Ultra-sensitive detection of extremely low level biological analytes using electrochemical signal amplification and biosensor

• US 9,624,532 B2
• Filed: 02/05/2014
• Issued: 04/18/2017
• Est. Priority Date: 02/05/2013
• Status: Active Grant

• Current Assignee: Neil Gordon
• Original Assignee: Neil Gordon
• Inventors: Gordon, Neil
• Primary Examiner(s): Kaur, Gurpreet
• Application Number:
  US14/173,064
• Publication Number:
  US 20150141272A1
• Time in Patent Office: 1,168 Days
• CPC Class Codes: C12Q 1/6804 Nucleic acid analysis using immunogens immunoassay G01N33/53
• CPC Class Codes: C12Q 1/682 Signal amplification
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• CPC Class Codes: C12Q 2563/113 the label being electroactive, e.g. redox labels
• CPC Class Codes: C12Q 2563/143 Magnetism, e.g. magnetic label
• CPC Class Codes: C12Q 2563/149 Particles, e.g. beads
• CPC Class Codes: C12Q 2565/102 Multiple non-interacting labels
• CPC Class Codes: C12Q 2565/607 being a sensor, e.g. electrode
• CPC Class Codes: C12Q 2565/629 being a microfluidic device
• CPC Class Codes: Y02A 90/10 Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Abstract

This invention allows ultra-low levels of virtually any biological analyte to be detected and quantified rapidly, simply and inexpensively with an electrochemical biosensor using a novel electrochemical signal amplification technique. The invention amplifies detection signals from low level analytes using an innovative sandwich ELISA structure that replaces optical labels with a massive amount of electrochemically detectable guanine rich oligonucleotide tags. Selective binding is achieved with matched pairs of either commercial or custom analyte binding materials such as monoclonal antibodies or single strand DNA. The guanine tags are eluted from the sandwich structures and hybridize with complementary cytosine rich oligonucleotide recognition probes attached to the surface of a biosensor working electrode. An electrochemical technique generates a signal in proportion to the guanine level on the working electrode which is also proportional to the analyte level in the sample. Magnetic separation and a nanosensor are used to improve the signal-to-noise ratio for measuring analyte levels 1,000,000 times lower than enzyme-linked immunosorbent assay (ELISA).

Claims

1. A signal amplification sandwich structure for amplifying, detecting and/or quantifying an analyte or multiple different analytes in a fluid sample, wherein said structure consists of:

(a) a first outer layer comprising a magnetic particle conjugated with a plurality of a first analyte binding material for binding the analyte;

(b) an inner layer comprising said analyte; and

(c) a second outer layer comprising a nonmagnetic particle conjugated with a plurality of a second analyte binding material for binding said analyte that is a matched pair with the first analyte binding material, and the nonmagnetic particle is also conjugated on its outer structure or temporarily filled in its inner structure with a plurality of an electrochemically detectable oligonucleotide tag in greater amounts than said analyte from said inner layer,

wherein;

(i) said electrochemically detectable oligonucleotide tags are for signal amplification, wherein the majority of nucleotides within said oligonucleotide tags are guanine, wherein said nucleotides within said oligonucleotide tags are selected from the group consisting of guanine, adenine, and thymine, and wherein the combination of said nucleotides produces a unique oligonucleotide tag that is used to amplify, detect and/or quantify said analyte or multiple different analytes;

(ii) analyte amplification performance of said signal amplification sandwich structure can be tuned to meet the desired limit of detection by adjusting one or more of the following parameters;

(a) the number of electrochemically detectable oligonucleotide tags per nonmagnetic particle;

(b) the number of guanines per electrochemically detectable oligonucleotide tag;

(c) the size of the nonmagnetic particle; and

(d) the surface area of the nonmagnetic particle for conjugating electrochemically detectable oligonucleotide tags;

(iii) the number of electrochemically detectable oligonucleotide tags per nonmagnetic particle ranges from 10 ² to 10¹³, the number of guanines per electrochemical detectable oligonucleotide tag ranges from 10 to 400, wherein the nonmagnetic particles are spherical and/or nonspherical, the diameter of spherical nonmagnetic particles ranges from 1 to 400 micrometers, the surface area of nonspherical nonmagnetic particles has an equivalent surface area of spherical nonmagnetic particles with ranges from 1 to 400 micrometers, and the surface of the nonmagnetic particles is smooth, rough, porous, or extended with attachments to other nonmagnetic particles; and

(iv) no optically detectable tags are used for amplification, detection or quantification.

2. The structure of claim 1, wherein the nonmagnetic particle in claim 1 (c) is selected from the group consisting of styrene, polystyrene, polymer, agarose, glass, ceramic, composite material, and combinations thereof, and the first analyte binding material in claim 1 (a) and the second analyte binding material in claim 1 (c) are selected from the group consisting of antibodies, monoclonal antibodies, polyclonal antibodies, amino acids, peptides, proteins, haptens, nucleic acids, oligonucleotides, DNA, RNA, aptamers, matched pairs thereof and combinations thereof.

3. A device for amplifying, detecting and/or quantifying an analyte or multiple different analytes in a fluid sample, wherein said device consists of:

(a) a magnetic separation unit configured to form a first outer layer and inner layer of signal amplification sandwich structures,

(b) an analyte amplification unit configured to form a second outer layer of signal amplification sandwich structures,

(c) a tag discharge unit configured to discharge electrochemically detectable oligonucleotide tags from signal amplification sandwich structures, and

(d) an electrochemical detection unit with at least one biosensor working electrode configured to measure detection signals from the electrochemically detectable oligonucleotide tags,

wherein said device employs the units from step (a), step (b), step (c) and step (d), collectively referred to as the device units, to form one or more signal amplification sandwich structures for amplifying detection signals from said analyte or multiple different analytes in a fluid sample, wherein said signal amplification sandwich structure consists of a first outer layer comprising a magnetic particle conjugated with a plurality of a first analyte binding material for binding said analyte, an inner layer comprising said analyte, and a second outer layer comprising a nonmagnetic particle conjugated with a plurality of a second analyte binding material for binding said analyte that is a matched pair with the first analyte binding material and the nonmagnetic particle is also conjugated on its outer structure or temporarily filled in its inner structure with a plurality of an electrochemically detectable oligonucleotide tag in greater amounts than said analyte from said inner layer,

wherein;

(i) said electrochemically detectable oligonucleotide tags are for signal amplification, wherein the majority of nucleotides within said oligonucleotide tags are guanine, wherein said nucleotides within said oligonucleotide tags are selected from the group consisting of guanine, adenine, and thymine, and wherein the combination of said nucleotides produces a unique oligonucleotide tag that is used to amplify, detect and/or quantify said analyte or multiple different analytes;

(ii) analyte amplification performance of said signal amplification sandwich structure can be tuned to meet the desired limit of detection by adjusting one or more of the following parameters;

(a) the number of electrochemically detectable oligonucleotide tags per nonmagnetic particle;

(b) the number of guanines per electrochemically detectable oligonucleotide tag;

(c) the size of the nonmagnetic particle; and

(d) the surface area of the nonmagnetic particle for conjugating electrochemically detectable oligonucleotide tags;

(iii) the number of electrochemically detectable oligonucleotide tags per nonmagnetic particle ranges from 10² to 10¹³, the number of guanines per electrochemical detectable oligonucleotide tag ranges from 10 to 400, wherein the nonmagnetic particles are spherical and/or nonspherical, the diameter of spherical nonmagnetic particles ranges from 1 to 400 micrometers, the surface area of nonspherical nonmagnetic particles has an equivalent surface area of spherical nonmagnetic particles with ranges from 1 to 400 micrometers, and the surface of the nonmagnetic particles is smooth, rough, porous, or extended with attachments to other nonmagnetic particles; and

(iv) no optically detectable tags are used for amplification, detection or quantification.

4. The device of claim 3, wherein the analyte amplification unit comprises one or more sets of nonmagnetic particles for creating electrochemically detectable oligonucleotide tag-nonmagnetic particle-analyte-magnetic particle structures if the analyte is present, wherein each set of nonmagnetic particles employs a plurality of a unique electrochemically detectable oligonucleotide tag for signal amplification, wherein the majority of the nucleotides within said oligonucleotide tags are guanine, wherein the nucleotides within the oligonucleotide tags are selected from the group consisting of guanine, adenine, and thymine, and wherein the combination of said nucleotides produces a unique oligonucleotide tag that is used to amplify, detect and/or quantify said analyte or multiple different analytes.

5. The device of claim 3, wherein the electrochemical detection unit consists of (a) an electrochemical biosensor or nanobiosensor comprising one or more working electrodes, wherein each working electrode is associated with said analyte from claim 3 that may be present in the sample and wherein each working electrode is conjugated with a plurality of an oligonucleotide recognition probe to bind or hybridize with associated electrochemically detectable oligonucleotide tags that is complementary to the oligonucleotide recognition probes, and (b) an electrochemical detection system that produces electrochemical signals on each working electrode in proportion to the quantity of said analyte if said analyte is present in the fluid sample, wherein the oligonucleotide recognition probes are oligonucleotides, wherein the majority of the nucleotides within said oligonucleotide recognition probes are cytosine, wherein the nucleotides within the oligonucleotide recognition probes are selected from the group consisting of cytosine, thymine, and adenine, wherein the combination of said nucleotides produces oligonucleotide recognition probes, and wherein each oligonucleotide recognition probe is complementary to a unique electrochemically detectable oligonucleotide tag defined in claim 3.

6. The device of claim 3, wherein the electrochemical detection unit produces a linear dynamic concentration range for quantifying the analyte in the fluid sample from known quantities of said analyte, and wherein said linear dynamic concentration range can be tuned by adjusting one or more of the following parameters:

the size of the working electrode, the surface area of the working electrode, the number of oligonucleotide recognition probes per working electrode, and the amplification ratio of electrochemically detectable oligonucleotide tags per analyte.

7. The device of claim 3, wherein multiple different analytes can be measured simultaneously from the said fluid sample:

(i) as multiple different analytes measured individually at unique biosensor working electrodes associated with each different analyte wherein each said analyte is associated with (a) a unique magnetic particle conjugated with a plurality of a first analyte binding material that binds with said analyte;

(b) a unique nonmagnetic particle conjugated with a plurality of a second analyte binding material that is a matched pair with the first analyte binding material and that binds with said analyte, and is also conjugated with a plurality of a unique electrochemically detectable oligonucleotide tag for signal amplification of said analyte, wherein the majority of the nucleotides within said oligonucleotide tags are guanine, wherein the nucleotides within the oligonucleotide tags are selected from the group consisting of guanine, adenine, and thymine, and wherein the combination of said nucleotides produces a unique oligonucleotide tag that is used to amplify, detect and/or quantify said analyte; and

(c) a unique working electrode conjugated with a plurality of a unique oligonucleotide recognition probe to bind or hybridize with the complementary electrochemically detectable oligonucleotide tag of said analyte to determine the quantity of said analyte;

or

(ii) as multiple different analytes measured as a group at a common biosensor working electrode associated with any analyte in said group of multiple different analytes wherein each said analyte in said group is associated with (a) a unique magnetic particle conjugated with a plurality of a first analyte binding material that binds with said analyte, (b) a unique nonmagnetic particle conjugated with a plurality of a second analyte binding material that is a matched pair with the first analyte binding material for said analyte, and is also conjugated with a plurality of a common electrochemically detectable oligonucleotide tag for signal amplification of any said analyte in said group, wherein the majority of the nucleotides within said oligonucleotide tags are guanine, wherein the nucleotides within the oligonucleotide tags are selected from the group consisting of guanine, adenine, and thymine, and wherein the combination of said nucleotides produces a unique oligonucleotide tag that is used to amplify, detect and/or quantify any analyte in said group; and

(c) a unique working electrode that is conjugated with a plurality of a unique oligonucleotide recognition probe to bind or hybridize with the common complementary electrochemically detectable guanine tag for any said analyte in said group to determine the combined quantity for all said analytes in said group.

8. The device of claim 3, wherein the electrochemical detection unit produces a linear dynamic concentration range for quantifying the analyte in the fluid sample from known quantities of said analyte in two or more standard samples, and wherein said linear dynamic concentration range can be increased in range by diluting a portion of one of the standard samples into a second standard sample, and diluting a portion of the second standard sample into a third standard sample, and diluting a portion of subsequent standard samples into derivative diluted standard samples.

9. The device of claim 3, wherein the device units in claim 3 are configured to comprise:

(a) one or more consumable test cartridges comprising portions of the device units for processing one or more samples; and

(b) a portable analyzer comprising portions of the device units for operating the one or more consumable test cartridges to process one or more samples.

10. The device of claim 9, wherein the one or more consumable test cartridges comprise one or more of microfluidics, a specimen inlet, sealable or nonsealable openings for magnetic particle and nonmagnetic particle solutions, reservoirs containing reagents, channels and mixing chambers, biosensors or nanobiosensors, heaters, magnet, valves, inlets for air connections, electrical connectors and circuitry for signal measurements and electrical systems, bar code, and Quick Response (QR) code.

11. The device of claim 9, wherein the one or more consumable test cartridges further provide one or more of dilution chambers, dilution reagents, and additional unique sets of working electrodes to create a larger linear dynamic concentration range for quantifying said analyte.

12. The device of claim 3, wherein the device units in claim 3 are configured to comprise:

(a) one or more consumable high throughput test panels comprising portions of the device units for processing one or more samples; and

(b) a high throughput analyzer comprising portions of the device units for operating the one or more consumable high throughput test panels to process one or more samples.

13. The device of claim 3, wherein the device units in claim 3 are configured to comprise:

(a) one or more consumable test cartridges comprising portions of the device units for processing one or more samples;

(b) an autonomous networked analyzer comprising portions of the device units for operating the one or more consumable test cartridges to process one or more samples;

(c) a sample collection and concentration unit; and

(d) a communications unit.

14. The device of claim 3, wherein the device units in claim 3 are configured to comprise:

(a) one or more consumable development cartridges comprising portions of the device units for processing one or more samples, wherein each consumable development cartridge has openings for inserting conjugated magnetic particles and conjugated nonmagnetic particles;

(b) a development analyzer comprising portions of the device units for operating the one or more consumable development cartridges to process one or more samples;

(c) algorithms for measuring the effectiveness of analyte binding materials, tag elution, and tag-probe hybridization, algorithms for generating concentration curves, and algorithms for identifying information associated with specific consumable development cartridges; and

(d) an insertion tool for inserting conjugated magnetic particles and conjugated nonmagnetic particles into the consumable development cartridges.

15. The device of claim 14, wherein the one or more consumable development cartridges comprise one or more of microfluidics, a specimen inlet, sealable or nonsealable openings for magnetic particle and nonmagnetic particle solutions, reservoirs containing reagents, channels and mixing chambers, biosensors or nanobiosensors, heaters, magnet, valves, inlets for air connections, electrical connectors and circuitry for signal measurements and electrical systems, bar code, and Quick Response (QR) code.

16. The device of claim 3, wherein the magnetic separation unit, the analyte amplification unit and the tag discharge unit in claim 3 are configured to comprise:

(a) one or more consumable amplification cartridges comprising portions of the magnetic separation unit, the analyte amplification unit and the tag discharge unit for processing one or more samples; and

(b) an amplification instrument comprising portions of the magnetic separation unit, the analyte amplification unit and the tag discharge unit for operating the one or more consumable amplification cartridges to process one or more samples.

17. A method for amplifying, detecting and/or quantifying an analyte or multiple different analytes in a fluid sample, wherein said method consists of the following steps performed sequentially:

(a) providing the fluid sample that may contain non-specific materials and an analyte or multiple different analytes;

(b) providing one or more sets of magnetic particles, wherein each set comprises a plurality of a magnetic particle conjugated with a plurality of a first analyte binding material to create analyte-magnetic particle complexes if said analyte or said multiple different analytes are present;

(c) providing one or more sets of nonmagnetic particles, wherein each set comprises a plurality of a nonmagnetic particle conjugated with a plurality of a second analyte binding material that is a matched pair with the first analyte binding material and is also conjugated with a plurality of a second electrochemically detectable oligonucleotide tag in greater amounts than said analyte to create electrochemically detectable oligonucleotide tag-nonmagnetic particle-analyte-magnetic particle structures if said analyte is present; and

(d) providing one or more working electrodes, wherein each working electrode is associated with said analyte or said group of multiple different analytes that may be present in said sample and wherein each working electrode is conjugated with a plurality of an oligonucleotide recognition probe to bind with associated electrochemically detectable oligonucleotide tags, and an electrochemical detection technique produces electrochemical signals on each working electrode in proportion to the quantity of said analyte or said group of multiple different analytes if said analyte or said group of multiple different analytes is present in the fluid sample;

wherein said method employs one or more signal amplification sandwich structures for amplifying detection signals from the analyte or multiple different analytes in the fluid sample, wherein said structure consists of a first outer layer comprising a magnetic particle conjugated with a plurality of a first analyte binding material for binding said analyte, an inner layer comprising said analyte, and a second outer layer comprising a nonmagnetic particle conjugated with a plurality of a second analyte binding material for binding said analyte that is a matched pair with the first analyte binding material and the nonmagnetic particle is also conjugated on its outer structure or temporarily filled in its inner structure with a plurality of an electrochemically detectable oligonucleotide tag in greater amounts than said analyte from said inner layer,

wherein;

(i) said electrochemically detectable oligonucleotide tags are for signal amplification, wherein the majority of nucleotides within said oligonucleotide tags are guanine, wherein said nucleotides within said oligonucleotide tags are selected from the group consisting of guanine, adenine, and thymine, and wherein the combination of said nucleotides produces a unique oligonucleotide tag that is used to amplify, detect and/or quantify said analyte or said group of multiple different analytes;

(ii) analyte amplification performance of said signal amplification sandwich structure can be tuned to meet the desired limit of detection by adjusting one or more of the following parameters;

(a) the number of electrochemically detectable oligonucleotide tags per nonmagnetic particle;

(b) the number of guanines per electrochemically detectable oligonucleotide tag;

(c) the size of the nonmagnetic particle; and

(d) the surface area of the nonmagnetic particle for conjugating electrochemically detectable oligonucleotide tags;

(iii) the number of electrochemically detectable oligonucleotide tags per nonmagnetic particle ranges from 10² to 10¹³, the number of guanines per electrochemical detectable oligonucleotide tag ranges from 10 to 400, wherein the nonmagnetic particles are spherical and/or nonspherical, the diameter of spherical nonmagnetic particles ranges from 1 to 400 micrometers, the surface area of nonspherical nonmagnetic particles has an equivalent surface area of spherical nonmagnetic particles with ranges from 1 to 400 micrometers, and the surface of the nonmagnetic particles is smooth, rough, porous, or extended with attachments to other nonmagnetic particles; and

(iv) no optically detectable tags are used for amplification, detection or quantification.

18. The method of claim 17, wherein the electrochemical detection technique in step (d) performs a first, a second and a third amperometric detection scan with an electron transport mediator on each working electrode, whereby

(e) the generated signal from guanine oxidation is measured as the difference in peak signal from a first scan minus peak signal from a second scan;

(f) said analyte is determined to be present if the generated signal from the associated electrochemically detectable oligonucleotide tags in step (e) is greater than the greatest variation in signal from a second scan minus a third scan; and

(g) the quantity of said analyte is determined by comparing the generated electrochemical signal from an associated electrochemically detectable oligonucleotide tag in step (e) with predetermined signals from known quantities of said analyte.

19. The method of claim 17, wherein said method further comprises:

(h) the analyte-magnetic particle complexes in step (b) are magnetically immobilized and the non-magnetically immobilized constituents of the fluid sample which may contain non-specific materials is washed and flushed away;

(i) the electrochemically detectable oligonucleotide tag-nonmagnetic particle-analyte-magnetic particle structures in step (c) are magnetically immobilized and unbound nonmagnetic particles conjugated with electrochemically detectable oligonucleotide tags are washed and flushed away;

(j) after step (c) the electrochemically detectable oligonucleotide tag-nonmagnetic particle-analyte-magnetic particle structures are magnetically immobilized and electrochemically detectable oligonucleotide tags are unbound from said structures, and washed and delivered to the working electrodes in step (d); and

(k) after step (a) the fluid sample may optionally be treated by one or more of the following;

a membrane, a chemical adherent, a disaggregation technique involving one or more of a chemical surfactant, sonication, and hydrodynamic cavitation to disaggregate clumps potentially containing said analytes, and a dilution technique to provide multiple concentrations of samples that can be separately processed as a larger range to quantify said analyte.

20. A method for amplifying an analyte or multiple different analytes in a fluid sample, wherein said method consists of the following steps performed sequentially:

(a) providing the fluid sample that may contain non-specific materials and an analyte or multiple different analytes;

(b) providing one or more sets of magnetic particles, wherein each set comprises a plurality of a magnetic particle conjugated with a plurality of a first analyte binding material to create analyte-magnetic particle complexes if said analyte or said multiple different analytes are present;

(c) providing one or more sets of nonmagnetic particles, wherein each set comprises a plurality of a nonmagnetic particle conjugated with a plurality of a second analyte binding material that is a matched pair with a first analyte binding material and is also conjugated with a plurality of a second electrochemically detectable oligonucleotide tag in greater amounts than said analyte to create electrochemically detectable oligonucleotide tag-nonmagnetic particle-analyte-magnetic particle structures if said analyte is present; and

(d) said electrochemically detectable oligonucleotide tag-nonmagnetic particle-analyte-magnetic particle structures are magnetically immobilized and said electrochemically detectable oligonucleotide tags are unbound from said structures, and washed and delivered as electrochemically detectable oligonucleotide tags for amplifying detection signals from said analytes in said fluid sample,

wherein said method employs one or more signal amplification sandwich structures for amplifying detection signals from the analyte or multiple different analytes in the fluid sample, wherein said structure consists of a first outer layer comprising a magnetic particle conjugated with a plurality of a first analyte binding material for binding said analyte, an inner layer comprising said analyte, and a second outer layer comprising a nonmagnetic particle conjugated with a plurality of a second analyte binding material for binding said analyte that is a matched pair with the first analyte binding material and the nonmagnetic particle is also conjugated on its outer structure or temporarily filled in its inner structure with a plurality of an electrochemically detectable oligonucleotide tag in greater amounts than said analyte from said inner layer,

wherein;

(i) said electrochemically detectable oligonucleotide tags are for signal amplification, wherein the majority of nucleotides within said oligonucleotide tags are guanine, wherein said nucleotides within said oligonucleotide tags are selected from the group consisting of guanine, adenine, and thymine, and wherein the combination of said nucleotides produces a unique oligonucleotide tag that is used to amplify said analyte or a group of multiple different analytes;

(ii) analyte amplification performance of said signal amplification sandwich structure can be tuned to meet the desired limit of detection by adjusting one or more of the following parameters;

(a) the number of electrochemically detectable oligonucleotide tags per nonmagnetic particle;

(b) the number of guanines per electrochemically detectable oligonucleotide tag;

(c) the size of the nonmagnetic particle; and

(d) the surface area of the nonmagnetic particle for conjugating electrochemically detectable oligonucleotide tags;

(iii) the number of electrochemically detectable oligonucleotide tags per nonmagnetic particle ranges from 10² to 10¹³, the number of guanines per electrochemical detectable oligonucleotide tag ranges from 10 to 400, wherein the nonmagnetic particles are spherical and/or nonspherical, the diameter of spherical nonmagnetic particles ranges from 1 to 400 micrometers, the surface area of nonspherical nonmagnetic particles has an equivalent surface area of spherical nonmagnetic particles with ranges from 1 to 400 micrometers, and the surface of the nonmagnetic particles is smooth, rough, porous, or extended with attachments to other nonmagnetic particles; and

(iv) no optically detectable tags are used for amplification.