Biochips with surfaces coated with polysaccharide-based hydrogels

• US 20030218130A1
• Filed: 04/14/2003
• Published: 11/27/2003
• Est. Priority Date: 05/02/2002
• Status: Abandoned Application

• Current Assignee: Bio-Rad Laboratories Incorporated
• Original Assignee: Ciphergen Biosystems Incorporated
• Inventors: Gurrier, Luc, Ding, Jian, Boschetti, Egisto, Girot, Pierre, Pohl, Christopher A., Grimes, Michael T.
• Application Number:
  US10/412,679
• Publication Number:
  US 20030218130A1
• Time in Patent Office: Days
• US Class Current: 250/288
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00315 Microtiter plates
• CPC Class Codes: B01J 2219/00454 by chemical cleavage from the solid support
• CPC Class Codes: B01J 2219/00497 Features relating to the solid phase supports
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00533 essentially rectangular
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00641 the porous medium being continuous, e.g. porous oxide substrates
• CPC Class Codes: B01J 2219/00644 the porous medium being present in discrete locations, e.g. gel pads
• CPC Class Codes: B01J 2219/00657 One-dimensional arrays
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00677 Ex-situ synthesis followed by deposition on the substrate
• CPC Class Codes: B01J 2219/00689 using computers
• CPC Class Codes: B01J 2219/00707 separated from the reactor apparatus
• CPC Class Codes: B01J 2219/00711 Light-directed synthesis
• CPC Class Codes: B01J 2219/00716 Heat activated synthesis
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01J 2219/00725 Peptides
• CPC Class Codes: B01J 2219/00731 Saccharides
• CPC Class Codes: B01J 2219/00734 : Lipids
• CPC Class Codes: B82Y 30/00 : Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C08B 11/20 : Post-etherification treatments of chemical or physical type, e.g. mixed etherification in two steps, including purification
• CPC Class Codes: C08B 15/00 : Preparation of other cellulose derivatives or modified cellulose , e.g. complexes
• CPC Class Codes: C08B 31/00 : Preparation of derivatives of starch derivatives of amylose C08B33/00; derivatives of amylopectin C08B35/00
• CPC Class Codes: C08B 33/00 : Preparation of derivatives of amylose
• CPC Class Codes: C08B 37/0021 : Dextran, i.e. (alpha-1,4)-D-glucan; Derivatives thereof, e.g. Sephadex, i.e. crosslinked dextran
• CPC Class Codes: C08B 37/0039 : Agar; Agarose, i.e. D-galactose, 3,6-anhydro-D-galactose, methylated, sulfated, e.g. from the red algae Gelidium and Gracilaria; Agaropectin; Derivatives thereof, e.g. Sepharose, i.e. crosslinked agarose
• CPC Class Codes: C08L 5/02 : Dextran; Derivatives thereof
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 40/10 : Libraries containing peptides or polypeptides, or derivatives thereof
• CPC Class Codes: C40B 40/12 : Libraries containing saccharides or polysaccharides, or derivatives thereof
• CPC Class Codes: C40B 40/14 : Libraries containing macromolecular compounds and not covered by groups C40B40/06 - C40B40/12
• CPC Class Codes: C40B 50/14 : Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support
• CPC Class Codes: C40B 60/14 : for creating libraries
• CPC Class Codes: G01N 33/5302 : Apparatus specially adapted for immunological test procedures
• CPC Class Codes: G01N 33/559 : through a gel, e.g. Ouchterlony technique
• CPC Class Codes: G01N 33/6848 : Methods of protein analysis involving mass spectrometry
• CPC Class Codes: G01N 33/6851 : Methods of protein analysis involving laser desorption ionisation mass spectrometry
• CPC Class Codes: H01J 49/0418 : for laser desorption, e.g. matrix-assisted laser desorption/ionisation [MALDI] plates or surface enhanced laser desorption/ionisation [SELDI] plates

Abstract

The present invention provides a substrate having a polymerized, polysaccharide-based hydrogel attached to the surface. The hydrogel can be derivatized with binding functionalities that bind analytes from a sample. The invention further provides methods of using the device and gels that are capable of selectively binding one or more analytes from a sample.

Claims

1. A device comprising:

(a) a substrate having a surface which comprises an anchor reagent covalently coupled to the surface, wherein the anchor reagent comprises a first polymerizable moiety; and

(b) a hydrogel comprising a soluble, non-ionic polysaccharide derivatized with a second polymerizable moiety at a plurality of hydroxyl groups;

wherein the polysaccharides are linked to each other and to the anchor reagent through bonds resulting from the polymerization of the first and second polymerizable moieties.

2. The device of claim 1, wherein said polysaccharide further comprises a binding functionality.

3. The device of claim 1, further comprising a co-polymerized mixture of a polymerizable monomer functionalized with a binding functionality and a cross-linking agent, wherein said mixture creates an interpenetrated network with said hydrogel.

4. The device of claim 1 wherein the polysaccharide is further derivatized with a polymerizable monomer comprising a binding functionality and a third polymerizable moiety, wherein the polymerizable monomer is linked to the polysaccharide through a bond resulting from the polymerization of the second and third polymerizable moieties.

5. The device of claim 1 wherein the surface comprises a metal oxide or a mineral oxide coating.

6. The device of claim 5 wherein the metal or mineral oxide is selected from the group consisting of silicon oxide, titanium oxide, zirconium oxide and aluminum oxide.

7. The device of claim 1 wherein the substrate comprises metal.

8. The device of claim 1 wherein the anchor reagent comprises an acryl group, an allyl group or a vinyl group.

9. The device of claim 1 wherein the polysaccharide is dextran.

10. The device of claim 1 wherein the polysaccharide is selected from the group consisting of hydroxy-ethyl-cellulose, starch, amylose and agarose.

11. The device of claim 1 wherein the polysaccharide is saturated with double bonds of about one per sugar unit to about one per one-thousand sugar units.

12. The device of claim 1 wherein the binding functionality is selected from the group consisting of a hydrophobic group, a hydrophilic group, reactive groups such as aldehydes, epoxy, carbonates and alike, a carboxyl, a thiol, a sulfonate, a sulfate, an amino, a substituted amino, a phosphate, a metal chelating group, a thioether, a biotin, a boronate, and complex structures such as dyes.

13. The device of claim 3 or 4 wherein the polymerizable monomer is a functionalized acrylic monomer.

14. The device of claim 4 wherein the polymerizable monomer is selected from the group consisting of glycidyl methacrylate, N-methyl-N-gycidyl-methylacrylamide 2-hydroxyethyl methacrylate and glycerol mono methacrylate.

15. The device of claim 4 further comprising contacting the polysaccharide with a spacer monomer comprising a third polymerizable moiety.

16. The device of claim 1, 2, 3 or 4 wherein the surface comprises a plurality of anchor reagents at different addressable locations and wherein the hydrogel is polymerized to the anchor reagent at a plurality of said locations.

17. The device of claim 1 wherein the anchor reagent comprises a silane selected from (3-acryloxypropyl)trimethoxysilane, (3-acryloxypropyl)methyldimethoxysilane, (3-acryloxypropyl)dimethylmethoxysilane, (3-acryloxypropyl)trichlorosilane, (3-acryloxypropyl)methyldichlorosilane, (3-acryloxypropyl)dimethylchlorosilane, (3-methacryloxypropyl)trimethoxysilane, (3-methacryloxypropyl)methyldimethoxysilane, (3-methacryloxypropyl)dimethylmethoxysilane, (3-methacryloxypropyl)trichlorosilane, (3-methacryloxypropyl)methyldichlorosilane, (3-methacryloxypropyl)dimethylchlorosilane, vinyloxytrimethylsilane, vinyltrichlorosilane, vinyltrimethoxysilane, allylchloromethyldimethylsilane, allylchlorodimethylsilane, allylbromodimethylsilane, allyldichloromethylsilane, allyldiisopropylaminodimethylsilane, allyloxy-tertbutyldimethylsilane, allyltrimethoxysilane and combinations thereof.

18. The device of claim 9 wherein the dextran has an average molecular weight of between about 1 kDa to about 2000 kDa.

19. The device of claim 9 wherein the dextran has an average molecular weight of about 500 kDa.

20. The device of claim 9 wherein the dextran is acryloyl dextran or methacryloyl dextran and the surface comprises acryloyl or metharcyloyl moieties.

21. The device of claim 9 wherein the dextran is cross-linked with bis-epoxide cross-linker.

22. The device of claim 3 and 4 wherein the cross-linking agent is selected from the group consisting of N,N′

-methylene-bis-acrylamide, N,N′

-methylene-bismethacrylamide, poly(ethylene glycol) dimethacrylate and diallyltartardiamide.

23. The device of claim 16 wherein the substrate is a probe that fits into a mass spectrometer and said locations are addressable by a laser beam.

24. The device of claim 21 wherein the bis-epoxide cross-linker is selected from the group consisting of BDDGE, EDGE and poly(ethyleneglycol)dimethacrylate.

25. The device of claim 13 wherein the acrylic monomer is selected from the group consisting of acrylamido-glycolic acid, acrylamido-methyl-propane-sulfonic acid, acrylamido-ethyl-phosphate, diethyl-aminoethyl-acrylamide, trimethyl-amino-propylmethacrylamide, N-octyl-acrylamide, N-phenyl-acrylamide and tert-butyl-acrylamide.

27. The device of claim 22 wherein said first functional group is a carboxyl and said second functional group is a primary amino.

28. The device of claim 22, wherein said first functional group is biotin and said second functional group is avidin.

29. The device of claim 1 wherein the hydrogel is attached to the surface at a plurality of addressable locations.

30. The device of claim 1, 2, 3 or 4 which comprises means for engaging a probe interface of a mass spectrometer.

66. A method of detecting an analyte comprising:

(a) contacting the hydrogel of a device of claim 1, 2, 3 or 4 with an analyte at an addressable location;

(b) introducing the device into a probe interface of a laser desorption mass spectrometer whereby the addressable location is positioned in an interrogatable relationship with a laser beam in a mass spectrometer;

(c) striking the hydrogel at the addressable location with a laser pulse to desorb and ionize the analyte; and

(d) detecting the desorbed and ionized analyte with the mass spectrometer.

67. The method of claim 66 wherein the analyte is a biomolecule selected from the group consisting of a protein, a peptide, a nucleic acid, a carbohydrate and a lipid.

68. The method of claim 66 wherein the analyte is a small organic molecule.

26. A device comprising:

(a) a substrate having a surface, wherein the surface comprises an anchor reagent covalently coupled to the surface and the anchor reagent comprises a first functional group; and

(b) a non-ionic polysaccharide derivatized at a plurality of hydroxyl groups with a second functional group for interacting with said first functional group, wherein said first and second functional groups interact to form a covalent bond.

31. A method of making a device comprising:

(a) providing a substrate having a surface, wherein the surface comprises an anchor reagent covalently coupled to the surface and wherein the anchor reagent comprises a first polymerizable moiety;

(b) contacting the anchor reagent with a soluble, non-ionic polysaccharide derivatized at a plurality of hydroxyl groups with a second polymerizable moiety; and

(c) co-polymerizing the polysaccharide and the anchor reagent, thereby producing a hydrogel covalently coupled to the surface via the first and second polymerizable moieties.

32. The method of claim 31 wherein the polysaccharide is further derivatized with a binding functionality, whereby the hydrogel is capable of binding an analyte.

33. The method of claim 31 further comprising contacting the anchor reagent with a polymerizable monomer functionalized with a binding functionality;

and wherein copolymerizing comprises copolymerizing the anchor reagent, the polysaccharide and the functionalized polymerizable monomer to form a composite polymer.

34. The method of claim 31 further comprising:

(d) contacting the material produced in (c) with a mixture of a polymerizable monomer functionalized with a binding functionality and a cross-linking agent; and

(e) co-polymerizing the polymerizable monomer and the cross-linking agent to create an interpenetrated network.

35. The method of claim 31 further comprising derivatizing the material produced in (c) with a binding functionality.

36. The method of claim 31 wherein the surface comprises a metal oxide or a mineral oxide coating.

37. The method of claim 33 wherein the polymerizable monomer is selected from the group consisting of glycidyl methacrylate, N-methyl-N-gycidyl-methylacrylamide, 2-hydroxyethyl methacrylate and glycerol mono methacrylate.

38. The method of claim 33 further comprising contacting the polysaccharide with a spacer monomer comprising a third polymerizable moiety.

39. The method of claim 36 wherein the metal or mineral oxide is selected from the group consisting of silicon oxide, titanium oxide, zirconium oxide and aluminum oxide.

40. The method of claim 31 wherein the substrate comprises metal.

41. The method of claim 31 wherein the anchor reagent comprises an acryl group, an allyl group or a vinyl group.

42. The method of claim 31 wherein the polysaccharide is dextran.

43. The method of claim 31 wherein the polysaccharide is selected from the group consisting of hydroxy-ethyl-cellulose, starch, amylose and agarose.

44. The method of claim 31 wherein the co-polymerizing is initiated with a light sensitive catalyst, a temperature sensitive catalyst, or a peroxide in the presence of an amine.

45. The method of claim 31 wherein the polysaccharide is saturated with double bonds of about one per sugar unit to about one per one-thousand sugar units.

46. The method of claim 32 wherein the binding functionality is selected from the group consisting of a carboxyl, a hydrophobic group, a hydrophilic group, reactive groups such as aldehydes, epoxy, carbonates, a carboxyl, a thiol, a sulfonate, a sulfate, an amino, a substituted amino, a phosphate, a metal chelating group, a thioether, a biotin, a boronate, and complex structures such as dyes.

47. The method of claim 32 wherein the polysaccharide is derivatized in situ with the binding functionality.

48. The method of claim 33 or 34 wherein the functionalized polymerizable monomer is a functionalized acrylic monomer.

49. The method of any of claim 31, 32, 33 or 34 wherein the surface comprises a plurality of anchor reagents at different addressable locations and wherein the hydrogel is polymerized to the anchor reagent at a plurality of said locations.

50. The method of claim 31 wherein the anchor reagent comprises a silane selected from the group consisting of (3-acryloxypropyl)trimethoxysilane, (3-acryloxypropyl)methyldimethoxysilane, (3-acryloxypropyl)dimethylmethoxysilane, (3-acryloxypropyl)trichlorosilane, (3-acryloxypropyl)methyldichlorosilane, (3-acryloxypropyl)dimethylchlorosilane, (3-methacryloxypropyl)trimethoxysilane, (3-methacryloxypropyl)methyldimethoxysilane, (3-methacryloxypropyl)dimethylmethoxysilane, (3-methacryloxypropyl)trichlorosilane, (3-methacryloxypropyl)methyldichlorosilane, (3-methacryloxypropyl)dimethylchlorosilane, vinyloxytrimethylsilane, vinyltrichlorosilane, vinyltrimethoxysilane, allylchloromethyldimethylsilane, allylchlorodimethylsilane, allylbromodimethylsilane, allyldichloromethylsilane, allyldiisopropylaminodimethylsilane, allyloxy-tert-butyldimethylsilane, allyltrimethoxysilane and combinations thereof.

51. The method of claim 43 wherein the dextran has an average molecular weight of between about 1 kDa to about 2000 kDa.

52. The method of claim 43 wherein the dextran has an average molecular weight of about 500 kDa.

53. The method of claim 43 wherein the dextran is acryloyl dextran or methacryloyl dextran and the surface comprises acryloyl or methacryloyl moieties.

54. The method of claim 43 wherein the dextran is reacted with glycidyl methacrylate, glycidyl acrylate, acryloyl-chloride, methacryloyl-chloride or allyl-glycidylether under alkaline conditions.

55. The method of claim 43 wherein the dextran is cross-linked with a bis-epoxide cross-linker.

56. The method of claim 32 wherein the polysaccharide is derivatized by

a) activating said polysaccharide with a molecule selected from the group consisting of carbonyl-di-imidazole, tosyl-chloride, tri-chloro-triazine and chloroformates;

and

b) reacting the activated polysaccharide with a binding reagent comprising said binding functionality.

57. The method of claim 32 wherein the binding functionality is carboxyl and the polysaccharide is functionalized by reacting the polysaccharide with chloroacetic acid.

58. The method of claim 33 or 34 wherein the cross-linking agent is selected from the group consisting of N,N′

-methylene-bis-acrylamide, N,N′

-methylene-bismethacrylamide, poly(ethylene glycol) dimethacrylat and diallyltartardiamide.

59. The method of claim 43 wherein the dextran is reacted with more than one chemical in a sequence of reactions.

60. The method of claim 49 wherein the substrate is a probe that fits into a mass spectrometer and said locations are addressable by a laser beam.

61. The method of claim 55 wherein the bis-epoxide cross-linker is selected from BDDGE, EGDGE and poly(ethylene glycol) dimethacrylat.

62. The method of claim 48 wherein the acrylic monomer is selected from the group consisting of acrylamido-glycolic acid, acrylamido-methyl-propane-sulfonic acid, acrylamido-ethyl-phosphate, diethyl-aminoethyl-acrylamide, trimethyl-amino-propylmethacrylamide, N-octyl-acrylamide, N-phenyl-acrylamide and tert-butyl-acrylamide.

63. A method for making a device comprising:

(a) providing a substrate having a surface, wherein the surface comprises one or more anchor reagent(s) covalently coupled to the surface and wherein the anchor reagent comprises a moiety having a first functional group; and

(b) contacting the anchor reagent with a soluble, non-ionic polysaccharide derivatized at a plurality of hydroxyl groups with a second functional group for interacting with said first functional group.

64. The method of claim 63, wherein said first functional group is a carboxyl and said second functional group is a primary amino.

65. The method of claim 63, wherein said first functional group is biotin and said second functional group is avidin.

69. A gel comprising an interpenetrated network of

a) a hydrogel;

and

b) a copolymerized mixture of a polymerizable monomer functionalized with a binding functionality and a cross-linking agent

70. The gel of claim 69, wherein said hydrogel is derivatized with a binding functionality.

71. A gel comprising

a) a non-ionic polysaccharide derivatized with a first polymerizable moiety at a plurality of hydroxyl groups;

and

b) a polymerizable monomer functionalized with a binding functionality and a second polymerizable moiety;

wherein the polymerizable monomer is linked to the polysaccharide through a bond resulting from the polymerization of the first and second polymerizable moieties.