Small molecule microarrays

• US 20030032203A1
• Filed: 07/10/2002
• Published: 02/13/2003
• Est. Priority Date: 07/10/2001
• Status: Abandoned Application

• Current Assignee: Whitehead Institute for Biomedical Research
• Original Assignee: Whitehead Institute for Biomedical Research
• Inventors: Stockwell, Brent R., Sabatini, David M.
• Application Number:
  US10/189,336
• Publication Number:
  US 20030032203A1
• Time in Patent Office: Days
• US Class Current: 436/518
• CPC Class Codes: G01N 33/543 with an insoluble carrier for immobilising immunochemicals

Abstract

Small molecule arrays, particularly small molecule microarrays, and methods of identifying a small molecule based on observing the effect of a small molecule on an observable characteristic of a biological sample or test element, such as a cell, protein, cell lysate, tissue slice or small organism.

Claims

1. A small molecule array which comprises a surface having affixed thereto or therein, in discrete, defined locations, one or more small molecules to be assessed for their effect(s) on one or more observable properties of a biological sample, wherein the small molecules are affixed to the surface by means of a polymer that immobilizes the small molecules to the surface, permits release of the small molecules, permits attachment of cells plated thereon or therein and is not toxic to cells plated thereon.

2. The small molecule array of claim 1 that is a microarray, wherein the biological sample is cells and the polymer is a hydrogel or a biodegradable polymer.

3. The microarray of claim 2, wherein the surface is a slide.

4. The microarray of claim 2, wherein the hydrogel is selected from the group consisting of:

a methacrylate-based polymer, a polycarboxylic acid, a cellulosic polymer, polyvinylpyrrolidone, maleic anhydride polymer, polyamide, polyvinyl alcohol and polyethylene oxide.

5. The microarray of claim 2, wherein the biodegradable polymer is selected from the group consisting of:

gelatin, poly (lactic acid), poly (glycolic acid) and poly lactide coglycolide.

6. The microarray of claim 2 that comprises from about 1 discrete, defined location per cm² to about 1,000,000 discrete, defined locations per cm².

13. The microarray of claim 1, wherein the polymer erodes in the presence of the cells plated thereon or therein, thereby releasing a portion of the small molecules.

14. The microarray of claim 1, wherein the polymer erodes at a measurable rate of erosion and the small molecules are released at a measurable rate of release, and wherein the rate of release is roughly proportional to the rate of erosion.

15. The microarray of claim 1, wherein the polymer adheres to the surface at the discrete, defined locations such that, after a 24 hour exposure to a cell culture medium, at least 95% of the discrete, defined locations have polymer adherent thereto or therein.

7. A small molecule microarray that comprises a slide having affixed thereto, in discrete, defined locations, small molecule-containing hydrogel spots.

8. The small molecule microarray of claim 7, wherein the hydrogel spots are methacrylate-based hydrogel disks and the microarray comprises from about 1 spot per cm² to about 1,000,000 disks per cm².

9. The small molecule microarray of claim 8 which comprises from about 10 spots per cm² to about 1,000,000 disks per cm².

10. A small molecule microarray that comprises a slide having affixed thereto or therein, in discrete, defined locations, small molecule-containing biodegradable polymer spots.

11. The small molecule microarray of claim 10, wherein the microarray comprises from about 1 spot per cm² to about 1,000,000 spots per cm².

12. The small molecule microarray of claim 11, wherein the microarray comprises from about 10 spots per cm² to about 1,000,000 spots per cm².

16. A small molecule-cell array which comprises:

(a) a small molecule to be assessed for its effect on a phenotypic characteristic of cells and (b) cells on which an effect of the small molecule is to be assessed, wherein the small molecule is affixed to or within the surface of the array in discrete, defined locations by means of a polymer that immobilizes the small molecule to or within the surface, permits release of the small molecule and attachment of cells plated thereon or therein and is not toxic to cells plated thereon or therein and the cells are plated thereon or therein.

17. The small molecule-cell array of claim 16 that is a small molecule-cell microarray, wherein the surface is a slide and the polymer is a hydrogel or a biodegradable polymer.

18. The small molecule-cell microarray of claim 17, wherein the hydrogel is selected from the group consisting of:

a methacrylate-based polymer, a polycarboxylic acid, a cellulosic polymer, polyvinylpyrrolidone, maleic anhydride polymer, polyamide, polyvinyl alcohol and polyethylene oxide.

19. The small molecule-cell microarray of claim 17, wherein the biodegradable polymer is selected from the group consisting of:

gelatin, poly (lactic acid), poly (glycolic acid) and poly lactide coglycolide.

20. The small molecule-cell microarray of claim 19 that comprises from about 1 discrete, defined location per cm² to about 1,000,000 discrete, defined locations per cm².

21. The small molecule-cell microarray of claim 20 that comprises from about 10 discrete, defined locations per cm² to about 1,000,000 discrete, defined locations per cm².

22. A small molecule-cell microarray that comprises a surface having affixed thereto or therein, in discrete, defined locations, test small molecule-containing hydrogel spots and cells plated thereon or therein.

23. The small molecule-cell microarray of claim 22, wherein the hydrogel spots are methacrylate-based hydrogel spots and the microarray comprises from about 1 spot per cm² to about 1,000,000 spots per cm².

24. A small molecule-cell microarray that comprises a surface having affixed thereto or therein, in discrete, defined locations, test small molecule-containing biodegradable polymer spots and cells plated thereon or therein.

25. The small molecule-cell microarray of claim 24, wherein the microarray comprises from about 1 spot per cm² to about 1,000,000 spots per cm².

26. The small molecule-cell microarray of claim 25, wherein the microarray comprises from about 10 spots per cm² to about 1,000,000 spots per cm².

27. A method of producing a small molecule array, wherein the small molecule array comprises test small molecule-containing hydrogel spots arrayed on a surface, comprising:

(a) arraying a test small molecule-hydrogel solution on or within a surface in discrete, defined locations, thereby producing a surface bearing or containing the test small molecule-hydrogel solution in discrete, defined locations and (b) subjecting the surface produced in (a) to conditions under which polymerization of the solution occurs, whereby the solution is polymerized and affixed to or within the surface as test small molecule-containing hydrogel spots, thereby producing the small molecule array.

28. The method of claim 27, wherein the surface is a slide and the hydrogel is a methacrylate-based hydrogel.

29. The method of claim 28, wherein the small molecule array is a small molecule microarray.

30. A method of producing a small molecule array, wherein the small molecule array comprises test small molecule-containing biodegradable spots arrayed on a surface, comprising:

(a) arraying a test small molecule-biodegradable polymer solution on or in a surface in discrete, defined locations, thereby producing a surface bearing the test small molecule-biodegradable polymer solution in discrete, defined locations and (b) subjecting the surface produced in (a) to conditions under which polymerization of the solution occurs, whereby the solution is polymerized and affixed to or in the surface as test small molecule-containing biodegradable polymer spots, thereby producing the small molecule array.

31. The method of claim 30, wherein the surface is a slide.

32. The method of claim 31, wherein the small molecule array is a small molecule mi cro array.

33. A method of identifying a small molecule that has an effect on a phenotypic characteristic of cells, comprising plating the cells on or in a small molecule array, wherein the small molecule array comprises a surface having affixed thereto or therein, in discrete, defined locations, test small molecule-containing hydrogel spots, thereby producing a small molecule-cell array;

maintaining the small molecule-cell array under conditions under which small molecule is released from the hydrogel spots and contacts membranes of vicinal cells;

observing effects of the small molecule on phenotypic characteristics of the vicinal cells, wherein if a phenotypic characteristic of vicinal cells is altered, the test small molecule is a small molecule that has an effect on a phenotypic characteristic of the cells.

34. The method of claim 33, wherein the small molecule array is a small molecule microarray and the surface is a slide.

35. The method of claim 34, wherein the hydrogel is a methacrylate-based hydrogel.

36. A method of identifying a small molecule that has an effect on a phenotypic characteristic of cells, comprising plating the cells on or in a small molecule array, wherein the small molecule array comprises a surface having affixed thereto or therein, in discrete, defined locations, test small molecule-containing biodegradable polymer spots, thereby producing a small molecule-cell array;

maintaining the small molecule-cell array under conditions under which small molecule is released from the biodegradable polymer spots and contacts membranes of vicinal cells;

observing effects of the small molecule on phenotypic characteristics of the vicinal cells, wherein if a phenotypic characteristic of vicinal cells is altered, the test small molecule is a small molecule that has an effect on a 5 phenotypic characteristic of the cells.

37. The method of claim 36, wherein the small molecule array is a small molecule microarray and the surface is a slide.

38. The method of claim 37, wherein the small molecule microarray comprises from about 1 discrete, defined location per cm² to about 1,000,000 discrete, defined locations per cm².

39. The method of claim 38, wherein the small molecule microarray comprises from about 10 discrete, defined locations per cm² to about 1,000,000 discrete, defined locations per cm² .