US20100260745A1 - Methods of using and constructing nanosensor platforms - Google Patents

Methods of using and constructing nanosensor platforms Download PDF

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US20100260745A1
US20100260745A1 US12/680,833 US68083308A US2010260745A1 US 20100260745 A1 US20100260745 A1 US 20100260745A1 US 68083308 A US68083308 A US 68083308A US 2010260745 A1 US2010260745 A1 US 2010260745A1
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nanosensor
silicon
disease
nanowire
nanomaterial
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Chongwu Zhou
Mark E. Thompson
Richard James Cote
Fumiaki Ishikawa
Marco Curreli
Hsiao-Kang Chang
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University of Southern California USC
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6816—Hybridisation assays characterised by the detection means
    • C12Q1/6825—Nucleic acid detection involving sensors
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B82—NANOTECHNOLOGY
    • B82Y—SPECIFIC USES OR APPLICATIONS OF NANOSTRUCTURES; MEASUREMENT OR ANALYSIS OF NANOSTRUCTURES; MANUFACTURE OR TREATMENT OF NANOSTRUCTURES
    • B82Y15/00—Nanotechnology for interacting, sensing or actuating, e.g. quantum dots as markers in protein assays or molecular motors
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B82—NANOTECHNOLOGY
    • B82Y—SPECIFIC USES OR APPLICATIONS OF NANOSTRUCTURES; MEASUREMENT OR ANALYSIS OF NANOSTRUCTURES; MANUFACTURE OR TREATMENT OF NANOSTRUCTURES
    • B82Y30/00—Nanotechnology for materials or surface science, e.g. nanocomposites
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N27/00—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means
    • G01N27/26—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means by investigating electrochemical variables; by using electrolysis or electrophoresis
    • G01N27/403—Cells and electrode assemblies
    • G01N27/414—Ion-sensitive or chemical field-effect transistors, i.e. ISFETS or CHEMFETS
    • G01N27/4146—Ion-sensitive or chemical field-effect transistors, i.e. ISFETS or CHEMFETS involving nanosized elements, e.g. nanotubes, nanowires
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/154—Methylation markers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10T—TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
    • Y10T436/00—Chemistry: analytical and immunological testing
    • Y10T436/14—Heterocyclic carbon compound [i.e., O, S, N, Se, Te, as only ring hetero atom]
    • Y10T436/142222—Hetero-O [e.g., ascorbic acid, etc.]
    • Y10T436/143333—Saccharide [e.g., DNA, etc.]

Definitions

  • the invention relates to the field of biotechnology; specifically, to nanosensor platforms and detection of a disease and condition.
  • a diversity of sensor architectures have been designed and fabricated during the last decade that utilize different nanomaterials as a sensing element (cantilevers, quantum dots, nanotubes, nanowires, nanobelts, nanogaps, and nanoscale films).
  • Some of these sensing devices such as those based on cantilevers and quantum dots are highly specific, ultra sensitive, and have short response times.
  • many of these devices require integration with optical components in order to translate surface binding phenomena into a readable signal.
  • the need for detection optics is expected to significantly increase the cost of operation for such a device.
  • Serum is a source of protein and nucleic acid biomarkers, and, by its very nature, can reflect organ-confined events.
  • Use of single biomarkers provides only a limited sensitivity and specificity for detection.
  • Prostate specific antigen (PSA) for prostate cancer screening for example, is one of the few examples of a single cancer marker that has been used in cancer screening, and it has been shown to be problematic due to its lack of specificity.
  • use of a multi-marker approach has been shown to add specificity and sensitivity to screening.
  • Many diseases and conditions, such as cancer are characterized by a number of molecular alterations and make multiple marker assays critical for successful, early detection of the disease and/or condition.
  • a nanosensor comprising a nanomaterial configured for electrical signaling, and one or more capture agents distributed on a surface of the nanomaterial, where the nanosensor is configured such that binding of a target molecule to one of the one or more capture agents causes a change in electrical signaling.
  • the change in electrical signaling is a change in conductance, current, transconductance, capacitance, threshold voltage, or combinations thereof.
  • the capture agent comprises a polynucleotide and/or polypeptide.
  • the capture agent comprises an aptamer, a receptor, a ligand, or a combination thereof.
  • the nanomaterial comprises a carbon nanotube.
  • the nanomaterial is fabricated by patterned growth of carbon nanotubes.
  • the nanomaterial may also comprise an In 2 O 3 nanowire.
  • the change in transconductance is calibrated by liquid gate measurement.
  • the target molecule comprises an analyte.
  • the target molecule comprises a biomolecule.
  • the presence or absence of the biomolecule is indicative of a molecular signature associated with a disease.
  • a complementary detection system comprising an orthogonal functionalization of a nanomaterial with a substrate.
  • the nanomaterial comprises a carbon nanotube and/or an In 2 O 3 nanowire.
  • the substrate comprises Si/SiO 2 .
  • inventions include a method of preparing a biosensor to detect the presence of a molecular signature associated with a disease, comprising providing a biosensor comprising one or more pairs of interdigitated source and drain electrodes, and fabricating a plurality of nanowires on the one or more pairs of interdigitated source and drain electrodes.
  • the nanowire comprises In 2 O 3 .
  • the IN 2 O 3 was grown on a substrate.
  • the one or more interdigitated source and drain electrodes each have a channel length of between 1 micron and 100 microns and a channel width of between 100 microns and 1000 microns.
  • the interdigitated source and drain electrodes each have a channel length of about 2.5 microns and a channel width of about 500, about 780, and/or about 2600 microns.
  • Other embodiments include a method of preparing a biosensor array, comprising placing a quantity of poly-silicon and/or a quantity of amorphous-silicon on an insulating substrate, and incorporating the quantity of poly-silicon and/or the quantity of amorphous-silicon as a component of the biosensor array.
  • biosensor array comprising a thin-film semiconductor patterned into one or more nanowires.
  • nanosensor platform comprising a field effect transistor configured with a plurality of interdigitated electrodes and nanowire, and a poly/amorphous silicon-on-insulator where the poly/amorphous silicon-on-insulator is a component of the field effect transistor.
  • the nanowire comprises In 2 O 3 .
  • Various embodiments include a method of fabricating a nanotube biosensor, comprising preparing a catalyst, growing aligned nanotubes by utilizing prepared catalyst; and defining metal electrodes separated by the aligned nanotubes.
  • growing aligned nanotubes comprises a chemical vapor deposition growth of the nanotube with methane, ethylene, hydrogen and/or CO as feedstock.
  • growing aligned nanotubes comprises using sapphire and/or quartz as a substrate.
  • Other embodiments include a method of attaching elastomer polydimethylsiloxane to a silicon/silica surface, comprising treating the silicon/silica surface with a linker molecule, and attaching the elastomer polymethylsiloxane to the silicon/silica surface.
  • the linker molecule comprises silicic acid and/or alkyl silane.
  • the linker molecule comprises a silicon compound.
  • Various embodiments include calibrating the response of a nanosensor platform, comprising extracting one or more electronic properties of the nanosensor platform, and calibrating the response from the one or more electronic properties extracted from the nanosensor platform.
  • one of the one or more electronic properties comprises transconductance.
  • transconductance is defined by dividing by dIds/dVg.
  • the transconductance is defined by dividing by dlogIds/dVg.
  • Various embodiments include an apparatus for detecting and/or monitoring a disease, comprising a nanomaterial, and a plurality of capture molecules bound to the nanomaterial, where the plurality of capture molecules are configured for recognizing one or more biomolecules associated with a molecular signature of the disease.
  • the capture molecule comprises a polypeptide.
  • the capture molecule comprises a polynucleotide.
  • the capture molecule comprises an aptamer.
  • the capture molecule comprises a polynucleotide complex.
  • Other embodiments include a method of determining the presence of a disease in an individual from whom a sample is obtained, comprising removing background noise from the sample, providing a nanosensor device configured to detect the presence or absence of a multimarker signature of the disease, and contacting the nanosensor device with the sample to determine the presence or absence of the multimarker signature of the disease, where the presence of the multimarker signature is indicative of the disease.
  • Other embodiments include removing the background noise by functionalization of the nanosensor device with one or more molecules that prevent binding of a nontarget entity.
  • Other embodiments include removing the background noise by amplifying binding signals of the nanosensor device.
  • Other embodiments include amplifying binding signals of the nanosensor device using a sandwich assay.
  • Other embodiments include removing the background noise by preprocessing the sample to remove a major interfering component.
  • Other embodiments include a method of treating a disease, comprising providing a nanosensor device configured to detect the presence or absence of a molecular signature of the disease, contacting the nanosensor device with the sample to determine the presence or absence of the molecular signature of the disease, and treating the disease.
  • Various embodiments also include a method of improving the sensitivity of a nanosensor, comprising providing a nanosensor, and performing biosensing measurements by liquid gate voltage and/or back gate voltage to improve the sensitivity of the nanosensor.
  • Other embodiments include a method of preparing a biosensor array, comprising placing a quantity of semiconductor film on a substrate, and incorporating the quantity of semiconductor film as a component of the biosensor array.
  • the semiconductor film comprises single-crystal silicon.
  • the semiconductor film comprises poly-crystal and/or amorphous silicon.
  • FIG. 1 depicts, in accordance with an embodiment described herein: (a) Optical micrograph of devices on complete 3′′ wafer. (b) optical micrograph of channel area with interdigitated source and drain electrodes. (c) SEM image of an In 2 O 3 NW between the source and drain electrodes. (d) family of source-drain current (I ds ) versus source-drain voltage (V ds ) plot under different gate voltage (V g ). The step of V g is 1 V. (e) I ds versus V g plots in linear (left) and log (right) scale.
  • FIG. 2 depicts, in accordance with an embodiment described herein, SEM image of In 2 O 3 nanowires dispersed on a Si/SiO 2 substrate with (a) high density and (b) low density. Statistical analysis of device yield with (c) high density nanowires and (d) low density nanowires.
  • FIG. 3 depicts, in accordance with an embodiment described herein, a histogram of threshold voltage of In 2 O 3 nanowire devices on a Si substrate capped with 50 nm SiO 2 .
  • FIG. 4 depicts, in accordance with an embodiment described herein, a process of making top-down fabrication of silicon nanowire using poly/amorphous silicon-on-insulator.
  • (a) depicts poly-silicon or amorphous-silicon 100 deposited on appropriate substrates, such as dielectric 101 and silicon 102 ;
  • (b) depicts active layer mesa defined using photolithography and reactive ion etching (RIE);
  • (c) depicts ion implantation done to create degenerate lead-in, and doped region 103 ;
  • RIE reactive ion etching
  • RIE reactive ion etching
  • (c) depicts ion implantation done to create degenerate lead-in, and doped region 103 ;
  • (d) depicts annealing done to activate the doped region 103 ;
  • (e) depicts e-beam writing and RIE is used to define nanowires with desired width;
  • (f) depicts metal contacts 104 created using
  • FIG. 5 depicts, in accordance with an embodiment described herein, schematic diagram of fabrication of biosensor arrays using aligned carbon nanotubes.
  • (a) depicts catalyst 105 preparation;
  • (b) depicts aligned carbon nanotube 106 growth
  • (c) depicts metal electrode 107 definition.
  • FIG. 6 depicts, in accordance with an embodiment described herein, images of biosensor array using aligned carbon nanotubes.
  • FIG. 7 depicts, in accordance with an embodiment described herein, (a) histogram of aligned nanotube device resistance, and (b) IgG detection using an anti-IgG antibody decorated aligned nanotube biosensor, where the inset shows the schematic diagram of the device structure.
  • FIG. 8 depicts, in accordance with an embodiment described herein, typical density of CNTs that yields high on/off ratio devices.
  • FIG. 9 depicts, in accordance with an embodiment described herein, typical electrical characteristics where source-drain current (Ids) versus source-drain voltage (Vds) under different gate voltage (Vg) are plotted. I-Vgf and I-Vdsf. The clearly separated curves indicate the good sensitivity of the device to the gate voltage, which led to improved sensitivity of the device. (a) depicts Vds(V); (b) depicts Vg(V).
  • FIG. 10 depicts, in accordance with an embodiment described herein; the sensing of SA with a device using semiconductive nanotube network.
  • the device showed ⁇ 1% conductance drop upon exposure to a solution of SA at 100 pM, and further addition of SA at higher concentrations gave large conductance drops as shown (a).
  • a device using mixed nanotube network showed only negligible response ( ⁇ 1%) when exposed to 2 nM SA as shown (b), indicating that the lowest detection limit of mixed nanotube network devices is at least lower by a factor of 20 compared to semiconductive nanotube network devices.
  • the comparison of magnitude of responses to SA at different concentrations revealed the enhanced sensitivity of semiconductive nanotube network devices over mixed nanotube network devices, confirming the advantage of the use of semiconductive nanotube network as biosensors.
  • FIG. 11 depicts, in accordance with an embodiment described herein, the general structure of a bifunctional molecule.
  • (a) depicts an example of a bifunctional molecule, as described herein.
  • (b) depicts an example of a bifunctional molecule as described herein.
  • the molecule may be SiCl 4; or for example, the molecule may be Si(OR) 4 where R is alkyl or H.
  • FIG. 12 depicts, in accordance with an embodiment described herein, (a) a schematic diagram of the measurement setup, where to extract parameters used to calibrate sensor responses, liquid gate measurement was employed; with (b) depicting a typical Ids-Vg curve.
  • FIG. 13 depicts, in accordance with an embodiment described herein, typical Ids-Vg curves before/after the exposure of the device to a solution of Streptavidin, with an inset of a SEM image, showing. Streptavidin molecules tagged with 10 nm Au nanoparticles captured by an In 2 O 3 nanowire functionalized with biotin.
  • FIG. 14 depicts, in accordance with, an, embodiment described herein, the successful normalization of the absolute response and relative response by dividing them by dIds/dVg and dlogIds/dVg, respectively.
  • (a) shows absolute responses plotted against device identification number together with an average of the response before the calibration.
  • the normalized device responses absolute response/dIds/dVg
  • the smaller deviation was verified by taking coefficient of variation (CV), which is one standard deviation divided by the mean.
  • CV coefficient of variation
  • FIG. 14 shows, in accordance with, an, embodiment described herein, the successful normalization of the absolute response and relative response by dividing them by dIds/dVg and dlogIds/dVg, respectively.
  • SA Streptavidin
  • SA Streptavidin
  • the device When the device was exposed to SA of 10, 100, and 1,000 nM, the device showed increased normalized conductance by 1, 2, and 10%, respectively.
  • FIG. 16 depicts the structure of some intercalating molecules.
  • FIG. 17 depicts, in accordance with an embodiment described herein, a schema of peptide nucleic acids binding modes for targeting double-stranded DNA.
  • FET field effect transistor
  • NT means nanotube
  • NW nanowire
  • SOI Silicon-On-Insulator
  • RIE reactive ion etching
  • CVD means chemical vapor deposition
  • DI de-ionized
  • CNT carbon nanotubes
  • PMMA poly(methyl methacrylate).
  • PDMS means elastomer polydimethylsiloxane
  • CV means coefficient of variation
  • SA Streptavidin
  • PNA peptide nucleic acid
  • aptamers are molecules that may bind to a target molecule with specificity.
  • top-down fabrication of nanowire technologies start with bulk materials and reduce the material dimensions using various techniques to cut, pattern, etch, and shape these materials into the desired geometry and order.
  • bottom-up approach involves preparing the nanowire from molecular precursors, rather than starting with the bulk semiconductor.
  • background noise refers to false or disruptive signals received when performing an assay to determine the presence or absence of analyte or a molecule of interest.
  • background noise may result when an analyte possesses a low net charge.
  • the analyte is present at trace levels in a complex mixture of biomolecules, such as blood, serum or urines.
  • “intercalating” refers to the ability to insert into an existing structure, such as a polynucleotide sequence.
  • Treatment and “treating,” as used herein refer to both therapeutic treatment and prophylactic or preventative measures, wherein the object is to achieve beneficial results even if the treatment is ultimately unsuccessful.
  • the inventors created nanobiosensors that are based on nanoscale FETs.
  • the inventors prepared the PEI with a desired nanomaterial between source and drain electrodes, and then coated the nanomaterial with a molecular coating designed to bind a specific biomolecule or analyte.
  • the binding of the target biomolecule and/or analyte to the nanobiosensor leads to a significant change in the environment surrounding the nanowire and/or nanotube, and a change in the transconductance of the device is detected.
  • the high sensitivity for the device stems from the high surface to bulk ratio for nanowires and nanotubes, such that a small amount of biomolecule or analyte binding leads to a significant shift in the electronic properties of the nanoscale semiconductor.
  • the inventors utilized complementary detection based on two material systems: carbon nanotubes and In 2 0 3 nanowires.
  • the inventors based their choice of nanomaterials on the need to achieve differential functionalization of the active sensing nanomaterials and the supporting substrates.
  • Si/SiO 2 substrates are the substrates of choice for most biosensing applications, using silicon nanowires would preclude selective functionalization of Si nanowires and Si/SiO 2 substrates with different functional groups, and an unwanted consequence is that antibodies and antigens, very often expensive and of minute quantity, would bind to both the nanowire and substrates.
  • orthogonal functionalization of carbon nanotubes, In 2 O 3 nanowires and Si/SiO 2 substrates can be easily achieved.
  • One aspect of the invention includes passivating the substrate and surrounding channel at the upper stream of the microfluidic channel with antibodies and aptamers that can bind to the high-concentration proteins in serum samples that are not relevant to cancer detection, therefore effectively providing filtration of the serum sample before arriving at the nanosensors.
  • the present invention provides a nanobiosensor where a nanomaterial is placed between a source and drain electrode.
  • the nanobiosensor is based on a nanoscale FET.
  • the nanomaterial is a nanowire and/or nanotube.
  • the nanomaterial is a carbon nanotube and/or In 2 0 3 .
  • the nanomaterial is coated with a molecular coating.
  • the molecular coating is designed to bind a specific biomolecule and/or analyte.
  • the binding of the target biomolecule and/or analyte causes a change in the environment surrounding the nanomaterial.
  • the binding of the target biomolecule and/or analyte causes a change in transconductance. In another embodiment, the binding of the target biomolecule and/or analyte causes a significant shift in the electronic properties of the nanoscale semiconductor.
  • the nanobiosensor utilizes a complementary detection system. In another embodiment, the complementary detection system undergoes an orthogonal functionalization of carbon nanotubes, In 2 O 3 nanowires and/or Si/SiO 2 substrates. In another embodiment, the nanosensor uses interdigitated electrodes. In another embodiment, there is a filtration of a sample before arriving at the nanobiosensor.
  • any number of molecular coatings that are designed to bind a specific biomolecule or analyte may be used in conjunction with the various embodiments described herein, such as a polynucleotide, polypeptide, antibody, PNA, aptamer, receptor, ligand, or any number of combinations thereof.
  • aptamers offer an advantage of being small in size and thus changes in charge distribution due to binding of target molecules can occur closer to the surface of the nanobiosensor and thus increase the signal intensity.
  • aptamers may tolerate harsher environmental changes which could result in longer shelf life and tolerate a wide variety of functionalization procedures.
  • the inventors used interdigitated electrodes to achieve an easy and reliable fabrication of nanowire field effect transistor biosensors with improved uniformity and yield, as compared to devices fabricated with non-interdigitated electrodes.
  • an analysis necessary to monitor the concentration of biomarkers associated with the progress of many diseases it is essential that there is a high yield of acceptable performing devices and uniform device performance (little device to device variation).
  • the inventors employed interdigitated electrodes to increase the effective channel width for the fabrication of nanobiosensor using a bottom up approach. Examples are depicted in FIGS. 1 , 2 and 3 .
  • interdigitated electrodes resulted in increasing the probability/number of the randomly dispersed nanowires to bridge between source and drain, while keeping the same footprint.
  • devices fabricated with interdigitated electrodes have a more uniform performance with higher yield compared to devices with non-interdigitated electrodes, and the yield and uniformity of the devices are comparable to those achieved with assembling assisted techniques.
  • This method has numerous advantages over the existing prior art, such as simplicity, scalability, reproducibility, high throughput, and room temperature processing.
  • the present invention provides a nanowire biosensor with interdigitated electrodes.
  • the interdigitated electrodes increase the probability and/or number of nanowire to bridge between source and drain.
  • the present invention provides a method of fabricating a nanowire biosensor by the following steps, or any combination thereof: (1) In 2 O 3 nanowire is suspended in isopropanol by sonication; (2) the solution is dispersed onto a complete 3′′ Si/SiO 2 substrate, followed by definition of Ti/Au source and drain electrodes by photolithography.
  • the In 2 O 3 nanowire is previously grown on a Si/SiO, substrate via a laser ablation process.
  • the interdigitated electrodes have a channel length of 1 micron to 20 microns, with a preferred length of about 2.5 microns.
  • the interdigitated electrodes have an effective channel width of 10 microns to 5000 microns.
  • the interdigitated electrodes have an effective channel width of about 500 microns, 780 microns and/or 2600 microns.
  • the inventors used a top-down fabrication of silicon nanowire using poly/amorphous silicon-on-insulator.
  • An example is depicted in FIG. 4 .
  • the inventors are able to reduce the cost significantly, while keeping the advantage of top-down, foundry compatible fabrication that results in high yield and small device-to-device variation.
  • amorphous-silicon can be deposited on unconventional rigid/flexible substrates such as glass and PET, which further reduces the cost of production.
  • the present invention provides a nanowire biosensor with a poly-silicon and/or amorphous silicon in a silicon-on-insulator wafer.
  • the amorphous silicon is deposited on an unconventional substrate.
  • the unconventional substrate is glass and/or PET.
  • the present invention provides a top-down fabrication of silicon nanowire using three kinds of samples: single-crystal silicon-on-insulator, polysilicon film deposited on a substrate, and amorphous silicon film deposited on a substrate.
  • the present invention provides a method of fabricating a nanowire biosensor by the following steps, or any combination thereof: (1) Poly-silicon and/or amorphous-silicon is deposited on an appropriate substrate, or single-crystal silicon-on-insulator wafer is used as the starting substrate; (2) an active layer mesa is defined using photolithography and reactive ion etching; (3) ion implantation is done to create degenerate lead-in; (4) annealing is performed to activate the dopants; (5) c-beam writing and reactive ion etching is used to define nanowires with the desired width; (6) metal contacts are created using photolithography and lift-off technique.
  • the present invention provides a method of fabricating a nanowire biosensor by patterning a semiconductor film deposited on a substrate into nanowires via patterning and etching.
  • the semiconductor film may include single-crystal silicon, polysilicon, amorphous silicon, or materials such as GaAs, InP, and/or GaN.
  • the inventors developed a novel and straightforward approach for manufacturable and scalable biosensor arrays based on patterned growth of aligned carbon nanotubes at desired locations.
  • An example is depicted in FIGS. 5 , 6 and 7 .
  • This approach has several advantages, such as the capacity for mass production due to the use of conventional fabrication processes without e-beam writing; uniform and reproducible device performance due to the use of multiple nanotubes; and deterministic construction of biosensor arrays at specific locations and at any array size.
  • Use of ordered nanotube arrays offers many important advantages, since the orientation control eases and increases the reproducibility of the sensor array fabrication.
  • the architecture is fault tolerant: the destruction of one channel leaves other channels open, providing a conduction pathway between source and drain. This approach to nanosensor array fabrication may be used as the basis for a multiplexed nanobiosensor array fabrication.
  • the present invention provides a biosensor array that utilizes highly aligned nanotubes as a semiconductor.
  • the nanotubes are single walled carbon.
  • the nanotubes are used for the detection of biomolecules.
  • the nanotube biosensor may be used to detect IgG antigen.
  • the nanotube biosensor may be functionalized with anti-IgG antibody by soaking in a solution of anti-IgG antibody in PBS buffer for about 12 hours at 4° C.
  • the present invention provides a method of fabricating a nanotube biosensor by the following steps, or any combination thereof: (1) catalyst preparation; (2) aligned carbon nanotube growth; and (3) metal electrode definition.
  • the catalyst preparation includes one or more of the following: Quartz substrates are photolithographically patterned to make openings for catalysts; a solution of ferritin (Sigma) in de-ionized (D.I.) water is dropped onto the substrates, and kept for 10 min; the substrates are rinsed with D.I. water, and the photoresist layer is lifted off in acetone; the substrate with ferritin particles is calcinated at 700° C. for 10 min to form iron oxide nanoparticles that act as catalysts.
  • D.I. de-ionized
  • the aligned carbon nanotube growth includes a chemical vapor deposition (CVD) growth of CNTs with 2,500 sccm of Methane, 10 sccm of Ethylene, and 600 sccm of Hydrogen at 900° C. for 10 min, resulting in allocation of oriented. CNTs at specific positions.
  • the metal electrode definition includes metal electrodes, 10 nm Ti and 30 nm Au, are defined using photolithography and lift off technique.
  • the spacing between adjacent devices is approximately 20 ⁇ m.
  • the inventors used semiconductive nanotube network as the active channel of biosensors to improve sensitivity. Examples are depicted herein as FIGS. 8 , 9 and 10 . Devices with high on/off ratio (indication of semiconductivity of the nanotube network) were successfully fabricated using carbon nanotube network where the density of the nanotube was carefully tuned.
  • the inventors employed semiconductive nanotube network as the active channel of a biosensor, and improved the sensitivity (lowest detection limit) by more than 20 times compared to devices with mixed nanotube (both metallic and semiconductive nanotubes) network. Preparation of such semiconductive network was done by controlling the nanotube density to overcome the percolation limit for semiconductive nanotubes and not to overcome that for metallic nanotubes. This method does not require any pre/post treatments on the devices, and is easily applicable to wafer scale or even larger scale production.
  • the present invention provides a biosensor array that utilizes a semiconductive nanotube network as the active channel.
  • the semiconductive nanotube network provides an improved sensitivity.
  • the present invention provides a method of fabricating a nanotube biosensor by growing single-walled carbon nanotubes on a degeneratively doped Si wafer with 500 nm SiO 2 on top via chemical vapor deposition method with Fe nanoparticles formed from ferritin molecules as catalysts.
  • the nanotube biosensor is made by one or more of the following steps: (1) Diluted solution of ferritin in De-ionized water (D.I. water) is put on the Si/SiO 2 wafer and kept for 1 h at room temperature, resulting in deposition of ferritin molecules onto the substrate; (2) the substrate is washed with D.I. water, followed by calcination in air at 700° C.
  • D.I. water De-ionized water
  • the substrate is placed in a quartz tube that was heated to 900° C. in hydrogen atmosphere, and once the temperature reaches 900° C., methane (1300 sccm), ethylene (20 sccm), and hydrogen (600 sccm) are flowed into the quartz tube for 10 min, which yields a CNT network on the substrate; (4) following the growth is patterning of source-drain electrodes, done by photolithography and lift off technique; (5) oxygen plasma is then performed for 1 min in order to etch unwanted CNTs while covering the channel areas with poly(methyl methacrylate) (PMMA).
  • the metal electrodes are made of 10 nm Cr and 30 nm Au.
  • the channel width and length of the resultant devices are 5 mm and 100 ⁇ m, respectively.
  • Nanosensor Platforms Attachment of PDMS Chips to Silicon/Silica Oxide Surfaces
  • the inventors have developed novel techniques to attach PDMS chips to a silicon/silica surface.
  • attachment of PDMS to silicon/silica surfaces has been achieved mostly via the generation of highly reactive radical species on the PDMS surface via oxygen plasma activation, which can react with OH group present on the silicon/silica surface.
  • the OH groups on the silicon/silica must be vertically aligned with the radicals on the PDMS surface.
  • the larger the number of successful reactions the stronger the adhesion of PDMS to silicon/silica.
  • the Si/SiO 2 chip at the end of nanowire/nanotube growth process is highly dehydrated with a significantly reduced number of OH groups on its surface.
  • a method to generate a large surface density of OH groups on the dehydrate Si/SiO 2 surface would be highly valuable.
  • the inventors have found that treating the Si/SiO 2 surface with a bifuntional molecule, bearing a silane terminal group (where W, Y.
  • Other linker molecules also useful for this purpose would include Si(OH) 4 and Si(OR) 4 as well as alkyl silanes; as used herein, R is an alkyl or H.
  • the present invention provides a method of attaching a PDMS microfluidic chip to a silicon and/or silica surface.
  • the PDMS microfluidic chip is attached by one or more of the following steps: (1) A silane derivative linker molecule is freshly distilled prior to its use; (2) a solution with a concentration of silane derivative in the 2-10% range in methanol is prepared; (3) the silicon/silica surface is cleaned using oxygen plasma (60 Ton O2, 1-10 minute(s)), where if any feature present of the Si/SiO 2 surface is sensitive to 0 2 plasma it can be protected with a layer of PMMA; (4) the silicon/silica surface is submerged in the silane-derivative methanolic solution overnight; (5) unbound silane derivative is washed away with methanol; (6) the PMMA is washed away with hot acetone or anisole; (7) the silicon/silica chip is baked for 1-2 hours at 120° C., and the Si/SiO 2 chip is ready for
  • the inventors have developed a data analysis method to calibrate the sensor response. Examples are depicted herein as FIGS. 12 , 13 and 14 . Because the variation of the sensor responses is decreased, and it is a simple analysis method that does not require intensive efforts, the method is complementary to producing uniform devices.
  • the inventors calibrated the response of In 2 O 3 nanowire biosensor using parameters extracted from transistor measurements, resulting in decrease in coefficient of variation.
  • the inventors have shown that two parameters can be extracted from transistor measurements that can be used to normalize the responses of In 2 O 3 nanowire biosensor. Two definitions of response were employed, one is absolute response, and the other is relative response.
  • the present invention provides a method of calibrating a sensor response.
  • the method of calibrating a sensor response includes extracting parameters from transistor measurements.
  • the parameters include dIds/dVg and/or dlogIds/dVg.
  • the sensor is an In 2 O 3 nanowire biosensor.
  • liquid gate measurement is used to calibrate the sensor response.
  • the calibration includes ⁇ I and/or ⁇ G. In another embodiment, the calibration includes ⁇ I/I and/or ⁇ G/G.
  • liquid gate can be used to tune the sensitivity of biosensors by applying different gate voltage to the liquid gate.
  • the method is applicable to field effect transistor type biosensors.
  • the present invention provides a method of tuning the sensitivity of a biosensor by using a liquid gate.
  • the biosensor includes an In 2 O 3 nanowire.
  • the liquid gate is used to tune the sensitivity of a biosensor by applying different gate voltage to the liquid gate.
  • the present invention provides an apparatus for tuning the sensitivity of a biosensor where a chemical cell made of teflon is mounted onto a device and filled with PBS, and a Pt wire is inserted into the PBS and serves as a gate electrode and/or liquid gate.
  • the inventors have created sensor devices, based on nanowires and/or nanotubes, designed for detection and monitoring of a disease and/or condition.
  • the device may recognize the unique molecular signatures arising upon development of a disease, bacterial or viral contamination, allergic reactions, etc.
  • These devices also use the capturing capabilities of any and all capture molecules such as antibodies, PNA, RNA, DNA and protein aptamers, oligonucleotides including RNA and DNA, receptors, ligands, and any other capture molecules that can detect biomolecules.
  • the detection platform can detect the unique molecular signatures of a specific disease as well as eliminate or reduce the need for multiple tests, thus reducing the total time required to have a final evaluation of the health status of a patient.
  • the present invention provides an apparatus for detecting and/or monitoring a disease and/or condition comprising a sensor device bound to a capture molecule, where the capture molecule may recognize a molecular signature associated with a disease and/or condition.
  • the sensor device includes nanowire and/or nanotube.
  • the capture molecule and/or molecules may be a polynucleotide, polypeptide, antibody, aptamer, receptor, ligand, or combinations thereof.
  • the disease and/or condition is cancer.
  • the present invention provides a method of detecting and/or monitoring a disease by binding a sensor device to a capture molecule, where the capture molecule may recognize a molecular signature associated with a disease and/or condition.
  • the sensor device includes nanowire and/or nanotube.
  • the capture molecule may be a polynucleotide, polypeptide, antibody, aptamer, receptor, ligand, or combinations thereof.
  • the disease and/or condition is cancer.
  • the present invention provides a method of analyzing one or more biomarker signals for the detection of a disease by the following steps, or combinations thereof: (1) Devices based on nanowires or nanotubes are obtained; (2) the surface of the nanomaterial is cleaned; (3) the surface of the each individual device or group of devices on a chip is then functionalized with a particular capture probe; (4) the conductance of the device is monitored over time, while the chip is then placed in contact with the solution under analysis where each single biomarker for a particular disease is captured by its corresponding probe molecule.
  • peptide aptamers and/or protein aptamers as capture agents in multiplex detection of the biomarker for a specific disease, as well as microbial/virus detection, in a sensor device based on nanowire/nanotube.
  • Peptide aptamers are sequences of peptides with a defined three dimensional structure that have shown to bind with high affinity and specificity to a particular biological molecule (protein, etc.).
  • a common example consists of a variable peptide attached at both ends to a protein scaffold, and the variable length is typically comprised of 10 to 20 amino acids.
  • peptide bond (of both peptide and protein aptamers) is stable over a large range of pH values, giving protein aptamers unique robustness. Moreover, peptide and protein aptamers are much smaller in size (2-3 nm and 2-6 KDa) than antibodies causing the captured molecule (analyte) to be spatially closer to the nanowire/nanotube. This analyte-nanowire closeness causes the electric field of the analyte to exert a greater influence on the charge carrier in the device.
  • the present invention is a sensor device for multiplex detection of a biomarker for a specific disease, where the capture molecule is a peptide aptamer and/or protein aptamer.
  • the peptide aptamer and/or protein aptamer is immobilized on the surface of a nanowire.
  • the present invention provides a method of fabricating a biosensor device for multiplex detection of biomarkers by the following steps, or combinations thereof: (1) Devices based on nanowires or nanotubes are obtained; (2) The surface of the nanomaterial is cleaned; (3) The surface of the nanomaterial is then functionalized with a linker molecule; (4) The peptide aptamer or protein aptamer is covalently bound to the linker molecule and thus is immobilized on the nanomaterial surface.
  • background noise can be a significant problem when performing the detection of an analyte in the case in which: (1) The analyte possesses a low net charge. In this case, a technique called sandwich assay can be used to amplify the binding signal. (2) The analyte is present at trace levels in a complex mixture of biomolecules such as blood, serum, or urine. In such mixtures background biomolecules might be present at concentration approaching up to a trillion times the concentration of the analyte.
  • the physiological solution can be preprocessed to remove major serum components (either using pre-processing chromatographic column or by functionalization of the microfluidic channels with “removing agents”) or the surface of the nanomaterial can be functionalized with one or more molecules that diminish any “non-specific” binding event.
  • the physiological solution may be preprocessed by utilizing a solid phase previously modified using capture agents with high affinity for major background components.
  • This solid phase could take on a number of different forms, including beads, modified PDMS microfluidic walls, or a patterned microarray (on a separate chip than the nanosensor array).
  • the capture component is mounted to a stationary support, which the sample is passed over before it reaches the nanosensor.
  • the major background components are removed from the sample, prior to the sample encountering the nanosensor.
  • the sandwich assay is used to amplify the signal from a binding event to detect molecules with low net charges.
  • Traditional nanowire biosensing has usually been done with a two-step approach: attachment of probe molecules followed by binding of the target biomolecules.
  • the inventors propose combining a sandwich antibody assay with nanowire biosensing.
  • the sandwich assay may be performed by one or more of the following steps: First, primary antibodies to target proteins are attached to the NWs. The analyte (containing target proteins) is then delivered to the NWs. After capture of the target proteins, secondary antibodies, directed to the target protein and conjugated to signal enhancer (charged nanoparticles or proteins) are introduced.
  • the secondary antibodies with signal enhancer can increase signal as well as specificity because the target proteins are recognized by two antibodies with the secondary antibodies attached to a signal enhancer.
  • a modified version of the sandwich assay can also be performed to amplify the binding signal when the analyte is a DNA/RNA nucleotide.
  • the hybridized DNA (forming a duplex on the NW surface) can be intercalated using highly charged intercalators such as YOYO1 (as depicted in FIG. 16 ). Small, highly charged molecules such as YOYO1 can insert in the DNA double helix and their molecular charge influences the device conductance.
  • the sandwich assay would not be restricted to the use of proteins.
  • the physiological solution may be preprocessed to remove major biological components;
  • the physiological solution is preprocessed by utilizing a microfluidic system.
  • the preprocessing includes a pre-processing chromatographic column for removal of non-specific proteins and molecules.
  • the physiological solution is pre-processed by attaching antibodies to the major serum proteins to the substrate and/or walls of a PDMS microfluidic channels in order to achieve a “on-chip” removal of non-specific proteins.
  • these techniques significantly reduce the concentration of background proteins in the physiological-sample containing the analyte, reducing the risk of false positives and false negatives.
  • the physiological solution is not-restricted in any way to serum.
  • the preprocessing of the physiological solution may be utilized in conjunction with a variety of molecules in addition to proteins.
  • PEG groups may be added to the nanowire surface to prevent nonspecific bindings of non-specific serum proteins. As disclosed herein, PEG groups on the nanowires will repel proteins that non-specifically might interact with the nanowire surface.
  • capture of double stranded DNA (dDNA) or double stranded RNA (dRNA) may be achieved using either a single strand PNA probe or a double stranded PNA probe immobilized on the surface of a nanowire FET sensor.
  • PNA probes are known to hybridize to double stranded DNA/RNA via “invasion”. An example is depicted herein as FIG. 17 . This invasion interaction will be detected by a nanowire/nanotube FET sensor due to the high molecular charge of the captured dDNA/dRNA.
  • PNA probes are known to hybridize to double stranded DNA/RNA via “invasion”.
  • duplex DNA instead of a single strand DNA allows for a more direct detection by eliminating a pre-analysis step that unfold/melt the dsDNA into two ssDNAs.
  • Another advantage of this strategy is given by the large molecular charge on the duplex DNA whose strong electric field can expert a vast influence on the current carries of the device.
  • the invention may detect a polynucleotide by using a PNA capture probe.
  • biomarkers may be used in conjunction with various embodiments described herein.
  • biomarkers include, but are not limited to, polypeptides, antigens such as glycosylated subunits and lipids, and polynucleotides including microRNA, microsatellite DNA, SNPs, and both genetic and epigenetic.
  • the various embodiments described herein may be used for any number of diseases and conditions.
  • diseases and conditions include, but are in no way limited to, cancer, cariac disease, autoimmune disease, endocrine disease, brain disease, reproductive disease, infectious disease including viruses, prions, bacteria, fungi, yeast, and methods to evaluate prenatal status.
  • Interdigitated electrodes were used to achieve an easy and reliable fabrication of nanowire field effect transistor biosensors with improved uniformity and yield compared to devices fabricated with non-interdigitated electrodes.
  • the inventors employed interdigitated electrodes to increase the effective channel width for the fabrication of nanobiosensor using bottom up approach. These interdigitated electrodes result in increasing the probability/number of the randomly dispersed nanowires to bridge between source and drain, while keeping same footprint.
  • devices fabricated with interdigitated electrodes have more, uniform performance with higher yield compared to devices with non-interdigitated electrodes, and the yield and uniformity of the devices are comparable to those achieved with assembling assisted techniques.
  • This method has several other advantages such as simplicity, scalability, reproducibility, high throughput, and room temperature processing.
  • the fabrication consists of three steps: First, In 2 O 3 NWs (previously grown on a Si/SiO 2 substrate via a laser ablation process developed previously 2 ) were suspended in isopropanol by sonication. The solution was then dispersed onto a complete 3′′ Si/SiO 2 substrate, followed by definition of the Ti/Au source and drain electrodes by photolithography.
  • the interdigitated electrodes were designed to have channel length of 2.5 mm and effective channel width of 500, 780, and 2600 mm.
  • the inventors presented an optical micrograph of In 2 O 3 NW devices with three different geometries on a complete 3′′ wafer, an optical micrograph of the interdigitated electrodes, and a SEM image of an In 2 O 3 NW bridging the source and drain, respectively. As disclosed herein, the inventors showed transport characteristics of a good device, where it is shown source-drain current (I ds ) versus source-drain voltage (V ds ) plots under different gate voltages (V g ), and I ds versus V g plots in linear and log scale.
  • I ds source-drain current
  • V g source-drain voltage
  • the I ds versus V ds plot exhibits transistor behavior similar to MOSFET, and I ds versus V g plot shows good gate dependence of the device with an on/off ratio ⁇ 10 6 .
  • the inventors achieved good device yield >70% by fine-tuning the nanowire density.
  • SEM images are shown of In2O3 nanowire samples with high density and low density. Devices fabricated with these nanowire samples were electrically characterized, and the yield of electrical connection (EC), yield of good devices out of electrically connected source and drain (GD), and total yield of good devices (TGD) were plotted versus the effective channel width.
  • the devices made with high density NWs exhibit 100% EC for the every channel width, while that for devices with low density NWs are from 75% for the smallest channel width to 98% for the longest channel width.
  • This increase in EC for higher density NWs and wider channels can be understood straightforward.
  • the yield of GD (and TGD as a result) decreases as the channel width increases for both high and low density NW samples, and the yields of GD for high density NWs are lower than that for low density NW samples with same channel widths. This may be explained by percolation of “bad” NWs, meaning NWs with little gate dependence, between source and drain electrodes, with analogy to the percolation of metallic nanotube pathway in networked carbon nanotube transistors.
  • the uniformity of the devices was analyzed. As disclosed herein, the distribution of threshold voltage of the devices made on a Si substrate capped with 50 nm SiO2 with a channel width of 2,600 ⁇ m. It exhibits an average value of ⁇ 0.65 V and a standard deviation of 0.25 V, which yield a coefficient of variance of 38.5%. This is only slightly higher than that of Si NW devices assembled with the langmuir Blodgett method (34.6%).
  • Nanowire Sensor Fabrication Top-Down Fabrication of Silicon Nanowire Using Single-Crystal Silicon, Poly-Silicon and/or Amorphous Silicon-on-Insulator
  • the inventors employed poly-silicon and amorphous-silicon as active materials to replace single crystal silicon in Silicon-on-Insulator (SOI) structure to fabricate high-density and uniform arrays of biosensors using a top-down approach.
  • SOI Silicon-on-Insulator
  • the cost is reduced significantly, while keeping the advantage of top-down, foundry compatible fabrication that results in high yield and small device-to-device variation.
  • amorphous-silicon can be deposited on unconventional rigid/flexible substrates such as glass and PET, which further reduces the device price.
  • Nanowire Sensor Fabrication Top-Down Fabrication of Silicon Nanowire Using Single-Crystal/Poly-Crystal/Amorphous Silicon-on-Insulator—Methods of Fabrication
  • the process consists of the following steps:
  • the inventors employed aligned carbon nanotubes to fabricate large, high-density arrays of sensors.
  • the inventors developed a novel and straightforward approach for manufacturable and scalable biosensor arrays based on patterned growth of aligned carbon nanotubes at desired locations. This approach has several advantages over competing techniques in terms of 1) mass production due to the use of conventional fabrication process without e-beam writing, 2) uniform and reproducible device performance due to the use of multiple nanotubes, and 3) deterministic construction of biosensor arrays at specific locations and at any array size.
  • Use of ordered nanotube arrays offer significant advantages, since the orientation control eases and increases the reproducibility of the sensor array fabrication.
  • the architecture is fault tolerant: the destruction of one channel leaves other channels still open, providing a conduction pathway between source and drain.
  • This approach may also be used as the basis for a multiplexed nanobiosensor array fabrication.
  • Biosensor arrays that utilize aligned carbon nanotubes as a semiconductor channel were successfully fabricated and used for the detection of a biomolecules, IgG.
  • the inventors have fabricated carbon nanotube FET arrays in a multistep process, illustrated herein.
  • the process consists of the following steps:
  • Catalyst preparation Quartz substrates were photolithographically patterned to make openings for catalysts. A solution of ferritin (Sigma) in de-ionized (D.I.) water was dropped onto the substrates, and kept for 10 min. The substrates were then rinsed with D.I. water, and the photoresist layer was lifted off in Acetone. The substrate with ferritin particles was calcinated at 700° C. for 10 min to form iron oxide nanoparticles that act as catalysts.
  • Aligned carbon nanotube growth A chemical vapor deposition (CVD) growth of CNTs was performed with 2,500 sccm of Methane, 10 sccm of Ethylene, and 600 sccm of Hydrogen at 900° C. for 10 min, resulting in allocation of oriented CNTs at specific positions.
  • Metal electrode definition Finally, metal electrodes (10 nm Ti and 30 nm Au) were defined using photolithography and lift off technique.
  • the inventors successfully fabricated aligned nanotube biosensor arrays.
  • the spacing between two adjacent devices was ⁇ 20 ⁇ m, and each device was clearly separated as is confirmed from the SEM images showing no nanotubes crossing between two devices.
  • the inventors have characterized the electrical property of aligned nanotubc devices, and the result is shown herein.
  • the device resistance showed mean value of 154.9 k ⁇ with a standard deviation of 132.2 k ⁇ . The distribution can be narrowed down by growing higher density of aligned nanotubes.
  • the inventors have further used those devices to detect IgG antigen.
  • the device was first functionalized with anti-IgG antibody by soaking in a solution of anti-IgG antibody in PBS buffer for 12 h at 4° C. The device was then exposed to a solution of IgG antigen at a concentration of 100 nM, and the device showed a conductance drop of ⁇ 8%. Upon exposure to 7 ⁇ M IgG antigen, the device showed further decrease in conductance by ⁇ 7%. This result confirms the successful use of aligned nanotube based biosensor.
  • the inventors used a semiconductive nanotube network as the active channel of biosensors to improve the sensitivity.
  • Single walled carbon nanotube can be categorized into two types, which are metallic and semiconductive nanotubes. It has been shown that semiconductive nanotube is more susceptible to the environment compared to metallic nanotube. This indicates that carbon nanotube based biosensors where the transport is dominated by the one through semiconductive nanotubes has a possibility to exhibit better sensitivity than biosensors where the transport happens through both metallic and semiconductive nanotubes. Based on this idea, the inventors have employed semiconductive nanotube network as the active channel of our biosensor, and improved the sensitivity (lowest detection limit) by more than 20 times compared to devices with mixed nanotube (both metallic and semiconductive nanotubes) network.
  • Preparation of such semiconductive network was done by controlling the nanotube density to overcome the percolation limit for semiconductive nanotubes and not to overcome that for metallic nanotubes. This method does not require any pre/post treatments on the devices, and is easily applicable to wafer scale or even larger scale production. Devices with high on/off ratio (indication of semiconductivity of the nanotube network) were successfully fabricated using carbon nanotube network where the density of the nanotube was carefully tuned.
  • CNTs were grown on a degenerately doped Si wafer with 500 nm SiO 2 on top via chemical vapor deposition (CVD) method with Fe nanoparticles formed from ferritin molecules as catalysts.
  • CVD chemical vapor deposition
  • Diluted solution of ferritin in De-ionized water (D.I. water) was put on the Si/SiO 2 wafer and kept for 1 h at room temperature, resulting in deposition of ferritin molecules onto the substrate.
  • the substrate was then washed with D.I. water, followed by calcination in air at 700° C. for 10 min, allowing formation of Fe nanoparticles.
  • the substrate placed in a quartz tube was heated to 900° C.
  • Source-drain current (Ids) versus source-drain voltage (Vds) under different gate voltage (Vg) are plotted and shows clearly separated curves under different Vg. These clearly separated curves indicate the good sensitivity of the device to the gate voltage, which led to the improved sensitivity of the device as shown later. This good sensitivity to gate voltage can be also observed in the Ids versus Vg curve shown herein. It should be noted that usually CNT devices using a network of mixture of semiconductive and metallic nanotubes show on/off ratio ⁇ 10.
  • Nanotube Sensor Fabrication Comparison of Sensitivity of Devices Using Semiconductive Nanotube Network and Mixed Nanotube Network
  • the inventors tested the sensitivity of both devices using Streptavidin (SA) as a model case.
  • SA Streptavidin
  • the devices were mounted in an electrochemical cell, and the cell was filled with phosphate saline buffer. The conductance of the devices was monitored while being exposed to solutions of SA at different concentrations.
  • the sensing of SA with a device using semiconductive nanotube network is disclosed herein. The device showed ⁇ 1% conductance drop upon exposure to a solution of SA at 100 pM, and further addition of SA at higher concentrations gave large conductance drops.
  • a device using mixed nanotube network showed only negligible response ( ⁇ 1%) when exposed to 2 nM SA, indicating that the lowest detection limit of mixed nanotube network devices is at least lower by a factor of 20 compared to semiconductive nanotube network devices. Furthermore, the comparison of magnitude of responses to SA at different concentrations revealed the enhanced sensitivity of semiconductive nanotube network devices over mixed nanotube network devices, confirming the advantage of the use of semiconductive nanotube network as biosensors.
  • the inventors developed a novel technique for attaching PDMS chips to silicone/silica oxide surfaces.
  • attachment of PDMS to silicon/silica surfaces has been achieved mostly via the generation of highly reactive radical species on the PDMS surface via oxygen plasma activation, which can react with OH group present on the silicon/silica surface.
  • the OH groups on the silicon/silica must be vertically aligned with the radicals on the PDMS surface.
  • the Si/SiO2 chip at the end of nanowire/nanotube growth process is highly dehydrated with a significantly reduced number of OH groups on it surface.
  • a method to generate a large surface density of OH groups on the dehydrate Si/SiO2 surface would be highly valuable.
  • the inventors have found that treating the Si/SiO2 surface with a bifuntional molecule, bearing a silane terminal group (where W, Y, or Z can be a methoxy, ethoxy, methyl, or etc.
  • linker molecules also useful for this purpose would includeSi(OH) 4 and Si(OR) 4 as well as alkyl silanes; as used herein, R is an alkyl or H.
  • Methods of fabrication include the following:
  • the inventors calibrated the response of In2O3 nanowire biosensor using parameters extracted from transistor measurements, resulting in decrease in coefficient of variation (CV).
  • the inventors have developed a data analysis method to calibrate the sensor responses. This method has an advantage that it can decrease the variation of the sensor responses. Furthermore, it is a simple analysis method that does not require intensive efforts often needed to make uniform devices. The method is complementary to those to make uniform devices.
  • the inventors have shown that two parameters that can be extracted from transistor measurements can be used to normalize the responses of In2O3 nanowire biosensor. Two definitions of response were employed, one is absolute response, and the other is relative response.
  • the inventors used Streptavidin and Avidin as model cases to verify the validity of their idea.
  • the devices were exposed to a solution of Streptavidin or Avidin (1 ⁇ M) in 100 times diluted PBS, and Ids-Vg measurement was done before/after the exposure. Absolute response and relative response were calculated from these curves.
  • Calibration of sensor response The inventors successfully normalized the absolute response and relative response by dividing them by dIds/dVg and dlogIds/dVg, respectively. As disclosed herein, the inventors show as an example absolute responses plotted against device identification number together with an average of the response before the calibration. In comparison, the normalized device responses (absolute response/dIds/dVg) showed smaller deviation from the average, which is after performing the calibration. The smaller deviation was verified by taking coefficient of variation (CV), which is one standard deviation divided by the mean. As disclosed herein, CV is shown for the absolute and relative responses before/after the calibration for Streptavidin and Avidin, respectively, where the decreased CV after calibration for every response is shown, in support for the validity of the idea.
  • CV coefficient of variation
  • the inventors tuned the sensitivity of In2O3 nanowire biosensors by using a liquid gate.
  • This method can increase the sensitivity of biosensors, and is applicable to the same type of biosensors, i.e. field effect transistor type biosensors.
  • the inventors have shown that liquid gate can be used to tune the sensitivity of biosensors by applying different gate voltage to the liquid gate.
  • Liquid gate configuration The schematic diagram of the measurement setup is shown herein.
  • a chemical cell made of teflon was mounted onto the device, and filled with phosphate saline buffer (PBS) diluted by 100 times with de-ionized water.
  • PBS phosphate saline buffer
  • a Pt wire was inserted into the buffer, and served as a gate electrode (liquid gate).
  • SA Streptavidin
  • the inventors fabricated sensor devices, based on nanowires or nanotubes, designed for the detection and monitor of a specific disease. Each of these devices recognize the unique molecular signatures arising upon development of a disease, bacterial or viral contamination, allergic reactions, etc. These devices may use the capturing capabilities of any and all capture molecules including antibodies, RNA, DNA and protein aptamers, oligonucleotides including RNA and DNA, receptors, ligands, and any other capture molecules that can detect biomolecules.
  • the detection platform can detect the unique molecular signatures of a specific disease. This device eliminates the need for multiple tests thus reducing the total time required to have a final evaluation of the health status of the patient.
  • Methods of use and fabrication include the following:
  • Peptide aptamers are sequences of peptides with a defined three dimensional structure that have shown to bind with high affinity and specificity to a particular biological molecule (protein, etc.).
  • An example may consist of a variable peptide attached at both ends to a protein scaffold, and the variable length is typically comprised of 10 to 20 amino acids.
  • the peptide bond (of both peptide and protein aptamers) is stable over a large range of pH values, giving protein aptamers unique robustness.
  • peptide and protein aptamers are much smaller in size (2-3 nm and 2-6 KDa) than antibodies causing the captured molecule (analyte) to be spatially closer to the nanowire/nanotube.
  • This analyte-nanowire closeness causes the electric field of the analyte to exert a greater influence on the charge carrier in the device.
  • the inventors have demonstrated that protein aptamers do work as capture molecules when immobilized on the surface of nanowire in a biosensor.
  • Peptide and/or Protein aptamers may be fabricated as capture agents or nanosensors by the following:
  • the conductance of the device was monitored over time, while the chip is then placed in contact with the solution under analysis where each single biomarker for a particular disease is captured by its corresponding probe molecule.
  • the analyte solution is washed away and replaced with PBS buffer.
  • a secondary ligand that also bind to the captured analyte is flown over the sensor surface.
  • This secondary ligand can be an aptamer or an antibody and it labeled with a highly charged tag or magnetic nanoparticle. The purpose of this tag is to increase the signal due to the binding of the analyte to the nanowire.
  • a step to cross link the analyte to the capture probe can be added to the procedure so the analyte is also covalently bound to the nanowire/nanotube device.
  • This cross linking step utilizes small, highly reactive molecules such as glutaraldehyde or formaldehyde.
  • the DNA analyte is allowed to hybridize with the DNA/PNA probe on the nanowire surface.
  • the solution containing the analyte is washed away with PBS buffer until a stable baseline is obtained.
  • a solution containing the intercalating molecule in PBS is flown over the sensor. The intercalator would insert in the PNA-PNA or DNA-DNA double helix. Depending on the type of charge carried by the intercalator, the conductance of the nanowire may increase or decrease (the intercalator may case either a carrier accumulation or depletion).
  • the solid phase is functionalized with capture agents (selectively binding to the background molecules to be removed from the solution).
  • This solid phase can be either on a separate chip or on the sidewalls of the microfluidic device.
  • the physiological solution is flown over the modified solid phase prior to get in contact with the nanosensors.
  • the surface of the nanomaterial is cleaned by standard procedure.
  • the surface of nanowire/nanotubes is coated with a linker molecule.
  • the linker molecule may be further activated for bioconjugation.
  • the surface of the each individual device or group of devices on a chip is then functionalized with a particular capture probe.
  • the capture probe being a biomolecule of relatively large size when compared to PEG short sequences, won't react with all the possible activated linker molecules on the surface.
  • a PEG chain with a terminal reactive group can be attached to the nanowires/nanotubes using the unreactive surface site, resulting in a passivation of the nanomaterial surface with PEG as well as capture molecules.

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