Microarray and uses therefor

• US 7,794,946 B1
• Filed: 02/04/1999
• Issued: 09/14/2010
• Est. Priority Date: 02/04/1998
• Status: Expired due to Fees

• Current Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Original Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: Nasoff, Marc S., Fernandez, Joseph M., Hoeffler, James P.
• Primary Examiner(s): Cook; Lisa V
• Application Number:
  US09/245,615
• Time in Patent Office: 4,240 Days
• Field of Search: 435/6, 435/7, 435/7.1, 435/7.21, 435/90, 435/91, 435/91.3, 435/91.5, 435/72, 435/188, 435/173.1, 435/174, 435/283.1, 435/285.1, 435/285.2, 435/288.7, 435/290.1, 435/292.11, 435/290, 435/291, 436/47, 436/94, 436/173, 436/501, 436/518, 436/524, 436/525, 436/528, 436/531, 436/532, 436/535, 436/63, 436/164, 436/165, 436/166, 436/169, 436/172, 436/175, 436/805, 422/50, 422/63, 422/55, 422/56, 422/57, 422/58, 422/68.1, 422/69, 422/82.01, 422/82.02, 422/129, 422/131, 422/138, 536/22.1, 536/360, 536/380
• US Class Current: 435/7.1
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00641 the porous medium being continuous, e.g. porous oxide substrates
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: G01N 33/543 with an insoluble carrier for immobilising immunochemicals
• CPC Class Codes: G01N 33/54393 Improving reaction conditions or stability, e.g. by coating or irradiation of surface, by reduction of non-specific binding, by promotion of specific binding
• CPC Class Codes: G01N 33/548 Carbohydrates, e.g. dextran
• CPC Class Codes: G01N 33/6845 Methods of identifying protein-protein interactions in protein mixtures
• CPC Class Codes: G01N 33/6854 Immunoglobulins

Abstract

The invention disclosed herein comprises methods of using microarrays to simplify analysis and characterization of genes and their function. In one aspect of the invention the methods are used to identify and characterize antibodies having binding affinity for a specific target antigen. The invention further comprises a method of determining gene expression at the protein level comprising contacting an array of characterized or uncharacterized antibodies on a solid surface with one or more proteins and identifying the antibodies to which said protein(s) binds. This method can be additionally used to compare the protein expression in two different populations of cells, such as normal cells and cancer cells or resting cells and stimulated cells. A further aspect of the invention comprises a method of determining gene expression at the protein level comprising contacting a microarray of nucleic acid samples derived from a variety of different sources with one or more nucleic acid probes then identifying the sample or samples to which the probe binds.

Claims

1. A kit comprising:

at least one antibody array, said antibody array comprising a plurality of discrete locations arrayed in a spatially addressable ordered matrix on a solid surface, wherein each of the discrete locations comprises one or more spots of an antibody bound to the solid surface, wherein a plurality of the discrete locations contain antibodies that are different from the antibodies of the other discrete locations;

a first detectable label for labeling a first protein sample;

optionally a second detectable label for detectably labeling a second protein sample, wherein the second detectable label is different from the first detectable label; and

instructions for using the kit to perform one or more of the following;

i. identifying antigens in the first or the second protein samples that bind to one or more of the antibodies bound to the solid surface;

ii. comparing the protein expression profiles of two or more protein samples;

iii. characterizing the first or the second protein samples based on the protein expression profile thereof; and

iv. determining the effect of varying binding conditions on the affinity of the bound antibodies to antigens present in first or second protein samples.

2. The kit according to claim 1, wherein the array comprises up to about 600 discrete locations per square centimeter.

3. The kit according to claim 1, wherein the array comprises up to about 1000 discrete locations.

4. The kit according to claim 1, wherein the array comprises at least 1000 discrete locations.

5. The kit according to claim 1, wherein each spot contains between about 1 ng to about 1 μ

g of antibody.

6. The kit according to claim 1, wherein the antibodies are covalently bound to the solid surface.

7. The kit according to claim 1, further comprising a second antibody array.

8. The kit according to claim 1, wherein each detectable label is a fluorescent dye, biotin, an epitope tag or a colorimetric enzyme.

9. The kit according to claim 1, wherein each detectable label is a fluorescent dye.

10. The kit according to claim 9, wherein each detectable label is selected from the list fluorescein isothiocyanate (FITC), fluorescein, rhodamine, tetramethyl-rhodamine-5-(and 6)-isothiocyanate (TRITC), Texas red, a cyanine dye, Cy3 and Cy5.

11. The kit according to claim 1, wherein each discrete location in the array comprises two or more discrete spots of an antibody bound to the solid surface.

12. The kit according to claim 11, wherein each of the two or more discrete spots contains a different amount of antibody bound to the solid surface.

13. The kit according to claim 11, wherein each of the two or more discrete spots contains the same amount of antibody bound to the solid surface.

14. The kit according to claim 1, wherein each discrete location in the array comprises three or more discrete spots of an antibody bound to the solid surface.

15. The kit according to claim 1, wherein the discrete locations on the solid surface contain different antibodies.

16. The kit according to claim 1, wherein at least a portion of the discrete locations on the solid surface contain the same antibodies.

17. The kit according to claim 1, wherein at least a portion of the antibodies bound to the solid surface are uncharacterized.

18. The kit according to claim 1, wherein at least a portion of the antibodies bound to the solid surface are characterized.

19. The kit according to claim 1, wherein the antibodies in each spot are independently polyclonal antibodies, monoclonal antibodies, antibody fragments, single claim antibodies, humanized antibodies or recombinant antibodies.

20. The kit according to claim 1, further comprising an aqueous solution for incubating a sample with the antibody array.

21. The kit according to claim 1, further comprising a blocking solution.

22. The kit according to claim 1, further comprising a washing buffer.

23. The kit according to claim 1, wherein the surface comprises one or more of a plastic, a complex carbohydrate, an acrylic resin, nitrocellulose, glass, silicon or nylon.