Methods for producing ligand arrays

• US 7,202,358 B2
• Filed: 07/25/2002
• Issued: 04/10/2007
• Est. Priority Date: 07/25/2002
• Status: Expired due to Fees

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Hargreaves, John S.
• Primary Examiner(s): Riley; Jezia
• Application Number:
  US10/206,877
• Publication Number:
  US 20040018498A1
• Time in Patent Office: 1,720 Days
• Field of Search: 435/6, 536/23.1, 536/25.3
• US Class Current: 536/25.3
• 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 2219/00608 DNA chips
• 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 2219/00677 Ex-situ synthesis followed by deposition on the substrate
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01J 2219/00725 Peptides
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• 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 40/10 Libraries containing peptides or polypeptides, or derivatives thereof
• CPC Class Codes: C40B 50/18 using a particular method of attachment to the solid support
• CPC Class Codes: G01N 33/54353 with ligand attached to the carrier via a chemical coupling agent coatings G01N33/54393

Abstract

Methods for producing ligand arrays, e.g., peptide and nucleic acid arrays, as well as the arrays produced thereby, methods for use of the arrays and kits that include the same are provided. In one embodiment of the subject methods, a substrate having a surface displaying acetate functional groups that produce surface bound hydroxyl functional groups upon hydrolysis is first provided, where the acetate groups are then hydrolyzed to hydroxyl functional groups. In another embodiment of the subject methods, a substrate having a surface displaying alkenyl functional groups is first provided, where the alkenyl functional groups are then converted to carboxylic functional groups. The resultant substrates, optionally after an additional functionalization step, are then contacted with ligands, e.g., via deposition of each different ligand onto a different region of the surface, resulting in covalent attachment of the contacted ligands to the surface. The subject methods find use in the preparation of a variety of different types of arrays, where the produced arrays find use in a variety of different applications, including both genomic and proteomic applications.

Claims

1. A method of producing an array of at least two different ligands covalently bonded to a surface of a substrate, said method comprising:

(a) contacting a surface of a substrate with a silanizing reagent comprising an acetate functional group to produce a surface displaying acetate functional groups;

(b) converting said acetate functional groups on said surface to hydroxyl functional groups by acid or alkali hydrolysis; and

(c) contacting said surface displaying hydroxyl functional groups with at least two different ligands to produce said army;

with the proviso that said method further comprises converting said hydroxyl functional groups to ligand reactive functional groups when said hydroxyl functional groups do not covalently bond to said ligands upon contact.

2. The method according to claim 1, wherein said silanizing reagent comprises silyl and acetate groups separated by an alkyl chain.

3. The method according to claim 2, wherein said alkyl chain is from about 6 to about 20 carbon atoms in length.

4. The method according to claim 3, wherein said silanizing reagent has the formula:

Ac-(L)-Si(R^LR^XR^Y) wherein;

R^L is a leaving group;

R^X and R^Y are independently lower alkyl or a leaving group;

L is a C₈–

C₁₈ alkyl chain; and

Ac is an acetate group.

5. The method according to claim 4, wherein said acetate group has the formula:

—

O(CO)CR¹R²R³;

wherein;

R¹, R², and R³ are independently chosen from H, halogen, alkyoxy, aryloxy, alkyl, alyl, heteroalkyl, heteroaryl.

6. The method according to claim 4, wherein said silane reagent is 11-trichlorosilyl-undecyl acetate.

7. The method according to claim 1, wherein said acetate functional groups are converted to said hydroxyl functional groups by hydrolysis.

8. The method according to claim 1, wherein said method comprises converting said hydroxyl functional group to a ligand reactive functional group.

9. The method according to claim 8, wherein said ligand reactive functional group is an aldehyde.

10. The method according to claim 1, wherein said substrate is glass.

11. The method according to claim 1, wherein said ligand are selected from the group comprising oligonucleotides, polynucleotides, peptide-nucleic acids or peptides.

12. The method according to claim 1, wherein said polynucleotides are cDNA.

13. A ligand array produced according to the method of claim 1.

14. A method of detecting the presence of an analyte in a sample, said method comprising;

(a) contacting a sample suspected of comprising said analyte with a ligand array according to claim 13;

(b) detecting any binding complexes on the surface of the said array to obtain binding complex data; and

(c) determining the presence of said analyte in said sample using said binding complex data.

15. The method according to claim 14, wherein said analyte is a nucleic acid.

16. The method according to claim 14, wherein said method further comprises a data transmission step in which a result from a reading of said array is transmitted from a first location to a second location.

17. A method according to claim 16, wherein said second location is a remote location.

18. A method comprising receiving data representing a result of a reading obtained by the method of claim 16.

19. A kit for use in an analyte detection assay, said kit comprising:

a ligand array according to claim 13.

23. The method according to claim 1, wherein a single silanizing reagent is used.

20. A method of producing an array of at least two different ligands covalently bonded to a surface of a substrate, said method comprising:

(a) contacting a surface of a substrate with a silanizing reagent comprising an acetate functional group to produce a surface displaying acetate functional groups;

(b) converting said acetate functional groups on said surface to hydroxyl functional groups; and

(c) converting said hydroxyl functional groups to aldehyde groups by controlled oxidation, wherein the controlled oxidation is a Moffat oxidation or is effected with Dess-Martin solution.

21. The method according to claim 20, wherein the controlled oxidation is a Moffat oxidation.

22. The method according to claim 20, wherein the controlled oxidation is effected with Dess-Martin solution.