Addressable protein arrays

• US 20030143616A1
• Filed: 01/22/2003
• Published: 07/31/2003
• Est. Priority Date: 04/03/1998
• Status: Abandoned Application

• Current Assignee: Adnexus Therapeutics, Inc. (Bristol-Myers Squibb Company)
• Original Assignee: Adnexus Therapeutics, Inc. (Bristol-Myers Squibb Company)
• Inventors: Kuimelis, Robert G., Wagner, Richard
• Application Number:
  US10/348,627
• Publication Number:
  US 20030143616A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: B01J 2219/00274 Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
• CPC Class Codes: B01J 2219/00378 Piezoelectric or ink jet dispensers
• CPC Class Codes: B01J 2219/00387 Applications using probes
• CPC Class Codes: B01J 2219/00497 Features relating to the solid phase supports
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• 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: B01J 2219/00662 Two-dimensional arrays within two-dimensional arrays
• CPC Class Codes: B01J 2219/00677 Ex-situ synthesis followed by deposition on the substrate
• CPC Class Codes: B01J 2219/00691 using robots
• CPC Class Codes: B01J 2219/00707 separated from the reactor apparatus
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01J 2219/00729 Peptide nucleic acids [PNA]
• CPC Class Codes: B82Y 30/00 : Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C03C 17/30 : with silicon-containing compounds
• CPC Class Codes: C03C 17/3405 : with at least two coatings of organic materials C03C17/36, C03C17/42 take precedence
• CPC Class Codes: C07B 2200/11 : Compounds covalently bound to a solid support
• CPC Class Codes: C07K 17/06 : attached to the carrier via a bridging agent
• CPC Class Codes: C12Q 1/6834 : Enzymatic or biochemical coupling of nucleic acids to a solid phase
• CPC Class Codes: C12Q 1/6837 : using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2525/203 : incorporating a composite nucleic acid containing a polypeptide sequence other than PNA
• CPC Class Codes: C12Q 2565/519 : characterised by the capture moiety being a single stranded oligonucleotide
• CPC Class Codes: C40B 30/04 : by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 60/14 : for creating libraries
• CPC Class Codes: G01N 2500/04 : Screening involving studying the effect of compounds C directly on molecule A (e.g. C are potential ligands for a receptor A, or potential substrates for an enzyme A)
• CPC Class Codes: G01N 33/552 : Glass or silica
• CPC Class Codes: G01N 33/6845 : Methods of identifying protein-protein interactions in protein mixtures

Abstract

Disclosed herein are arrays of nucleic acid-protein fusions which are immobilized to a solid surface through capture probes which include a non-nucleosidic spacer group and an oligonucleotide sequence to which the fusion (such as an RNA-protein fusion) is bound. Also disclosed herein are solid supports on which these arrays are immobilized as well as methods for their preparation and use (for example, for screening for protein-compound interactions such as protein-therapeutic compound interactions).

Claims

1. A solid support having a linker layer on its surface, said linker layer being linked to an array of immobilized capture probes, each of said capture probes comprising a non-nucleosidic spacer group located proximal to the linker layer and an oligonucleotide sequence located distal to the linker layer, wherein said oligonucleotide sequence is bound to a nucleic acid-protein fusion.

2. The solid support of claim 1, wherein said nucleic acid-protein fusion is an RNA-protein fusion.

3. The solid support of claim 1, wherein said oligonucleotide sequence is bound to said nucleic acid-protein fusion by base pairing.

4. The solid support of claim 1, wherein the protein is encoded by the nucleic acid.

5. The solid support of claim 1, wherein said spacer group comprises polyalkylene oxide.

6. The solid support of claim 1, wherein said spacer group comprises polyethylene oxide.

7. The solid support of claim 1, wherein said spacer group comprises hexaethylene oxide.

8. The solid support of claim 1, wherein said capture probe comprises a photocleavable linker.

9. The solid support of claim 1, wherein said oligonucleotide sequence comprises a modified base.

10. The solid support of claim 9, wherein said modified base is 5-propyne pyrimidine.

11. The solid support of claim 1, wherein said oligonucleotide sequence comprises an internucleotide analog.

12. The solid support of claim 11, wherein said internucleotide analog is a 3′

-phosphoramidate linkage.

13. The solid support of claim 1, wherein said oligonucleotide sequence comprises a carbohydrate modification.

14. The solid support of claim 13, wherein said carbohydrate modification is a 2′

-O-methyl group.

15. The solid support of claim 1, wherein said nucleic acid-protein fusion comprises a hybridization tag sequence.

16. The solid support of claim 15, wherein said hybridization tag sequence comprises a modified base.

17. The solid support of claim 15, wherein said hybridization tag sequence comprises an intemucleotide analog.

18. The solid support of claim 1, wherein each of said capture probes further comprises a reactive moiety.

19. The solid support of claim 18, wherein said reactive moiety is a primary amino group.

20. The solid support of claim 1, wherein said solid support is a glass or silica-based chip.

21. The solid support of claim 1, wherein said nucleic acid-protein fusion is covalently linked to said capture probe.

22. The solid support of claim 21, wherein said capture probe comprises one or more psoralen moieties.

23. A solid support having a linker layer on its surface, said linker layer being linked to an array of immobilized capture probes, wherein each of said capture probes is attached to the linker layer of said solid support through a non-nucleosidic spacer group, and wherein each of said capture probes comprises an oligonucleotide sequence to which a nucleic acid-protein fusion is bound.

24. The solid support of claim 23, wherein said nucleic acid-protein fusion is an RNA-protein fusion.

25. A solid support comprising an array of immobilized capture probes, each of said capture probes comprising a non-nucleosidic spacer group and an oligonucleotide sequence to which a ribosome display particle is bound.

26. A method for preparing a solid support, said method comprising the steps of:

(a) preparing a capture probe by linking a spacer group to an oligonucleotide sequence;

(b) attaching said capture probe to said solid support; and

(c) binding a nucleic acid-protein fusion to said capture probe.

27. The method of claim 26, wherein said nucleic acid-protein fusion is an RNA-protein fusion.

28. A method for preparing a solid support, said method comprising the steps of:

(a) attaching a spacer group to a surface of said solid support;

(b) attaching a bifunctional linker to said spacer group;

(c) attaching a capture probe to said bifunctional linker; and

(d) binding a nucleic acid-protein fusion to said capture probe.

29. The method of claim 28, wherein said nucleic acid-protein fusion is an RNA-protein fusion.