Process to detect binding events on an electrode microarray using enzymes

• US 20070231794A1
• Filed: 09/21/2005
• Published: 10/04/2007
• Est. Priority Date: 09/21/2005
• Status: Abandoned Application

• Current Assignee: CustomArray, Inc. (Genscript Biotech Corp.)
• Original Assignee: CombiMatrix Corporation
• Inventors: Cooper, John, Roth, Kristian, Dill, Kilian, Ghindilis, Andrei
• Application Number:
  US11/232,479
• Publication Number:
  US 20070231794A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/001 Enzyme electrodes
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2537/149 Sequential reactions
• CPC Class Codes: C12Q 2563/125 the label being enzymatic, i.e. proteins, and non proteins, such as nucleic acid with enzymatic activity
• CPC Class Codes: C12Q 2565/607 being a sensor, e.g. electrode
• CPC Class Codes: G01N 33/5438 Electrodes

Abstract

The present invention provides a process to detect binding events on an electrode microarray. A microarray is provided having addressable electrodes and two or more different types of capture complexes at sites corresponding to the electrodes. The capture complexes capture analytes. Enzymes are attached to form a reporter complex. Substrate solutions are sequentially contacted to make enzyme products that are detectable at the electrodes by a difference in the electrical response at electrodes having the enzyme product and those not having the enzyme product. The enzyme product may be a solid deposition product. The electrical properties of electrodes on the microarray are read for the presence of the enzyme product by sequentially switching each electrode held at a constant voltage to ground and then back to the constant voltage.

Claims

1. A process to detect binding events on an electrode microarray using enzymes comprising:

(a) providing a microarray having a plurality of electrodes and a plurality of capture complexes of at least two different types and attached at sites corresponding to the electrodes, wherein a first capture complex type has affinity for a first analyte type and subsequent capture complex types have affinity for subsequent analyte types, wherein the electrodes are electronically addressable;

(b) administering a plurality of analytes of at least one type to the capture complexes to form bound complexes of types corresponding to each type of the analytes captured by the capture complexes;

(c) attaching enzymes to the bound complexes to form reporter complexes, wherein the reporter complexes are of a type corresponding to each type of the analytes captured by the capture complexes;

(d) sequentially contacting a plurality of substrate solutions to the microarray and measuring for the presence or absence of an enzymatic product at the sites using an electrical signal, wherein each substrate solution corresponds to the reporter complex type, wherein the presence of the electrical signal is a measure of the binding event.

2. The process of claim 1, wherein the capture complexes are comprised of a plurality of probe oligonucleotides, the analytes are comprised of a plurality of target oligonucleotides, the bound complexes are formed by hybridization of the target oligonucleotides to the probe oligonucleotides, and the enzymes are bound to the target oligonucleotides by an attaching method, wherein the attaching method comprises attaching the enzymes through molecular groups selected from the group consisting of (a) an antibody, anti-antibody, and anti-idiotype antibody combination, (b) a biotin and streptavidin or avidin combination, and (c) an oligonucleotide and complementary oligonucleotide combination, and combinations thereof.

3. The process of claim 2, wherein the probe oligonucleotides are synthesized by in situ electrochemical synthesis.

4. The process of claim 1, wherein the capture complexes are comprised of probe oligonucleotides hybridized to target oligonucleotides having antibody tags, the bound complexes are formed by capture of the analytes by the antibody tags, and the enzymes are bound to the analytes by an attaching method, wherein the attaching method comprises a reporter antibody attached to the analyte and the enzyme attached to the reporter antibody through molecular groups selected from the group consisting of (a) an antibody, anti-antibody, and anti-idiotype antibody combination, (b) a biotin and streptavidin or avidin combination, and (c) an oligonucleotide and complementary oligonucleotide combination, and combinations thereof.

5. The process of claim 4, wherein the probe oligonucleotides are synthesized by in situ electrochemical synthesis.

6. The process of claim 1, wherein the capture complexes are made by a method selected from the group consisting of in situ electrochemical synthesis, spotting, ink-jet printing, electric field deposition, and in situ photolithography synthesis.

7. The process of claim 1, wherein the capture complexes are comprised of molecules selected from the group consisting of oligonucleotides, polypeptides, antibodies, glycosylated polypeptides, polysaccharides, peptide nucleic acids, and mixed molecules having monomers from a plurality of the foregoing molecules.

8. The process of claim 1, wherein the analytes are comprised of molecules selected from the group consisting of antigens, haptens, viruses, bacteria, cells, proteins, polysugars, biological polymer molecules, lipids, glycoproteins (alpha-1-acid glycoprotein,) ricin, M13 phage, Bacillus globigii (BG) spores, fluorescein, rabbit IgG, goat IgG, DNA, RNA, single-stranded DNA, ribosomal RNA, mitochondrial DNA, cellular receptors, glycosylated membrane-bound proteins, non-glycosylated membrane-bound proteins, polypeptides, glycosylated polypeptides, antibodies, cellular antigenic determinants, organic molecules, metal ions, salt anions and cations, and organometallics, and combinations thereof.

9. The process of claim 1, wherein the enzymes are selected from the group consisting of horseradish peroxidase, laccase, beta-galactosidase, glucose oxidase, alkaline phosphatase, glucose-6-phosphate dehydrogenase, catalase, lactate oxidase, and peroxidase, and combinations thereof.

10. The process of claim 1, wherein the substrate solutions are comprised of an aqueous solution having a buffer, a salt, and an enzymatic substrate solution, wherein the enzymatic substrate solution has substrates that are reactive with the enzyme.

11. The process of claim 1, wherein the enzymatic product comprises a molecule that is electrochemically reducible or oxidizeable.

12. The process of claim 1, wherein the electrical signal comprises a difference response, wherein the difference response is a measure of the difference between a product response and a base response, wherein the product response is measured on the sites having enzyme and the base response is measured on sites not having enzyme, wherein the product response and the base response are selected from the group consisting of current, voltage, and resistance, wherein the difference response is a measure of binding of the analytes to the capture complexes.

13. A process to detect binding events on an electrode microarray using enzymes comprising:

(a) providing a microarray having a plurality of electrodes and a plurality of capture complexes attached at sites corresponding to the electrodes, wherein the electrodes are electronically addressable;

(b) administering a plurality of analytes to the capture complexes to form bound complexes, wherein the capture complexes have affinity to the analytes;

(c) attaching enzymes to the bound complexes to form reporter complexes;

(d) contacting to the microarray a substrate solution having substrates reactive to the enzymes, wherein a solid enzyme product deposits on the sites having enzymes; and

(e) measuring for the presence or absence of the solid enzyme product at the sites using a measurement solution and an electrical signal, wherein the presence of the electrical signal is a measure of the binding event.

14. The process of claim 13, wherein the capture complexes are comprised of a plurality of probe oligonucleotides, the analytes are comprised of a plurality of target oligonucleotides, the bound complexes are formed by hybridization of the target oligonucleotides to the probe oligonucleotides, and the enzymes are bound to the target oligonucleotides by an attaching method, wherein the attaching method comprises attaching the enzymes through molecular groups selected from the group consisting of (a) an antibody, antiantibody, and antiidiotype antibody combination, (b) a biotin and streptavidin or avidin combination, and (c) an oligonucleotide and complementary oligonucleotide combination, and combinations thereof.

15. The process of claim 14, wherein the probe oligonucleotides are synthesized by in situ electrochemical synthesis.

16. The process of claim 13, wherein the capture complexes are comprised of probe oligonucleotides hybridized to target oligonucleotides having antibody tags, the bound complexes are formed by capture of the analytes by the antibody tags, and the enzymes are bound to the analytes by an attaching method, wherein the attaching method comprises attaching the enzymes through molecular groups selected from the group consisting of (a) an antibody, antiantibody, and antiidiotype antibody combination, (b) a biotin and streptavidin or avidin combination, and (c) an oligonucleotide and complementary oligonucleotide combination, and combinations thereof.

17. The process of claim 16, wherein the probe oligonucleotides are synthesized by in situ electrochemical synthesis.

18. The process of claim 13, wherein the capture complexes are made by a method selected from the group consisting of in situ electrochemical synthesis, spotting, ink-jet printing, electric field deposition, and in situ photolithography synthesis.

19. The process of claim 13, wherein the capture complexes are comprised of molecules selected from the group consisting of oligonucleotides, polypeptides, antibodies, glycosylated polypeptides, polysaccharides, and mixed molecules having monomers from a plurality of the foregoing molecules.

20. The process of claim 13, wherein the analytes are comprised of molecules selected from the group consisting of antigens, haptens, viruses, bacteria, cells, proteins, polysugars, biological polymer molecules, lipids, glycoproteins (alpha-1-acid glycoprotein,) ricin, M13 phage, Bacillus globigii (BG) spores, fluorescein, rabbit IgG, goat IgG, DNA, RNA, single-stranded DNA, ribosomal RNA, mitochondrial DNA, cellular receptors, glycosylated membrane-bound proteins, non-glycosylated membrane-bound proteins, polypeptides, glycosylated polypeptides, antibodies, cellular antigenic determinants, organic molecules, metal ions, salt anions and cations, and organometallics, and combinations thereof.

21. The process of claim 13, wherein the enzymes are selected from the group consisting of horseradish peroxidase, laccase, beta-galactosidase, glucose oxidase, alkaline phosphatase, and glucose dehydrogenase, and combinations thereof.

22. The process of claim 13, wherein the substrate solutions are comprised of an aqueous solution having a buffer, a salt, and an enzymatic substrate solution, wherein the enzymatic substrate solution has substrates that are reactive with the enzyme.

23. The process of claim 22, wherein the enzyme is horseradish peroxidase and the substrate is hydrogen peroxide and a chemical selected from the group consisting of oxidizeable aromatics, ferrocene derivatives, and oxidizeable inorganic compounds, pyrrole, and combinations thereof.

24. The process of claim 13, wherein the solid enzyme product is non-reactive and the measurement solution is an aqueous solution having an electron mediator.

25. The process of claim 24, wherein the electron mediator is a mixture of potassium ferrous cyanide and potassium ferric cyanide having a mixture proportion of approximately 10:

90 to 90;

10 and a concentration of approximately 0.1 to 1000 millimolar.

26. The process of claim 13, wherein the solid enzyme product is reducible or oxidizeable and the measurement solution is an aqueous solution having a buffer and a salt.

27. The process of claim 26, wherein the buffer is a phosphate-citrate buffer and the salt is sodium chloride.

28. The process of claim 13, wherein the solid enzyme product is a conductive material.

29. The process of claim 28, wherein the conductive material is polypyrrole.

30. The process of claim 13, wherein the electrical signal comprises a difference response, wherein the difference response is a measure of the difference between a product response and a base response, wherein the product response is measured on the sites having enzyme and the base response is measured on sites not having enzyme, wherein the product response and the base response are selected from the group consisting of current, voltage, conductivity, and resistance, wherein the difference response is a measure of binding of the analytes to the capture complexes.

31. A process to detect binding events on an electrode microarray using enzymes comprising:

(a) providing a microarray having a plurality of electrodes, wherein the electrodes are electronically addressable;

(b) applying a constant initial voltage to the electrodes while maintaining an open circuit to the electrodes; and

(c) measuring an electrical response of each electrode by sequentially switching each electrode to approximately ground or a voltage substantially different from the constant initial voltage for a measurement time, recording current flow at each electrode during the measurement time, and returning each electrode to the constant initial voltage before setting the next electrode to ground or the voltage substantially different from the constant initial voltage.

32. The process of claim 31, wherein the constant initial voltage is approximately 0.1 millivolts absolute value to 5 volts absolute value.

33. The process of claim 31, wherein the measurement time is approximately 0.1 milliseconds to 1 second.