Compositions and methods for capturing, isolating, detecting, analyzing and quantifying macromolecules

• US 20040018642A1
• Filed: 05/21/2003
• Published: 01/29/2004
• Est. Priority Date: 02/18/2000
• Status: Active Grant

• Current Assignee: Cooley Godward LLP
• Original Assignee: Cooley Godward LLP
• Inventors: Huang, Chin-Shiou
• Granted Patent: US 7,288,415 B2
• Time in Patent Office: Days
• US Class Current: 436/518
• CPC Class Codes: B01J 20/268 Polymers created by use of a template, e.g. molecularly imprinted polymers
• CPC Class Codes: G01N 2600/00 Assays involving molecular imprinted polymers/polymers created around a molecular template
• CPC Class Codes: G01N 33/544 the carrier being organic
• CPC Class Codes: Y10S 436/804 Radioisotope, e.g. radioimmunoassay
• CPC Class Codes: Y10S 436/805 Optical property
• CPC Class Codes: Y10S 436/809 Multifield plates or multicontainer arrays
• CPC Class Codes: Y10S 977/927 Diagnostic contrast agent

Abstract

The present invention provides imprint compositions useful for capturing, isolating, detecting and/or quantifying macromolecules in a sample, methods of making and using the same. Generally, the imprint compositions comprise a matrix material defining an imprint of a template molecule, and the template molecule typically corresponds to a portion of a macromolecule of interest.

Claims

1. An imprint composition comprising a matrix, said matrix defining an imprint cavity of a template molecule that corresponds to a portion of a macromolecule of interest.

2. The imprint composition of claim 1 in which the matrix material comprises a polymer.

3. The imprint composition of claim 2, wherein the polymer comprises a polymerized monomer selected from the group consisting of styrene, methyl methacrylate, 2-hydroxyethyl methacrylate, 2-hydroxyethyl acrylate, methyl acrylate, acrylamide, vinyl ether, vinyl acetate, divinylbenzene, ethylene glycol dimethacrylate, ethylene glycol diacrylate, pentaerythritol dimethacrylate, pentaeiythritol diacrylate, N,N′

-methylenebisacrylamide, N,N′

-ethylenebisacrylamide, N,N′

-(1,2-dihydroxyethylene)bis-acrylamide and trimethylolpropane trimethacrylate.

4. The imprint composition of claim 1 in which the matrix material comprises a heat-sensitive compound.

5. The imprint composition of claim 4 in which the heat-sensitive compound is selected from the group consisting of hydrogels, agarose, gelatins and moldable plastics.

6. The imprint composition of claim 1, wherein the template molecule corresponds to a terminal portion of the macromolecule.

7. The imprint composition of claim 1, wherein the macromolecule is a polynucleotide and the template molecule is an oligonucleotide.

8. The imprint composition of claim 1, wherein the macromolecule is a polypeptide and the template molecule is an oligosaccharide.

9. The imprint composition of claim 1, wherein the macromolecule is a polypeptide and the template molecule is a peptide.

10. The imprint composition of claim 9, wherein the sequence of the peptide corresponds to a contiguous sequence of the polypeptide.

11. The imprint composition of claim 10, wherein the peptide is between 3 and 30 amino acids in length.

12. The imprint composition of claim 10, wherein the peptide is between 4 and 15 amino acids in length.

13. The imprint composition of claim 10, wherein the peptide is between 4 and 7 amino acids in length.

14. The imprint composition of claim 10, wherein the portion of the polypeptide comprises the C-terminus of the polypeptide.

15. The imprint composition of claim 1 further including the macromolecule, wherein the macromolecule is bound or associated with an imprint cavity.

22. A plurality of imprint compositions according to claim 1.

23. The plurality of claim 22, in which at least two compositions of the plurality are unique.

24. The plurality of claim 22, in which each composition defines imprint cavities of at least two different template molecules.

25. The plurality of claim 24, wherein each different template molecule corresponds to a different portion of the same macromolecule.

26. The plurality of claim 24, wherein each different template molecule corresponds to a different macromolecule.

27. The plurality of claim 22, wherein the compositions are arranged in a spatially-identifiable array or pattern.

28. The plurality of claim 27 in which the array is one-dimensional.

29. The plurality of claim 27 in which the array is two-dimensional.

30. The plurality of claim 27 in which the array is three-dimensional.

31. The plurality of claim 22 in which each template molecule is a peptide of from 3 to 7 amino acids in length.

32. The plurality of claim 22 which comprises imprint compositions defining imprints of the complete set of peptides of 7 amino acids in length.

39. A method of capturing a macromolecule, comprising contacting the macromolecule with an imprint composition of claim 1 under conditions in which the macromolecule binds the imprint.

40. A method of isolating a macromolecule, comprising the steps of:

(a) contacting the macromolecule with an imprint composition according to claim 1 under conditions in which the macromolecule binds the imprint; and

(b) recovering the macromolecule from the imprint.

16. An imprint composition comprising a matrix, said matrix defining a plurality of imprint cavities of a plurality of template molecules, wherein at least two of the template molecules are unique.

17. The imprint composition of claim 16 in which least one template molecule is a molecule that corresponds to a portion of a macromolecule of interest.

18. The imprint composition of claim 16 in which each template molecule of the plurality is unique.

19. The imprint composition of claim 16 in which the plurality of imprint cavities are arranged in a spatially identifiable pattern or array.

20. The imprint composition of claim 16 in which each template molecule is a peptide of from 3 to 7 amino acids in length.

21. The imprint composition of claim 16 in which the plurality of template molecules comprises the complete set of peptides of 7 amino acids in length.

48. A method of screening a plurality of macromolecules, comprising contacting the plurality of macromolecules with the imprint composition of claim 16, under conditions in which at least one macromolecule of the plurality binds the substrate.

49. A method of screening a plurality of macromolecules, comprising contacting the plurality of macromolecules with the plurality of imprint compositions of claim 20, under conditions in which at least one macromolecule of the plurality binds a substrate.

33. A method of making an imprint composition capable of capturing a macromolecule of interest, comprising the steps of:

(a) solidifying a fluidic matrix material capable of retaining shaped cavities when in a solid or semis-solid form in the presence of a template molecule that corresponds to a portion of the macromolecule, thereby yielding a solid or semi-solid matrix material having template molecules entrapped therein; and

(b) removing the template molecules from the solid or sem-solid matrix material, yielding an imprint composition capable of capturing the macromolecule.

34. The method of claim 33 in which the fluidic-matrix material is a heat-sensitive composition and the solidifying step comprises lowering the temperature of the heat-sensitive composition from above its melting point to below its melting point.

35. The method of claim 33 in which the fluidic matrix material is a composition comprising a polymerizable compound and the solidifying step comprises polymerizing the polymerizable compound.

36. The method of claim 33 in which the template molecule is immobilized on a solid support or substrate.

37. The method of claim 33 in which the solidifying step is carried out under conditions which are denaturing with respect to the template molecule.

38. The method of claim 33 in which the solidifying step is carried out under conditions which are native with respect to the template molecule.

41. A method of capturing a plurality of macromolecules, comprising contacting the plurality of macromolecules with a spatially identifiable array of imprint cavities, wherein each imprint cavity is of a template molecule that corresponds to a portion of one of the macromolecules of the plurality, under conditions in which the macromolecules bind their corresponding imprint cavities.

42. A method of quantifying the relative amounts of a plurality of different macromolecules in a sample, comprising the steps of:

(a) contacting the sample with a spatially identifiable array of imprint cavities, wherein each imprint cavity is of a template molecule that corresponds to a portion of one of the macromolecules of the plurality, under conditions in which the macromolecules bind their corresponding imprint cavities; and

(b) quantifying the amount of macromolecule bound to at least a subset of the plurality of imprints.

43. A method of making a spatially-identifiable array of imprint cavities, comprising the steps of:

(a) solidifying a fluidic matrix material capable of retaining shaped cavities when in a solid or semis-solid form in the presence of a spatially-identifiable array of immobilized template molecules, thereby yielding a solid or semi-solid matrix material having template molecules entrapped therein; and

(b) removing the template molecules from the solid or sem-solid matrix material, yielding a spatially-identifiable array of imprint cavities.

44. The method of claim 43 in which at least one immobilized template molecule corresponds to a portion of a macromolecule of interest.

45. The method of claim 43 in which each template molecule of the array of immobilized template molecules is unique.

46. The method of claim 43 in which each immobilized template molecule corresponds to a portion of a macromolecule of interest.

47. The method of claim 43 in which each immobilized template molecule corresponds to a portion of a different macromolecule of interest.