Photoactivatable silane compounds and methods for their synthesis and use

• US 6,773,888 B2
• Filed: 07/09/2002
• Issued: 08/10/2004
• Est. Priority Date: 04/08/2002
• Status: Expired due to Fees

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Li, Handong, McGall, Glenn
• Primary Examiner(s): Riley, Jezia
• Application Number:
  US10/192,598
• Publication Number:
  US 20030194715A1
• Time in Patent Office: 763 Days
• Field of Search: 536/23.1, 435/6
• US Class Current: 435/6.12
• 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 2219/00378 Piezoelectric or ink jet dispensers
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00628 Ionic
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00711 Light-directed synthesis
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C07B 2200/11 Compounds covalently bound to a solid support
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 50/18 using a particular method of attachment to the solid support
• CPC Class Codes: C40B 60/14 for creating libraries
• CPC Class Codes: G03F 7/165 Monolayers, e.g. Langmuir-Blodgett
• CPC Class Codes: Y10T 428/31663 As siloxane, silicone or silane

Abstract

In one aspect of the invention, photoactivatable silane compounds and methods for their synthesis and use are provided. In one embodiment, the photoactivatable silane compounds synthesized are represented by a formula: PG-LS-SN, wherein PG is a photoactivatable group, LS is a linkage and spacer group, and SN is a silane group. The silanes allow the photoactivatable silane compounds to be covalently bound to the surface of a substrate such as silica. The photoactivatable group forms a hydrophobic layer that can be photochemically cross-linked with a layer of hydrophilic functional polymers. In another embodiment, a method is disclosed to synthesize a substrate of hydrophobic layers and hydrophilic functional polymer layers thereafter onto glass surfaces. An array of biopolymers such as nucleic acids and peptides may then be covalently attached to the substrate using photolithography and biopolymer synthesis.

Claims

1. A photoactivatable silane compound of the formula PG-LS-SN wherein PG is a photoactivatable group for photochemically crosslinking, LS is a linkage and spacer group and SN is a silane group.

2. A photoactivatable silane compound according to claim 1 wherein said photoactivatable group for photochemically crosslinking is selected from a group consisting of the following moieties:

3. A photoactivatable silane compound according to claim 1 wherein said photoactivatable group for photochemically crosslinking comprises a photoreactive benzophenone.

4. A photoactivatable silane compound according to claim 1 wherein said saline group comprises an activated silicon group.

5. A photoactivatable silane compound according to claim 1 wherein said activated silicon group is capable of reacting with a functional group on a surface of a substrate.

6. A photoactivatable silane compound according to claim 4 wherein said saline group is selected from a group consisting of

7. A photoactivatable silane compound according to claim 1 wherein said photoactivatable silane compound is 4-(3′

-triethoxysily)propylamidobenzophenone or 4-(3′

-triethoxysilyl)propyloxybenzophenone.

8. A photoactivatable silane compound according to claim 1 wherein said LS group is selected from the group consisting of

9. An array of biopolymers comprising:

a substrate,

a photoactivatable silane compound covalently attached to said substrate, said photoactivatable silane comprising the formula PG-LS-SN wherein PG is a photoactivatable group for photochemically crosslinking, LS is a linkage and spacer group, and SN is a silane group said substrate attached to said photoactivatable silane compound through said silane group,

a functionalized polymer having reactive functionalized groups attached to said photoactivatable silane compound via photochemical cross-linking of said functionalized polymer to said photoactivatable group through photoactivation of said photoactivatable group; and

a plurality of biopolymers attached to said functionalized polymer through said reactive functional groups.

10. An array of biopolymers according to claim 9 wherein said photoactivatable group for photochemically crosslinking is hydrophobic and said functionalized polymer is hydrophilic.

11. An array of biopolymers according to claim 9 wherein said reactive functional groups are selected from the group consisting of hydroxyl, amino, carboxyl, thiol and amide.

12. An array of biopolymers according to claim 9 wherein said functionalized polymer is selected from the group consisting of polyvinyl alcohol, dextran, hydroxyethylcellulose, poly(2-hydroxylpropyl)methacrylate, 88% hydrolyzed polyvinyl alcohol, 80% ethoxylated plyethylenimine, poly(vinylalcohol-co-ethylene), hydrogenated poly(phenyl vinyl ketone), reduced poly-glutaldehyde, hydroxyethylacrylamide and 2-hydroxyethylacrylamide-methylacrylamide.

13. An array of biopolymers according to claim 9 wherein said photoactivatable group for photochemically crosslinking is selected from a group consisting of

14. An array of biopolymers according to claim 9 wherein said photoactivatable group comprises a photoreactive benzophenone.

15. An array of biopolymers according to claim 9 wherein said saline group comprises an activated silicon group.

16. An array of biopolymers according to claim 14 wherein said activated silicon group is capable of reacting with a functional group on said substrate.

17. An array of biopolymers according to claim 15 wherein said saline group is selected from a group consisting of

18. An array of biopolymers according to claim 9 wherein said LS group is selected from the group consisting of

19. An array of biopolymers according to claim 9 wherein said photoactivatable silane compound is 4-(3′

-triethoxysily)propylamidobenzophenone or 4-(3′

-triethoxysilyl)propyloxybenzophenone.

20. An array of biopolymers according to claim 9 wherein said substrate is glass.

21. An array of biopolymers according to claim 9 wherein said biopolymers are polynucleotides.

22. An array of biopolymers according to claim 20 wherein said polynucleotides are oligonucleotides.

23. An array of biopolymers according to claim 9 wherein said biopolymers are proteins.

24. An array of biopolymers according to claim 9 wherein said biopolymers are peptides.

25. A method of making an array of biopolymers comprising the steps of providing a substrate having a surface,

silanating said surface of said substrate with a photoactivatable silane compound having the formula PG-LS-SN wherein PG is a photoactivatable group for photochemically crosslinking, LS is a linkage and spacer group, and SN is a silane group wherein said surface of said substrate is attached to said photoactivatable silane compound through said silane group;

providing a functionalized polymer having reactive functionalized groups;

photochemically crosslinking said photoactivatable silane compound with said functionalized polymer via photoactivation of said photoactivatable group; and

attaching a plurality of biopolymers to said functionalized polymer via said reactive functionalized groups.

26. A method of making an array of biopolymers according to claim 25 wherein said photoactivatable group is a hydrophobic and said functionalized polymer is hydrophillic.

27. A method of making an array of biopolymers according to claim 25 wherein said functionalized polymer is selected from the group consisting of polyvinyl alcohol, dextran, hydroxyethylcellulose, poly(2-hydroxylpropyl)methacrylate, 88% hydrolyzed polyvinyl alcohol, 80% ethoxylated plyethylenimine, poly(vinylalcohol-co-ethylene), hydrogenated poly(phenyl vinyl ketone), reduced poly-glutaldehyde, hydroxyethylacrylamide and 2-hydroxyethylacrylamide-methylacrylamide.

28. A method of making an array of biopolymers according to claim 25 wherein said saline group comprises an activated silicon group.

29. A method of making an array of biopolymers according to claim 25 wherein said activated silicon group is capable of reacting with a functional group on said surface of said substrate.

30. A method of making an array of biopolymers according to claim 25 wherein said synthesizing said plurality of biological polymer on said functionalized polymer requires an activation of said functionalized polymer.

31. A method of making an array of biopolymers according to claim 25 wherein said biopolymer is a nucleic acid.

32. A method of making an array of biopolymers according to claim 31 wherein said nucleic acid is an oligonucleotide.

33. A method of making an array of biopolymers according to claim 25 wherein said biopolymer is a protein.

34. A method of making an array of biopolymers according to claim 25 wherein said biopolymer is a peptide.

35. A method of making an array of biopolymers according to claim 25 wherein said array of biopolymers is synthesized in situ using a photolithographic method or a reagent deposition method.

36. A method of making an array of biopolymers according to claim 25 wherein said ray of biopolymers is synthesized in situ using an inkjet printing method.

37. A method of making an array of biopolymers according to claim 25 wherein said array of biopolymers is synthesized by spotting the biopolymer onto the functionalized polymer.

38. A method of making an array of biopolymers according to claim 25 wherein said photoactivatable group is selected from a group consisting of

39. A method of making an array of biopolymers according to claim 25 wherein said photoactivatable group comprises a photoreactive benzophenone.

40. A method of making an array of biopolymers according to claim 25 wherein said saline group comprises an activated silicon group.

41. A method of making an array of biopolymers according to claim 25 wherein said activated silicon group is capable of reacting with a functional group on said substrate.

42. A method of making an array of biopolymers according to claim 25 wherein said saline group is selected from a group consisting of

43. A method of making an array of biopolymers according to claim 25 wherein said LS group is selected from the group consisting of

44. A method of making an array of biopolymers according to claim 25 wherein said photoactivatable silane compound is 4-(3′

-triethoxysily)propylamidobenzophenone or 4-(3′

-triethoxysilyl)propyloxybenzophenone.

45. A method of making an array of biopolymers according to claim 25 wherein said substrate is glass.