Molecular detection and assay by electrobiochip micro-array

• US 20050053996A1
• Filed: 10/18/2004
• Published: 03/10/2005
• Est. Priority Date: 11/29/2001
• Status: Active Grant

• Current Assignee: Sun-Wing Tong
• Original Assignee: Sun-Wing Tong
• Inventors: Tong, Sun-Wing
• Granted Patent: US 7,632,671 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• CPC Class Codes: G01N 33/54326 Magnetic particles
• CPC Class Codes: G01N 33/5438 Electrodes

Abstract

The presence of a nucleic acid target, molecule or ligand can be detected by hybridization, antigen-antibody reaction or receptor-ligand binding. This is reported by the strategic positioning of a first probe and a second probe attached to a small particle of electrical conductor, which closes an electrical circuit, thereby reporting the event. A myriad of potential applications of this technique include the identification and detection of small amounts of nucleic acids by hybridization, the detection of molecules such as toxins and carcinogens by antigen-antibody reaction and the detection of other molecules by receptor-ligand interaction. The method can also be adapted to assay the quantity of a given substance using the principle of competitive binding.

Claims

1. A method of detecting trace quantities of a molecular target by exploiting a specific interaction between the target and two molecular probes, comprising:

attaching one of said molecular probes to an electrically conductive magnetic bead,

fixing the other of said probes in a gap between two electrodes,

applying a perpendicular magnetic field to the base of the gap,

applying an electric potential to said electrodes, and monitoring for an increase in electrical current from one of the electrodes to the other as might occur if said conductive bead is drawn into said gap by said specific interaction and fixed between the electrodes by said magnetic field.

2. The method of claim 1 wherein one of the probes is physically bound to a “

well”

between the electrodes.

3. The method of claim 1 wherein the conductive bead is an iron bead.

4. The method of claim 1 wherein the conductive bead is demagnetized prior to attachment of said one of the molecular probes.

5. The method of claim 4 wherein said demagnetization is by heating in an environment shielded from the Earth'"'"'s and other magnetic field(s).

6. The method of claim 1 wherein the conductive bead is prevented from rusting by removing all oxygen from the carrier fluid by heating or displacement with Nitrogen gas.

7. The method of claim 1 wherein the physical positioning of the iron beads between the electrodes causes a circuit to close.

8. The method of claim 1 wherein specificity of the reaction between the probe and the target is the basis of detection.

9. The method of claim 1 when adopted to detect multiple agents/molecules in a microprocessor-controlled microarray.

10. The method of claim 1 when adopted to assay the concentration of a given substance.

15. The method of claim 1 engineered into two or three-dimensional microarrays and used to detect multiple different molecules of different chemical nature, including but not limited to nucleic acids, proteins, carbohydrates, lipids and inorganic molecules.

16. The method of claim 15 including built-in duplications or triplications for quality control.

17. The method of claim 15 including an electronic self-check and/or pre-analytic test run with negative controls.

18. The method of claim 15 including a post-analytic test run with positive controls should the test result be negative.

11. A method of detecting trace quantities of a molecular target by exploiting a specific interaction between the target and two molecular probes, comprising the steps of:

(a) preparing a specimen by putting a gas or solid into solution or otherwise preparing an agent to be identified,

(b) introducing the specimen into a detecting device including a gap between two electrodes, which contains bound probes, and allowing for binding/hybridization to occur,

(c) before, during or after step (b) adding a second probe that is bound to an electrically conductive bead and allowing for specific binding/hybridization to occur,

(e) fixing any electrically conductive magnetic beads between the two electrodes by the application of a magnetic field, and

(f) determining if binding of the conductive bead to the gap has occurred by detecting a change in any electrical current between the electrodes.

12. The method of claim 11 wherein step (e) is preceded by:

(d) adjusting chemistry and/or temperature of the solution to optimize reaction conditions.

13. The method of claim 11 wherein step (f) employs the use of a microprocessor.

14. The method of claim 11 wherein step (a) includes physically and/or chemically reducing a cell to its components to liberate them for detection.

19. A method for assaying the concentration of a given substance, comprising:

providing an array of individual chips, each providing a closed electrical circuit including bound analyte and conductive beads between a pair of electrodes, wherein the chips differ in the size of the gap between the electrodes and the quantity of bound analyte and hence quantity of said beads, introducing a sample containing an unknown quantity of analyte to the microarray,

whereby the analyte displaces the bead-bound probes competitively in chips containing a given amount or less of bound analyte but not those containing a larger amount of bound analyte, and chips that have sufficient beads displaced will be converted to an open circuit.

20. The method of claim 19 wherein prior calibration with standards of known concentrations permits the assay of the concentration of analyte in the sample.

21. A method for assaying the concentration of a given substance, comprising:

providing an array of identical chips, with a small gap between two electrodes that accept only one conducting bead each and with well-bound probes, introducing a sample containing an unknown quantity of analyte to the microarray within a cassette that contains known amounts of added bead-bound probes in lesser quantity than the analyte in the sample, whereby

a free analyte competes with analyte-bound bead-bound probes (formed after introduced analyte react with bead-bound probes inside the cassette) for binding with said well-bound probes on a limited number of said electrobiochips.

22. The method of claim 21 comprising computation of a concentration of the analyte in the sample using prior knowledge of the amount of bead-bound probe, the proportion of “

on”

to “

off”

signals registered by the microprocessor and prior calibration with standards of known concentrations of analyte.

23. Apparatus for detecting trace quantities of a molecular target by exploiting a specific interaction between the target and two molecular probes, comprising:

a well having two electrodes spaced apart to form a gap and one of said probes attached to the well, means for applying an electric potential to said electrodes,

means for applying a magnetic field to the well to thereby fix any beads if bound between the electrodes, and

means for monitoring for an increase in electrical current from one of the electrodes to the other as might occur if a conductive bead having the other of said molecular probes attached thereto is drawn into said gap by said specific interaction and fixed therein by said magnetic field.

24. The apparatus of claim 23 in combination with a plurality of other identical apparatus in micro-arrays thereof.

25. The combination of claim 24 wherein the micro-arrays are housed within a cassette.

26. The combination of claim 25 further in combination with a portable device constructed with a slot that accepts the cassette.

27. The combination of claim 26 further including a microprocessor that reads the contents of the cassette from an identifier on the cassette.

28. A method of quantitatively determining the level of gene expression in a living organism as set out in example 3.

29. A method of detection of point mutations and single nucleotide polymorphisms as set out in example 4.

30. A method of detection of chimeric nucleic acid molecules as set out in example 5.

31. A method of quantitative viral load assay as set out in example 6.

32. A method of measurement of the size of repetitive DNA sequences (or their transcripts) as set out in example 9.

33. A method of detection of microsatellite instability as set out in example 9.

34. Methods of studying protein-protein interaction as set out in example 10.

35. A method of quantitating the amount of proteins in a given proteome as set out in example 10.

36. A method of identifying drug-protein interaction as set out in example 11.