidyl ester	Molecular Probes	P130	PPE
Biotin PEO Amine	Thermo Scientific	EZ- Link PEG2 Biotin, # 21346	PPE
Streptavidin	Invitrogen	S 888	PPE
Dimethylformamide	MP Biomedicals	0219514791	PPE
Polydimethylsiloxane Elastomer Base and Curing Agent	Dow Corning	Sylgard 184 Elastomer Kit	PPE
SU-8 2015	Microchem	Y111064	PPE
SU-8 Developer	Microchem	Y020100	PPE
Silanizing agent	Sigma Aldrich	452807	PPE
Hydrogen	Purity Plus	LNF
Ethylene	Purity Plus	LNF
Argon	Purity Plus	LNF
Phosphate Buffer Saline System	Sigma Aldrich	PBS1
EQUIPMENT
Equipment provided by Lurie Nanofabrication Facility (University of Michigan) is denoted as LNF in Catalogue column.
GCA 200 Autostepper	GCA	LNF
Low Pressure Chemical Vapor Deposition Tool	Tempress	LNF
e-beam Evaporator	Enerjet	LNF
CNT growth Furnace	First Nano	Easy Tube 3000 (LNF)
Photomasks	Nanofilm	LNF
Petri dish (150mm)		LNF
Desiccator	Bel-Art	F420100000
Biopsy Punch	Ted Pella	15071/78
Scalpel	Ted Pella	548
Polyethylene Tubing PE-50	VWR	20903-414
Syringe Pump	New Era Pump Systems	NE-1000
Syringe	Fisher Scientific	BD Safety-Lok Syringes
Syringe Needles	Fisher Scientific	14-821-13A
DAQ card	National Instruments	779111-01
GPIB connector	National Instruments	778032-51
Lock-in Amplifier	Stanford Research Systems	SR 830
Frequency Generator	HP Agilent	8648B, 9kHz -2GHz
Bias Tee	Picosecond	5575A-104
Current Preamplifier	DL Instruments, LLC	DL 1211
BNC cables	Allied Electronics	665-xxxx
SMA cables	Sentro Tech Corp	SCF65141