CA2619000A1

CA2619000A1 - Biofet based microfluidic system

Info

Publication number: CA2619000A1
Application number: CA002619000A
Authority: CA
Inventors: M. Jamal Deen; Ponnambalam Selvaganapathy; M. Waleed Shinwari
Original assignee: McMaster University
Current assignee: McMaster University
Priority date: 2007-12-28
Filing date: 2007-12-28
Publication date: 2009-06-28
Anticipated expiration: 2027-12-28
Also published as: CA2619000C

Abstract

Biological field-effect transistors are configured to optimize their sensitivity as label-free DNA microarrays. Different circuit configurations allow for highly sensitive biosensors to be realized using the transistors, including an electronic DNA microarray chip in an industry standard silicon technology.

Description

BioFET Based Microtluidic System FIELD OF THE INVENTION

[001] This invention pertains to integrated bio-sensor systems and in particular to those based on label-free detection of oligonucleotides or protein fragments in a multiplexed microarray format, namely an electronic DNA microarray chip in an industry standard silicon CMOS
technology.
BACKGROUND TO THE INVENTION

[002] Food and water-borne pathogens constitute a major public health problem globally. Therefore, early detection and containment of pathogens, such as Salmonella, E-coli and Campylobacter Jejuni, a bacterium responsible for gastroenteritis, will prevent the rapid spread of this communicable diseases and the otherwise inevitable contamination of other consumable goods. Fast, reliable, sensitive and inexpensive methods of detecting biological contaminants are therefore of great importance and appreciated by many areas of research, including but not limited to, water and food monitoring for public health.

[003] The use of mainstream electronics is an appealing technique for DNA hybridization detection. Metal-oxide-semiconductor field-effect transistors (MOSFETs) can be modified to act as DNA hybridization biosensors. By removing the gate metal and polysilicon off a FET device, and functionalizing the underlying dielectric with a tether molecule, ssDNA probes can be immobilized onto the dielectric surface. If target DNA molecules hybridize to these probes, the underlying FET structure will be affected by this increase of DNA density, due to the intrinsic negative charges on the DNA backbone. The excess charge induces a counter-charge from the surroundings, including the underlying silicon substrate. Electronically, the result of this action is as a shift in the threshold voltage of the biosensor. Such a modified transistor is referred to herein as a biological field-effect transistor (bioFET).

[004] There are many advantages of this technique. A direct method of label-free electrical detection of DNA hybridization is provided using relatively inexpensive, mainstream complementary metal-oxide-semiconductor (CMOS) silicon technology. As such, precise and controlled silicon-based fabrication environments are carried over to the biosensor. The biosensor array is integrated with the accompanying electronics for signal processing on the same chip. In addition, the continued scaling down of CMOS technology allows DNA microarrays with higher sensitivity, and higher density, to be realized. CMOS
technology can also be used to manufacture low-power components.
Combined with dense integration capabilities, DNA microarrays built in this manner are good candidates for a potentially portable DNA analysis and pathogen detection device.

[005] A bioFET consists of a field effect transistor, the current through which can be modulated by the gate potential. The gate provides the interface between the electronic and biological domains. A solution of biomolecules, such as single stranded DNA, RNA and proteins ligands, is put in contact with the bioFET and are covalently fixed on a gate electrode. The association of complimentary DNA, RNA or protein from the sample solution increases the charge and hence the potential of the gate electrode. This is reflected as a change in the current and sensing of the association. This type of detector is widely used for sensing ions, organic compounds both in the gaseous and liquid phase. However the sensitivity of the device is based solely on the non-linear I-V
characteristics of the transistor.

[006] There remains a need for DNA microsensors that operate with very low power, and can be incorporated into handheld devices for direct detection of pathogens from environmental samples. A system using label-free electrical detection would eliminate the need for expensive and cumbersome laser scanning systems required in current microarray technology and would lead to advantages in terms of portability and cost, making it more amenable to deployment in the field.

SUMMARY OF THE INVENTION

[007] An object of the present invention is to provide a biological sensor system which is cost-effective, easy to operate and maintain, and which employs highly sensitive means for detecting biological molecules in water or food.

[008] Another object of the present invention is to provide a circuit interface system to the bioFET which produces linear, temperature-insensitive, and environment insensitive, biosensors that are highly sensitive to DNA charges.

[009] Another object of the present invention is to provide a model and interface of CMOS-based electronic biosensors to develop highly sensitive label-free DNA microarrays compatible with mainstream silicon-based microelectronics.

[0010] Another object of the present invention is to provide different interface circuit topologies to enhance the sensitivity and performance of the bioFET. Such circuit techniques are utilized to enhance the sensitivity of the bioFET sensor, and are suitable for implementation in DNA
microarrays. The use of feedback systems, both positive and negative, as well as non-conventional techniques, such as floating nodes and clocked circuits, is provided.

[0011] Another object of the present invention is to provide a design of a biochip DNA array in an industry standard silicon CMOS technology.
BRIEF DESCRIPTION OF THE DRAWINGS

[0012] Fig. 1 is a configuration of a CMOS inverter, biased as an inverting amplifier.

[0013] Fig. 2 is a configuration of a CMOS inverter as an inverting amplifier with active, diode connected load.

[0014] Fig. 3 is a configuration of a CMOS inverter as an inverting amplifier with active, independently biased load.

[0015] Fig. 4 is a configuration of a CMOS common-source amplifier with negative resistance load.

[0016] Fig. 5 is a configuration of a CMOS ring oscillator with bioFET as an inverter stage.

[0017] Fig. 6 is a configuration of a feedback operational amplifier with offset voltage due to hybridization.

[0018] Fig. 7 is a schematic representation of a charge sensing system, including an embodiment of a bioFET of the present invention.

[0019] Fig. 8 shows schematic diagrams of circuits implemented on the microarray chip of the present invention.

[0020] Fig. 9 shows the design layout of the microarray chip of the present invention.

[0021] Fig. 10 depicts a schematic diagram of a folded cascode operational amplifier of the present invention.

[0022] Fig. 11 shows the a) Frequency response of the operational amplifier, and b) Voltage transfer characteristics of the designed operational amplifier of the present invention.

[0023] Fig. 12 depicts the schematic diagram of Fig. 10 with the addition of compensation capacitor.

[0024] Fig. 13 shows a compact layout of an operational amplifier of the present invention.
DETAILED DESCRIPTION OF THE INVENTION

[0025] BioFETs are based on the principle that adsorption of charged biomolecules, such as DNA fragments (oligonucleotides), on the gate dielectric of a FET will modulate the transistor's surface potential and ultimately its current. If the dielectric is appropriately functionalized with an oligonucleotide of a given sequence, hybridization of an oligonucleotide with the complementary sequence will give rise to an electrical signal in the FET. The fabrication of bioFETs requires the controlled deposition of high quality, high dielectric constant insulators of nano-scale thickness and methods for the chemical functionalization of these ultrathin dielectric layers for biomolecule attachment.

[0026] DNA hybridization causes a shift in the threshold voltage of the bioFET. This shift is equivalent to a change in the voltage of the reference electrode. For constant biasing, the change in the threshold voltage causes a change in the amount of drain current, via the transconductance of the bioFET. In addition, the threshold change in the bioFET causes a shift in its electrical characteristics such as the C-V characteristics or the I-V
characteristics.

[0027] The following characteristics of the bioFET sensor allow a determination of three different sensor circuit families:

[0028] Potentiometric sensors: These sensors aim at sensing the change in the threshold voltage by maintaining a constant current for the drain of the BioFET, while measuring the shift in the gate-source voltage (VGS) directly via a high input impedance readout circuit, such as an operational amplifier. These sensors can offer better linearity in measurements, as the output can be fed to linear amplifiers for sensitivity enhancement. Another characteristic of this type of sensor is that the sensitivity is limited by the limits of validity of the one dimensional solution, and not by the device sizing.

[0029] Amperometric sensors: In this regime, the change in the current of the bioFET due to DNA hybridization is sensed while VGS is kept constant. If the bioFET is in the linear region of operation, the sensor works as a resistance sensor, monitoring the change in the channel resistance as the DNA is immobilized. In saturation, amperometric sensors would be equivalent to common-source amplifiers, offering a high degree of sensitivity to hybridization. Higher aspect ratios of the bioFET will, in general, cause higher sensitivities due to the higher transconductance values. However, the output resistance can also be lowered by this, and a compromise must be made to maintain a high sensitivity value.

[0030] Capacitance sensors: The change in the small signal capacitance due to a shift in the threshold voltage can affect the operation of different AC circuits, particularly amplifiers and oscillators. DNA hybridization can, therefore, change the oscillation frequency of an oscillator or the gain of an amplifier. The sensitivity of the capacitance due to the DNA
hybridization scales as the area of the bioFET, which may be challenging in terms of miniaturization.

[0031] Many different interface circuits have been proposed for ion sensitive field effect transistors, including both potentiometric and amperometric sensors, which are equally applicable for the bioFETs.
These circuits are concerned with interfacing to the transistorm, as opposed to the actual sensitivity of the device. The more sensitive a circuit is, the more possible it is to reduce the density of DNA probes, thereby allowing the sensor to detect very dilute concentrations of the DNA molecules.

[0032] The configurations of bioFETs shown in Figs. 1-6 are implemented to fabricate hybrid devices employing functionalized carbon nanotubes or nanowires on the surface of the gate oxide to increase the effective surface area for hybridization and signal generation. The resulting biosensor can be integrated within a commercial CMOS
technology, leading to low-cost devices integrated with on-chip amplifiers and signal conditioning/ processing electronics, further enhancing the overall sensitivity of the bioFET system.

[0033] The bioFET configuration of the invention comprises several basic bioFET units combined in networks to enhance the sensitivity of the biomolecule association.

1. CMOS inverter, biased as an inverting amplifier

[0034] A set of bioFETs (PMOS and NMOS) are configured as an inverter and share a reference electrode. The inverter is biased at the point where both transistors are saturated for maximum gain. Hybridization on both transistors results in the output voltage changing by a large amount.

[0035] As shown in Fig. 1, a set of BioFETs (PMOS and NMOS) are configured as an inverter, sharing the reference electrode. The inverter can then be biased at the point where both transistors are saturated for maximum gain. Hybridization on both transistors results in the output voltage changing by a significant amount.

[0036] The amplification in this circuit is dependant on the transconductances of the transistors, the output conductance, and the amount of threshold voltage change due to DNA hybridization. Assuming that AVth is constant, which is the case for specific parameters of the device (electrolyte concentration, pH, probe density), then only the transconductances and output conductances will affect the amplifier's gain.
Changing the transconductance by changing the device size or changing the DC bias current will not help much in increasing the gain, because the output resistance will decrease as well.

gm = 2KID
~
rout = (XID 1

[0037] One method that would enhance the gain in this stage would be to operate the inverter in subthreshold, since such a high output swing is not needed, and since subthreshold bias would give extremely high output resistances. A simple simulation has shown that gains of around 100 (40 dB) are obtainable.

[0038] The output of such an amplifier would have to be taken from a low-output impedance buffer. A unity gain opamp can be used for this purpose.

2. CMOS inverter configured as an inverting amplifier with active, diode connected to load

[0039] This design provides the same performance as the previous one but reduces the area of hybridization from two transistors to one.

[0040] In an attempt to reduce the bio-sensitive area, one might use a simple amplifier configuration with a diode connected load. This can also be seen as a MOSFET inverter biased to operate as an inverting amplifier.
Fig. 2 shows this configuration.
[00411 This can be a very small gain, because gõ'p;' is generally much smaller than the output resistances of the two transistors and will therefore dominate, reducing the overall gain of the circuit. Thus, this circuit shares the advantages of the previous one.
3. CMOS inverter configured as an inverting amplifier with active independently biased load [0042] In this configuration, shown in Fig. 3, only one of the transistors is a bioFET which can undergo hybridization while the other transistor is biased at a constant point. This configuration allows a wider choice of biasing points for the bioFET, which is somewhat independent of the power supply, but lower gain than the first configuration.

[0043] The gain in this case can be much higher than that in the second configuration, but not as high as the first configuration, described above.

4. CMOS common-source amplifier with negative resistance load [0044] In this configuration, the gain of the amplifier is made high over a voltage range by using negative resistance loads, such as resonant tunneling diodes or other MOSFET circuits.

[0045] The gain of a single-stage bioFET amplifier can be increased using negative-resistance loads. Using one of the several negative-resistance techniques (resonant tunneling diodes or MOSFET circuits for negative resistance), the gain of the amplifier can be made very high (ideally infinite) over a voltage range. If the transistor is biased around that range, then the sensitivity to the bioFET is superb. Fig. 4 depicts a schematic diagram of one implementation.
[0046] In this configuration, extremely high gains can be obtained through optimization of the component values and biasing conditions.

[0047] Similar to the previously described circuits, this circuit would also require an output buffer opamp to read the voltage. This circuit uses only a single bioFET and may achieve gains higher than that of the first configuration.

5. CMOS ring oscillator with bioFET as an inverter stage [0048] In this configuration, all the inverters of a ring oscillator are replaced by bioFET inverters. The hybridization of the biomolecule causes a capacitance change which affects the oscillation frequency.

[0049] In order to establish the effect of DNA hybridization on the ring oscillator's characteristics, it is important to find the relationship between both the threshold voltage and the input capacitance, and frequency of oscillation.

[0050] A ring oscillator can be seen as a regular phase shift oscillator, but with loop gain that is higher than 1, such that the circuit oscillates between the rail voltages. One can think of the ring oscillator as starting at the equilibrium point, and then starting to oscillate due to some disturbance.
Under small-signal conditions, the Barkhausen criteria for oscillation can be evaluated. This will give the frequency of oscillation of the ring oscillator. Of course, this will only apply under small-signal conditions.

This is why the best sensitivity of the ring oscillator to hybridization might be under small-signal oscillation. This can be done with heavy enough capacitive loads. Fig. 5 shows a schematic diagram of a small-signal ring oscillator's simplified equivalent circuit.
[0051] In Fig. 5, the resistance R is the parallel combination of the saturated output resistances of the pullup PMOS and pulldown NMOS, and the capacitance C is the parallel combination of the gate capacitances for the PMOS and NMOS of the next stage. Without these delay elements, the circuit would not oscillate, but would rather stabilize at an equilibrium voltage where the input and output of the inverters has the same voltage (called the inverter's threshold voltage).

[0052] From determining the mathematical condition, it can be guaranteed that the ring oscillator will oscillate.

[0053] By replacing the standard inverters with bioFET inverters, the oscillation frequency will be affected by the capacitance change due to hybridization, and not by the threshold voltage shift. The threshold voltage shift will merely cause the DC average stable point around the ring to deviate. Biasing the bioFETs around its threshold voltage results in a change in the inverter's oscillation properties due to the capacitance changes upon hybridization.

[0054] Subthreshold operation will allow higher gains of the inverter stage, allowing more frequency deviation per change in capacitance due to DNA hybridization.

6. CMOS ring oscillator with bioFET as a load capacitor [0055] Another manifestation of the first configuration is where a MOSFET inverter stage is replaced by a bioFET inverter. The expression for the sensitivity is again:

dco -C 1 + G3 dCl R ~C2 +2CCl l3 [0056] Another manifestation is to have only one of the inverter MOSFETs functionalized as a bioFET. This way, upon hybridization, the gain of the inverting amplifier stage will change, and this will cause a change in the frequency of the output. In this configuration, if the oscillator is operated in its oscillation mode, then hybridization will change it oscillation properties:

7. General LC oscillator with bioFET as a load capacitor [0057] In this configuration, tunable oscillators such as RF VCO, Colpitts, Hartley or Clapp oscillators are used with the capacitance obtained from the bioFET. Hybridization changes the capacitance and hence the oscillation frequency of the device. Similar analysis as that of the ring oscillator can be carried out to find the frequency deviation.

8. Mismatched analog circuits [0058] The effects of mismatch can be studied in particular circuits. In this configuration, an operational amplifier in open loop is provided a stable input and another input from the bioFET. The inputs are matched in the unhybridized state. Upon hybridization the inputs become mismatched and the mismatch is amplified in the output signal by the amplifier gain.

[0059] It seems that operational amplifiers might have the best sensitivity to mismatch, even under feedback. An entire analysis of opamp-based mismatch can be carried out, depending on the opamp's topology.
Mismatch would introduce an output offset voltage, whose value would be dependant on the open-loop gain of the amplifier. Under closed loop unity feedback, the change in the output voltage would be:

dVout __ -A
dVoffset 1 + A

[0060] This value is less than 1. See Fig. 6. Thus, under closed-loop, a feedback opamp might not provide that much gain. However, one can utilize the opamp in open-loop. Then, the gain due to mismatch will be that of the open-loop gain A.

9. Leakage component modulation for a floating charge device (eg.
Dynamic logic circuit) [0061] This configuration utilizes the effects of hybridization in the leakage current of MOSFET devices. In this configuration, the modulation of the leakage current by the hybridization is used as a signal.
When a charge is stored in a floating node, substrate leakage currents lead to its depletion over time. Hybridization of the biomolecule causes further inversion of a channel and an increase of leakage current and hence discharge in a shorter time. This leakage is used as an indication of hybridization.
[0062] This is because the inversion might not cause conduction along the channel, but rather increase the area of the effective PN-junction and thus increase the leakage current. This is be very noticeable for floating charges.

[0063] These configurations lead to significant enhancement in the sensitivity of the device. An individual configuration is what is termed as a BioPixel. The device itself consists of an array of BioPixels. Each pixel is configured by the biomolecule present in its sensing layer to identify its complementary target associated with a particular disease biomarker.

[0064] One example of a bioFET in a 1 milliMolar solution shows electrical current changes of 20 nA for hybridization of around 4,080 molecules of 17 base pairs on a bioFET with 12,000 square micron gate area fabricated in an industry standard silicon complementary metal-oxide-semiconductor (CMOS). Experiments with the bioFET sensor are with purified and amplified nucleic acids in order to demonstrate functionality, determine sensitivity limits and to calibrate the existing theoretical model. In practical applications, the bioFET sensor is packaged with microfluidic pre-processing modules. These preprocessing modules perform a number of steps to transform the analyte from its naturally occurring state to a form that is suitable for detection by the bioFET sensor.

[0065] An example of a microfluidic/MEMS based system that performs all the required preprocessing steps including filtration, concentration, cell lysing, DNA extraction, processing and amplification is represented schematically at Fig. 7.

[0066] This system combines the physical and chemical modeling of the electrolyte/DNA system with semiconductor technology to establish a physical model that relates the change in current due to DNA
hybridization to the density of DNA probes. This measure gives quantitative characterization of the sensitivity of the bioFET, which is used to compare bioFET-based sensing to other mainstream methods, such as optical DNA microarrays.

[0067] The linearization of the entire physical model of the bioFET gives good approximations to the response of the bioFET to DNA hybridization.
Moreover, the simplification shows that the response to DNA
hybridization can be quantified as a shift in the threshold potential, the amount of which can be given in closed form, as a function of the ionic strength, DNA strand length, DNA probe density, degree of hybridization, adsorption affinity of the insulator surface, and permittivity of the electrolyte and membrane areas.

[0068] Since these biosensors require that the sample presented to them is pure, an integrated microfluidic sample purification system is essential for the device's operation. Microfluidic chips are attractive for processing field samples because many of the sample processing steps can be integrated into a single module, minimizing the dilution of intracellular components following cell lysis. Furthermore, sample handling in microfluidics is gentle which minimizes DNA shearing effects, which are important for high molecular weight DNA fragments. The pre-processing module performs a number of essential steps including sample filtration, cell lysing, biomolecule extraction and concentration.
[0069] Sample filtration is critical because particulate matter present in the environment pose a serious challenge to the functioning of microfluidic system due to channel blockage and also provide sites for accumulation of other- particulates. Selective filtration and concentration of the biological material of interest can be done using size-based retention of cells on microfabricated filters. Microfabricated porous monoliths with defined pore sizes allow construction of a series of filters which are used to isolate biological materials like cells, which are in a characteristic size range, from other particulate matter. This methodology is further used to isolate sub-populations in cells. For example white blood cells can be isolated from red blood cells using this method due to their size difference. However, microfabricated filters has small capacity and are prone to become clogged. Active filter regeneration is achieved by generating counter flow using an electrokinetic mechanism. In electrokinetics, electrical fields are used to direct flows through microchannels and microporous materials such as filters. Since electrical fields are easily controlled, modulated and reversed using computer generated signals, they could be used for dynamic cleaning of a clogged filter. The active filter consists of a microporous membrane of a defined pore size with a pair of electrodes on either side of the membrane.
Application of a positive potential across the membrane drives flow through the membrane and leads to accumulation of particulate matter.
Subsequently, reversal of potential across the membrane generates counter flow, clearing the filter. The concentrated particulate matter is moved to a waste reservoir and the filtering process continued. This process regenerates the filter and allows higher capacity. A series of stacked filter designs can be developed to size-separate the particles for further analysis.
[0070] The same design can be used for concentration of the collected biological material. The collected material (cells) consist of the information containing biomolecule packaged along with other biomaterials such as DNA, RNA, proteins, lipids and cellular materials.
The cell membrane is broken and its contents exposed for the biomolecule to be extracted and analyzed. Cell lysis is performed using osmotic shock on exposure to pure water. In this method, a porous material inside a microchannel is used to concentrate the cells of interest. Subsequently, the buffer solution is replaced with distilled water using the microfluidic solvent exchange. Cells present in DI water undergo osmotic shock due to the large concentration gradient present across their cell membrane.
Subsequently, the solvent is once again replaced by buffer solution.

[0071] Since the cell lysate consists of the biomolecule of interest along with other contaminants, a microscale solid phase extraction is performed to concentrate and isolate the DNA. This is especially important when a subsequent PCR stage is included as PCR is inhibited by certain proteins.
The cell lysate is electrokinetically passed through another silica sol-gel porous region microfabricated on chip. Silica surfaces have preferential adsorption of DNA over other proteins, lipids and other containments. The concentrator is subsequently washed with a propanol/water mixture to further purify the extracted DNA. Release of concentrated DNA is performed using the low ionic concentration solution or DI water.
Amplification of the section of DNA of interest from the extracted DNA is performed using standard PCR protocol subsequent to which the DNA is passed on to the detector stage.

Design of a DNA Microarray Chip in CMOS 0.8 m Technology [0072] The chip was designed using an industry standard silicon CMOS
technology which also supports microelectromechanical systems (MEMS)/microfluidic device control and high-voltage integrated circuit (HVIC) control and power systems.

[0073] All circuit simulations were conducted using simulation software.
All layouts were built using a custom design platform. The models for the transistors and the design layers were included in the design kit and technology file for the industry-standard silicon process. The transistor models were based on a standard industry modeling architecture. The only components to be simulated were the operational amplifiers. The BioFET
transistors were simulated once with a gate contact to verify normal transistor operation and proper construction, but the gate contact was subsequently removed to facilitate direct exposure of the polysilicon, which would be etched during post-processing.

[0074] Several different microarrays were required in the construction.
For example, for each microarray cell, the bioFET transistor was expected to occupy a square area of 50 mX50 m. This size is needed to accommodate the array spotter requirements. The spotter resolution limitations also required that the spacing between the cells be set at 200 m, edge to edge. Such spacing allows a lot of unused space between the cells that is sufficient to incorporate any auxiliary circuits. Therefore, all operational amplifiers and differential circuits were placed within these spaces. Several different microarrays were implemented in the design.
Each of these microarrays was required to be electrically isolated from all others. Examples of the arrays constructed were the following:

1. A 7x7 Array of 50 mX50 m P-type bioFETs, with separate drain connections but shared source and body connections.
2. A 7x7 Array of 50 mX50 m N-type bioFETs, with separate drain connections but shared source and body connections.
3. A 7x7 Array of 50 mX50 m P-type bioFETs, with separate drain connections but shared source and body connections. Each bioFET
was connected in a common-source fashion to a high-impedance active load. The output was read using an operational amplifier configured as a unity gain buffer.
4. A 7x7 Array of 50 mX 1 mX2l P-type multi-fingered bioFETs, with separate drain connections but shared source and body connections.
Each bioFET was connected in a common-source fashion to a high-impedance active load. The output is read using an operational amplifier configured as a unity gain buffer.
5. A 14x7 array, consisting of 7x7 pairs of bioFETs. Each bioFET was connected in common source mode, and the outputs of each pair were passed to differential amplifiers. The output of the differential was read by a unity gain buffer. Only one of the two bioFETs would undergo hybridization. This array is designed to reject any signal fluctuations that are common to both bioFET devices, such as those created by temperature and pH variations.

[0075] Fig. 8 shows schematic diagrams of the circuits that were implemented in these arrays. In addition, a large square area of 2.5mmx2.5mm was required for monitoring the etch process during post-processing. This region consisted of bare polysilicon deposited on top of the substrate, with the insulator in between. A connection was provided to the periphery of this area to drain away any charges that might leak into the substrate during the etch process. Etch monitoring is important to ensure that the insulator underneath the polysilicon is not damaged during the etching process.

[0076] The layout of the final chip is shown in Fig. 9. The chip has a size of l Ommx 10mm, and is surrounded by 260 pads, in addition to two pads that are placed closer to the center of the chip. These two pads are introduced to serve as reference electrodes when the electrolyte is applied to thp surface of the chip. The number of pads was not sufficient for all different arrays and some of them had to be shared by two different arrays.
Specifically, the drain connections of each of the bioFETs in arrays 1 and 2 share a single pad.

[0077] To facilitate post processing, several alignment marks were placed on the chip. These consisted of squares of the top metal layer, located in different areas around the chip. These marks provided landmarks that were used for aligning the etch mask with the chip during post-processing.
Finally, it is important that there be clearance spacing between the outermost pads and the sliced edge of the chip. A clearance of 0.75mm was required to guard against edge bead formation during the deposition of PDMS onto the chip during post-processing.

[0078] The main circuit component that required proper design in this chip was the operational amplifier. Many different topologies for CMOS
operational amplifiers exist. The topology chosen was that of a folded cascode op-amp. This topology allowed for higher gains to be achieved from a single stage. The body effect in the cascode transistor enhances the gain performance of the amplifier, contrary to the case of cascaded amplifiers. Finally, compensation capacitors in a cascade transistor need not be as large as that for a regular two stage op-amp. This is because the capacitance can be placed across two stages, which are the output node and the cascode stage, as opposed to one stage in the cascaded two stage amplifier case. One challenge of using this topology was that it allowed for some common-mode gain, even with perfectly matched differential transistors and current sources.
[0079] Fig. 10 shows the schematic diagram of the operational amplifier.
Transistors M1 and M2 form the input differential pair, with M3 and M4 as active loads. Transistors M5 and M6 form the cascode pair, and a feedback connection to the gates of the active load provide the differential to single-ended conversion. The single ended output was applied to an output common source stage, which provided the final output pin of the amplifier. Using a common source output stage instead of a common-drain mode is justified because the operational amplifier operates in unity feedback mode. Thus, its output resistance is roughly divided by the open-loop gain, which will be quite high. The reason for using an amplifying stage at the output is to obtain a high output dynamic range, which will be limited only by the onset of linear operation of the output transistors. If this last stage were a common-drain stage, then the factor that would determine the dynamic range would be the overdrive voltage of the output transistor, which would be determined by the gate bias. If high dynamic range is required, then the gate bias of the output PMOS would have to be quite high, necessitating a higher gate bias for the cascode transistors to keep them saturated. However, it was desired to have a cascode bias of zero volts to minimize the extra circuitry required to bias voltage generation.
[0080] The current driving requirement for the operational amplifier was chosen at 100 A. Given the large number of op-amps in the chip, higher output drive capabilities may heat up the chip and cause undesirable effects to the bioFET sensors. To find the required gate bias voltage of the output PMOS transistor, a value of 100 A was used as the quiescent drain current, and set the output voltage to zero. This minimizes the offset voltage of the op-amp. Recognizing the presence of large-signal variations at the output, the calculated bias was adjusted to keep the output transistor in saturation under the harshest signal swings (chosen here as 1 volt).
From hereon, the analysis continued backwards, with the cascode transistors, active loads, and finally the input differential pair. In each step, conditions were imposed to guarantee that the device stayed saturated, the appropriate voltage values were determined, and the sizes were calculated based on the currents that flowed in the branches. The total current consumption in the internal stages of the op-amp was also chosen as 100 A, divided equally among the different conduction paths. Based on these current values and the DC voltages on the nodes that would guarantee saturation, the sizing of the different devices was deduced. The current sources in Fig. 10 were implemented using a stacked transistor pair. This had the effect of increasing the output resistance and made the circuit behave more like an ideal current source. The biasing of these transistors was chosen so as to maintain the saturation region of operation. The biasing was kept as low as possible so that the current source had a higher range of operation. This further enhanced the dynamic range of the device.

[0081] Figs. lla) and b) show the simulated frequency response and the voltage transfer characteristics of the designed op-amp, respectively. The dynamic range spanned around 4 volts, and the low frequency gain was simulated at 83 dB. The bandwidth for the uncompensated op-amp is shown to be around 35kHz. However, to guarantee stability of the op-amp with unity feedback, a Miller compensation capacitor was added at the terminals shown in Fig. 12. The cascode configuration allowed for the placement of the capacitor over a large inverting gain, consisting of the output stage and the cascode stage. This resulted in a smaller capacitance value and higher stability. The compensated op-amp had a bandwidth of 8kHz, a gain margin of 7.633 dB, and a phase margin of 35 . Fig. 13 shows a compact layout of the op-amp, in which it is clear that the compensating capacitor occupies a considerable area of the design. The following table shows the performance parameters of a sample operational amplifier of the invention, compared with typical values of general purpose CMOS op-amps.

Sample Performance Parameters of a Designed Operational Amplifier Parameter Designed Op-Amp Typical Open-loop gain 85dB 74dB
CMRR 124dB 80dB
Open-loop bandwidth 35kHz (5kHz with 100Hz-100kHz compensation) Output resistance 7.8kS2 3000-lOks2 Slew rate 12.5V/ s (9.5 V/ s with 2-20V/ s IOpF load) Offset voltage -0.58mV 0.1-1mV
Gain margin 7.63dB -Phase margin 35.3 >60 Power consumption imW 0.5-10mW
PSRR 74dB 80dB

[0082] The foregoing has constituted a description of specific embodiments showing how the invention may be applied and put into use.
These embodiments are only exemplary. The invention in its broadest, and more specific aspects, is further described and defined in the claims which now follow.

[0083] These claims, and the language used therein, are to be understood in terms of the variants of the invention which have been described. They are not to be restricted to such variants, but are to be read as covering the full scope of the invention as is implicit within the invention and the disclosure that has been provided herein.

Claims

THE EMBODIMENTS OF THE INVENTION IN WHICH AN
EXCLUSIVE PROPERTY OR PRIVILEGE IS CLAIMED ARE
DEFINED AS FOLLOWS:

1. A microarray comprising one or more electrical configurations of bioFET's arranged in a manner as to enhance sensitivity of the device to charge sensing due to the presence or hybridization of biomolecules, wherein said configurations are chosen from the group consisting of:

a) CMOS inverter configuration, biased as an inverting amplifier;
b) CMOS inverter configured as an inverting amplifier with active, diode connected to load;
c) CMOS inverter configured as an inverting amplifier with active independently biased load;
d) CMOS common-source amplifier configuration with negative resistance load;
e) CMOS ring oscillator configuration with bioFET as an inverter stage ;
f) CMOS ring oscillator configuration with bioFET as a load capacitor;
g) General LC oscillator configuration with bioFET as load capacitor;
h) Mismatched analog circuit configuration; and i) Floating charge device configuration with leakage current monitoring.

2. The microarray of claim 1 further having a pre-processing module comprising filtration, cell lysis, biomolecule concentration and amplification sections.

3. The microarray of claim 1 further having a post processing module comprising RF transmission and reception sections, power source and antenna.

4. The microarray of claim 2, wherein said pre-processing module consists of an electrokinetic filtration section using active reverse flow of fluid for filter regeneration to increase filter capacity.

5. The microarray of claim 2, wherein said pre-processing module consists of a cell lysis section constructed with a porous region and solvent exchange capability.

6. The microarray of claim 2, wherein said pre-processing module consists of a biomolecule concentration region constructed with a porous region which has preferential adsorption of and retention of biomolecules in certain chemical condition and release in other condition.